WorldWideScience

Sample records for european bioinformatics institute

  1. The European Bioinformatics Institute in 2017: data coordination and integration

    Science.gov (United States)

    Cochrane, Guy; Apweiler, Rolf; Birney, Ewan

    2018-01-01

    Abstract The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI’s approach to data integration and service development as genomics begins to enter the clinic. PMID:29186510

  2. The European Bioinformatics Institute in 2017: data coordination and integration.

    Science.gov (United States)

    Cook, Charles E; Bergman, Mary T; Cochrane, Guy; Apweiler, Rolf; Birney, Ewan

    2018-01-04

    The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI's approach to data integration and service development as genomics begins to enter the clinic. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.

    Science.gov (United States)

    Wright, Victoria Ann; Vaughan, Brendan W; Laurent, Thomas; Lopez, Rodrigo; Brooksbank, Cath; Schneider, Maria Victoria

    2010-11-01

    Today's molecular life scientists are well educated in the emerging experimental tools of their trade, but when it comes to training on the myriad of resources and tools for dealing with biological data, a less ideal situation emerges. Often bioinformatics users receive no formal training on how to make the most of the bioinformatics resources and tools available in the public domain. The European Bioinformatics Institute, which is part of the European Molecular Biology Laboratory (EMBL-EBI), holds the world's most comprehensive collection of molecular data, and training the research community to exploit this information is embedded in the EBI's mission. We have evaluated eLearning, in parallel with face-to-face courses, as a means of training users of our data resources and tools. We anticipate that eLearning will become an increasingly important vehicle for delivering training to our growing user base, so we have undertaken an extensive review of Learning Content Management Systems (LCMSs). Here, we describe the process that we used, which considered the requirements of trainees, trainers and systems administrators, as well as taking into account our organizational values and needs. This review describes the literature survey, user discussions and scripted platform testing that we performed to narrow down our choice of platform from 36 to a single platform. We hope that it will serve as guidance for others who are seeking to incorporate eLearning into their bioinformatics training programmes.

  4. Lecture 10: The European Bioinformatics Institute - "Big data" for biomedical sciences

    CERN Multimedia

    CERN. Geneva; Dana, Jose

    2013-01-01

    Part 1: Big data for biomedical sciences (Tom Hancocks) Ten years ago witnessed the completion of the first international 'Big Biology' project that sequenced the human genome. In the years since biological sciences, have seen a vast growth in data. In the coming years advances will come from integration of experimental approaches and the translation into applied technologies is the hospital, clinic and even at home. This talk will examine the development of infrastructure, physical and virtual, that will allow millions of life scientists across Europe better access to biological data Tom studied Human Genetics at the University of Leeds and McMaster University, before completing an MSc in Analytical Genomics at the University of Birmingham. He has worked for the UK National Health Service in diagnostic genetics and in training healthcare scientists and clinicians in bioinformatics. Tom joined the EBI in 2012 and is responsible for the scientific development and delivery of training for the BioMedBridges pr...

  5. European Institutions?

    NARCIS (Netherlands)

    Meacham, Darian

    2016-01-01

    The aim of this article is to sketch a phenomenological theory of political institutions and to apply it to some objections and questions raised by Pierre Manent about the project of the European Union and more specifically the question of “European Construction”, i.e. what is the aim of the

  6. Report on the EMBER Project--A European Multimedia Bioinformatics Educational Resource

    Science.gov (United States)

    Attwood, Terri K.; Selimas, Ioannis; Buis, Rob; Altenburg, Ruud; Herzog, Robert; Ledent, Valerie; Ghita, Viorica; Fernandes, Pedro; Marques, Isabel; Brugman, Marc

    2005-01-01

    EMBER was a European project aiming to develop bioinformatics teaching materials on the Web and CD-ROM to help address the recognised skills shortage in bioinformatics. The project grew out of pilot work on the development of an interactive web-based bioinformatics tutorial and the desire to repackage that resource with the help of a professional…

  7. Bioinformatics

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren

    , and medicine will be particularly affected by the new results and the increased understanding of life at the molecular level. Bioinformatics is the development and application of computer methods for analysis, interpretation, and prediction, as well as for the design of experiments. It has emerged...

  8. European Bioinformatics Institute: Research Infrastructure needed for Life Science

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    The life science community is an ever increasing source of data from increasing diverse range of instruments and sources. EMBL-EBI has a remit to store and exploit this data, collected and made available openly across the world, for the benefit of the whole research community. The research infrastructure needed to support the big data analysis around this mission encompasses high performance networks, high-throughput computing, and a range of cloud and storage solutions - and will be described in the presentation.

  9. Turkey and European Security Institutions

    Science.gov (United States)

    2009-03-01

    relationships between Turkey, the United States, the Kurds, and Europe. As a source often critical of Turkey and the United States ( Noam Chomsky ...2008, http://consilium.europa.eu/uedocs/cmsUpload/080220Altheaupdate10. pdf . 129 Ibid. 130 Ibid. 131 Ibid. 132 The Council of the European Union...Factsheet, “EU Police Mission in Bosnia and Herzegovina (EUPM),” March 2006, http://consilium.europa.eu/uedocs/cmsUpload/Factsheet_060312. pdf . 48

  10. European Institutional Developments and Evolutions Post‑Lisbon Treaty

    Directory of Open Access Journals (Sweden)

    Cristian Sorin Dumitrescu

    2014-11-01

    Full Text Available The current article aims at analysing the main difficulties the European institutions were confronted to and identifying the axes of urgent reforms of the European construction, which are claimed to be applied, immediately, after the recent parliamentary elections from 25 of May together with the installation of the new decision teams in Brussels. While the first part of the article examine the action of the various European institutions within the new constitutional architecture, the second part will cover some axes needed which could be followed by the Union starting with the new term. In the context of the economic and financial crisis, the first European institutional cycle under the terms of the Lisbon Treaty –2009-2014, became an important challenge for the application of the provisions concerning the functioning of the European institutions. An objective assessment of the ways regarding the practical implementation of the Treaty must take into consideration the negative influence of the economic crisis upon the decisions assumed by the high national and European responsibles.

  11. Experiences with Learning Management Systems in 113 European Institutions

    Directory of Open Access Journals (Sweden)

    Morten Flate Paulsen

    2003-10-01

    Full Text Available This article presents the major findings from six regional analyses conducted within the framework of the European Web-edu project (http://www.nettskolen.com/in_english/webedusite/index.html. It analyses the experiences of European institutions with the Learning Management Systems that they have purchased or developed themselves. Data was collected from in-depth interviews with 113 European experts, usually the systems managers in the institutions, in 17 countries. The analyses of the interviews revealed as many as 52 different commercial and 35 self-developed LMS systems. The article presents the data from these interviews and includes a series of important findings from the study. One conclusion is that there is a host of commercial and self-developed systems that seem to work satisfactorily in various educational institutions throughout Europe. The systems are not able to handle all the functions the institutions want, and they can be improved in many ways. But most systems encountered in the analyses seem to be good enough for handling online education successfully. Another conclusion is that the European market is not dominated by the American LMS systems. In countries that do not use English as the first language, locally developed LMS systems have successfully ousted the American products. Remarkably, a large number of the LMS systems used in Europe are commercial systems developed locally, or self-developed systems built by the institutions.

  12. Institutional pioneers in world politics: Regional institution building and the influence of the European Union

    Science.gov (United States)

    Lenz, Tobias; Burilkov, Alexandr

    2016-01-01

    What drives processes of institution building within regional international organizations? We challenge those established theories of regionalism, and of institutionalized cooperation more broadly, that treat different organizations as independent phenomena whose evolution is conditioned primarily by internal causal factors. Developing the basic premise of ‘diffusion theory’ — meaning that decision-making is interdependent across organizations — we argue that institutional pioneers, and specifically the European Union, shape regional institution-building processes in a number of discernible ways. We then hypothesize two pathways — active and passive — of European Union influence, and stipulate an endogenous capacity for institutional change as a key scope condition for their operation. Drawing on a new and original data set on the institutional design of 34 regional international organizations in the period from 1950 to 2010, the article finds that: (1) both the intensity of a regional international organization’s structured interaction with the European Union (active influence) and the European Union’s own level of delegation (passive influence) are associated with higher levels of delegation within other regional international organizations; (2) passive European Union influence exerts a larger overall substantive effect than active European Union influence does; and (3) these effects are strongest among those regional international organizations that are based on founding contracts containing open-ended commitments. These findings indicate that the creation and subsequent institutional evolution of the European Union has made a difference to the evolution of institutions in regional international organizations elsewhere, thereby suggesting that existing theories of regionalism are insufficiently able to account for processes of institution building in such contexts. PMID:29400350

  13. A Legal Institutional Perspective on the European External Action Service

    DEFF Research Database (Denmark)

    Van Vooren, Bart

    2011-01-01

    This article provides a legal perspective on the new European External Action Service (EEAS), and positions this new body in the reshuffled institutional balance of EU external relations. Towards that end, the paper examines the EEAS’ legal nature as compared to that of Council, Commission...

  14. Polish Accession to the European Union: Participating Institutions

    Directory of Open Access Journals (Sweden)

    Tomaszewski Waldemar

    2015-06-01

    Full Text Available In May 2014 it was aready ten years since Poland’s accession to the European Union. The accession was preceded by a long period of political action and negotiations between the Polish and the EU institutions. The process of integration was extremely complex. It covered almost all areas of economic, legal and civil aspects of the aspiring country’s economy, in which all necessary requirements had to be met. The aim of the article was to present the institutional framework created for efficient implementation of the process of accession. The considerations involved especially an institutional method. The research resulted in poining out both the actually efficient and less efficient bodies participating in the process of integration.

  15. IBWS: IST Bioinformatics Web Services.

    Science.gov (United States)

    Zappa, Achille; Miele, Mariangela; Romano, Paolo

    2010-07-01

    The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa has been involved since many years in the development and maintenance of biomedical information systems. Among them, the Common Access to Biological Resources and Information network services offer access to more than 130,000 biological resources, like strains of micro-organisms and human and animal cell lines, included in 29 collections from some of the most known European Biological Resource Centers. An Sequence Retrieval System (SRS) implementation of the TP53 Mutation Database of the International Agency for Research on Cancer (Lyon) was made available in order to improve interoperability of this data with other molecular biology databases. 'SRS by WS (SWS)', a system for retrieving information on public SRS sites and for directly querying them, was also implemented. In order to make this information available through application programming interfaces, we implemented a suite of free web services (WS), called the 'IST Bioinformatics Web Services (IBWS)'. A support web site, including a description of the system, a list of available WS together with help pages, links to corresponding WSDLs and forms for testing services, is available at http://bioinformatics.istge.it/ibws/. WSDL definitions can also be retrieved directly at http://bioinformatics.istge.it:8080/axis/services.

  16. Liability of the European Union for acts of its Institutions

    OpenAIRE

    Mihaescu, Bucura Catalina

    2011-01-01

    The following article will assess the real extent of the potential liability of the European Union. It will fi rstly focus on the recognition and the development by the EU Courts of the conditions which must be fulfi lled in order for the EU to incur liability for the acts of its institutions. It will be emphasised in this regard that, as the EU Courts’ case-law currently stand, the criteria for Union liability can differ, depending on a number of variables including whether the c...

  17. Islamic Symbols in Europe: the European Court of Human Rights and the European Institutions

    Directory of Open Access Journals (Sweden)

    Sara Tonolo

    2014-02-01

    Full Text Available Il contributo, sottoposto a valutazione, è destinato alla pubblicazione nel volume, a cura di   R. Scarciglia, Islamic Symbols in European Courts,Quaderni giuridici del Dipartimento di Scienze politiche e sociali, Cedam – Kluwer, Trieste, 2014SUMMARY: 1. Preliminary Remarks - 2. The veil before the European Court of Human Rights – 3. Religious Symbols in Article 9 ECHR case law and women’s religious freedom in Europe – 4. Islamic Symbols and European Institutions. Indirect Discrimination? – 5. Conclusive Remarks. AbstractReligious freedom within Europe and the place of Islam within Europe are of particular contemporary interest. The focus of recent case law developed by the European Court of Human Rights (ECtHR has been on national laws which proscribe the wearing of religious symbols in certain aspects of the public sphere, and on the claims more generally to religious and cultural freedom of Muslim minorities in European states. Stepping back from these cases, this Article aims at a theoretical analysis of the subject, involving the contrast between value pluralism as a basis for religious freedom in international law, and other fundamental rights, i.e. women’s or children’s rights. By recognizing the intrinsic connection between individual rights and communal goods, value pluralism opens new pathways for enforcing human rights.

  18. [Factors affecting the adoption of ICT tools in experiments with bioinformatics in biopharmaceutical organizations: a case study in the Brazilian Cancer Institute].

    Science.gov (United States)

    Pitassi, Claudio; Gonçalves, Antonio Augusto; Moreno Júnior, Valter de Assis

    2014-01-01

    The scope of this article is to identify and analyze the factors that influence the adoption of ICT tools in experiments with bioinformatics at the Brazilian Cancer Institute (INCA). It involves a descriptive and exploratory qualitative field study. Evidence was collected mainly based on in-depth interviews with the management team at the Research Center and the IT Division. The answers were analyzed using the categorical content method. The categories were selected from the scientific literature and consolidated in the Technology-Organization-Environment (TOE) framework created for this study. The model proposed made it possible to demonstrate how the factors selected impacted INCA´s adoption of bioinformatics systems and tools, contributing to the investigation of two critical areas for the development of the health industry in Brazil, namely technological innovation and bioinformatics. Based on the evidence collected, a research question was posed: to what extent can the alignment of the factors related to the adoption of ICT tools in experiments with bioinformatics increase the innovation capacity of a Brazilian biopharmaceutical organization?

  19. What direction for the European Council? Institutional reforms and counter-reforms in EU

    Directory of Open Access Journals (Sweden)

    Gheorghe Ciascai

    2012-12-01

    Full Text Available The aim of this paper is to analyse the political and institutional impact of the juridical consecration of the European Council that official institution of European Union by the Lisbon Treaty. Until 1 December 2009, the European Council was a political body with a strong informal role within the european decision making process, but with ambiguous institutional and legal powers. After entry in force of the Lisbon Treaty, European Council becomes an institution that try to exercise a collective leadership in EU.

  20. A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning.

    Science.gov (United States)

    Via, Allegra; Attwood, Teresa K; Fernandes, Pedro L; Morgan, Sarah L; Schneider, Maria Victoria; Palagi, Patricia M; Rustici, Gabriella; Tractenberg, Rochelle E

    2017-09-26

    Demand for training life scientists in bioinformatics methods, tools and resources and computational approaches is urgent and growing. To meet this demand, new trainers must be prepared with effective teaching practices for delivering short hands-on training sessions-a specific type of education that is not typically part of professional preparation of life scientists in many countries. A new Train-the-Trainer (TtT) programme was created by adapting existing models, using input from experienced trainers and experts in bioinformatics, and from educational and cognitive sciences. This programme was piloted across Europe from May 2016 to January 2017. Preparation included drafting the training materials, organizing sessions to pilot them and studying this paradigm for its potential to support the development and delivery of future bioinformatics training by participants. Seven pilot TtT sessions were carried out, and this manuscript describes the results of the pilot year. Lessons learned include (i) support is required for logistics, so that new instructors can focus on their teaching; (ii) institutions must provide incentives to include training opportunities for those who want/need to become new or better instructors; (iii) formal evaluation of the TtT materials is now a priority; (iv) a strategy is needed to recruit, train and certify new instructor trainers (faculty); and (v) future evaluations must assess utility. Additionally, defining a flexible but rigorous and reliable process of TtT 'certification' may incentivize participants and will be considered in future. © The Author 2017. Published by Oxford University Press.

  1. Edge Bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    2015-08-03

    Edge Bioinformatics is a developmental bioinformatics and data management platform which seeks to supply laboratories with bioinformatics pipelines for analyzing data associated with common samples case goals. Edge Bioinformatics enables sequencing as a solution and forward-deployed situations where human-resources, space, bandwidth, and time are limited. The Edge bioinformatics pipeline was designed based on following USE CASES and specific to illumina sequencing reads. 1. Assay performance adjudication (PCR): Analysis of an existing PCR assay in a genomic context, and automated design of a new assay to resolve conflicting results; 2. Clinical presentation with extreme symptoms: Characterization of a known pathogen or co-infection with a. Novel emerging disease outbreak or b. Environmental surveillance

  2. THE ROLE OF THE EUROPEAN EXTERNAL ACTION SERVICE IN THE EU’S INSTITUTIONAL SYSTEM

    Directory of Open Access Journals (Sweden)

    DAN VATAMAN

    2012-05-01

    Full Text Available European External Action Service (EEAS is a new institution of the European Union, whose foundation was laid by the Treaty of Lisbon with the role to support the High Representative of the Union for Foreign Affairs and Security Policy in fulfilling his mandate and, also to assist the President of the European Council, European Commission, President and other Commissioners to exercise their powers in international relations. Since the establishment of the European External Action Service (EEAS is relatively recent, this article tries to highlight the crucial role of the European External Action Service (EEAS in the European Union's institutional system and its contribution to strengthening the coherence and increasing impact and visibility of European Union action at international level and thus the one of the Member States.

  3. Designing fiscal and monetary institutions for a European Monetary Union

    NARCIS (Netherlands)

    Beetsma, R.M.W.J.; Bovenberg, A.L.

    1995-01-01

    This paper explores under what conditions a European Monetary Union (EMU) is an optimum currency area. The scope for an EMU increases with convergence of structural and fiscal policies, small money holdings, a conservative European Central Bank, and dependent national central banks. How national

  4. RATIONAL CHOICE INSTITUTIONALISM AND THE EUROPEAN NEIGHBOURHOOD POLICY

    OpenAIRE

    Andrei Cristian Balasan; Andreea Maha

    2013-01-01

    The aim of this paper is to highlight the main aspects regarding the rational choice theory in neo-institutionalism, and the role the EU Neighbourhood Policy has nowadays. The protagonist of the rational choice theory in the new institutionalism remains homo-economicus. The theory of rational choice institutionalism challenges the perfect rationality of the individual, rather than the principle of rational choice itself. ENP is a framework for consolidating the Union's relations with neighbou...

  5. Aptamer Bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew B. Kinghorn

    2017-11-01

    Full Text Available Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment, an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection. This review will discuss the advancements made in several enclaves of aptamer bioinformatics, including simulation of aptamer selection, fragment-based aptamer design, patterning of libraries, identification of lead aptamers from high-throughput sequencing (HTS data and in silico aptamer optimization.

  6. Aptamer Bioinformatics

    Science.gov (United States)

    Kinghorn, Andrew B.; Liang, Shaolin; Tanner, Julian A.

    2017-01-01

    Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment), an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection. This review will discuss the advancements made in several enclaves of aptamer bioinformatics, including simulation of aptamer selection, fragment-based aptamer design, patterning of libraries, identification of lead aptamers from high-throughput sequencing (HTS) data and in silico aptamer optimization. PMID:29186809

  7. Aptamer Bioinformatics.

    Science.gov (United States)

    Kinghorn, Andrew B; Fraser, Lewis A; Lang, Shaolin; Shiu, Simon Chi-Chin; Tanner, Julian A

    2017-11-24

    Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment), an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection. This review will discuss the advancements made in several enclaves of aptamer bioinformatics, including simulation of aptamer selection, fragment-based aptamer design, patterning of libraries, identification of lead aptamers from high-throughput sequencing (HTS) data and in silico aptamer optimization.

  8. A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC

    Directory of Open Access Journals (Sweden)

    Ashokkumar A. Patel

    2007-01-01

    Full Text Available Background: The Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC, http://www.pcabc.upmc.edu is one of the first major project-based initiatives stemming from the Pennsylvania Cancer Alliance that was funded for four years by the Department of Health of the Commonwealth of Pennsylvania. The objective of this was to initiate a prototype biorepository and bioinformatics infrastructure with a robust data warehouse by developing a statewide data model (1 for bioinformatics and a repository of serum and tissue samples; (2 a data model for biomarker data storage; and (3 a public access website for disseminating research results and bioinformatics tools. The members of the Consortium cooperate closely, exploring the opportunity for sharing clinical, genomic and other bioinformatics data on patient samples in oncology, for the purpose of developing collaborative research programs across cancer research institutions in Pennsylvania. The Consortium’s intention was to establish a virtual repository of many clinical specimens residing in various centers across the state, in order to make them available for research. One of our primary goals was to facilitate the identification of cancer specific biomarkers and encourage collaborative research efforts among the participating centers.Methods: The PCABC has developed unique partnerships so that every region of the state can effectively contribute and participate. It includes over 80 individuals from 14 organizations, and plans to expand to partners outside the State. This has created a network of researchers, clinicians, bioinformaticians, cancer registrars, program directors, and executives from academic and community health systems, as well as external corporate partners - all working together to accomplish a common mission. The various sub-committees have developed a common IRB protocol template, common data elements for standardizing data collections for three organ sites, intellectual

  9. Science on the net: an analysis of the websites of the European public research institutions

    National Research Council Canada - National Science Library

    Laura Massoli

    2007-01-01

    This article introduces a study on the websites of several European public research institutions that aims at identifying the science communication model chosen and implemented online with the purpose...

  10. Entrepreneurship, institutions and growth in European regions : a uniform mechanism

    NARCIS (Netherlands)

    Bruns, K.; Bosma, N.S.; Sanders, M.W.J.L.; Schramm, M.C.

    2015-01-01

    In this paper we present an alternative empirical strategy that sheds light on the importance of institutional quality for regional economic growth. The fundamental problem in this type of research is that institutional quality cannot be measured directly. Existing proxies are typically highly

  11. Economic and labor rights in the European Union after Lisbon: an institutional approach

    OpenAIRE

    Konstantinos Margaritis

    2013-01-01

    Economic and labor rights belong to the core of business action, since they constitute the institutional framework for actors involved in business, employers and workers. Since the European integration is progressing, we may speak of a European environment for business, a common market in European legal terms, which became the main aim for the Communities since 1957. At the end of 2009, with the enforcement of the Lisbon Treaty amendments, important changes were brought in the fundamental rig...

  12. Academic Entrepreneurialism vs. Changing Governance and Institutional Management Structures in European Universities (Chapter 5)

    OpenAIRE

    Kwiek, Marek

    2013-01-01

    In this chapter we will discuss a historically relatively new phenomenon in European higher education systems: academic entrepreneurialism – especially with regard to governance and management. Entrepreneurial universities seem to be increasingly important points of reference for international and European-level policy discussions about the future of higher education. Entrepreneurial institutions, functionally similar although variously termed, currently seem to be an almost natur...

  13. Competitive Universities? The Impact of International and European Trends on Academic Institutions in the "New Europe"

    Science.gov (United States)

    Dakowska, Dorota

    2017-01-01

    This contribution examines the domestic reinterpretations of international and European recommendations in Central and Eastern European countries (CEECs). It asks under what conditions these institutional recommendations, but also global processes such as the university rankings, affect domestic public policies. The countries of Central and…

  14. European Commission, the Institution which brings Europe closer

    Directory of Open Access Journals (Sweden)

    Enertila Bekteshi

    2016-11-01

    Full Text Available This paper presents a brief story of the establishment and function of the European Commission. Why European Commission is considered the shortest way toward Europe? This material recalls the agreements concluded since the beginning of the creation of the European Commission, scope of cooperation among member countries aiming a single and economic and political unit which directs and develops the Continent. The role of Commission stands at the center of explanations regarding the nature of the path toward the European integration. Obviously the debate is made for EU. In case the Commission is seen as an autonomous actor, the argument that EU is an intergovernmental organization will be diminished. So far, the Commission has been at the center of critiques in the role as manager of the policies of the Community and finances. Meanwhile the policy of implementation is not having a rectilinear motion within the member countries. Any member country may sue another country for breach of the Commission’s obligations. The Commission is still depending on the national governments and administrations, the achievement of the policy goals at an EU inclined to expansion, is difficult. This has made more difficult the job of the Commission. Another aspect being noticed is that EU can make an effective policy in the enterprising area, setting out some basic criteria for the efficiency of decisions taken and demonstrate capacities to correct the eff ects of failure. Also, the Commission role in managing the budget deficit should be obvious.

  15. The Effects of Institutional Change in European Soccer

    NARCIS (Netherlands)

    Haan, Marco A.; Koning, Ruud H.; van Witteloostuijn, Arjen

    The last decades have seen two profound changes in European soccer. First, international trade in talent has increased markedly. Second, international competitions such as the Champions League have become much more important. Using a theoretical model, we study how these changes affect competitive

  16. RATIONAL CHOICE INSTITUTIONALISM AND THE EUROPEAN NEIGHBOURHOOD POLICY

    Directory of Open Access Journals (Sweden)

    Andreea Maha

    2013-09-01

    Full Text Available The aim of this paper is to highlight the main aspects regarding the rational choice theory in neo-institutionalism, and the role the EU Neighbourhood Policy has nowadays. The protagonist of the rational choice theory in the new institutionalism remains homo-economicus. The theory of rational choice institutionalism challenges the perfect rationality of the individual, rather than the principle of rational choice itself. ENP is a framework for consolidating the Union's relations with neighbouring countries and aims therefore intensifying cooperation with them in order to establish a zone of prosperity, good neighbourliness, stability and security.

  17. Polish credit institutions within the European Union: a cross-country survey

    Directory of Open Access Journals (Sweden)

    Mariusz Dybał

    2011-06-01

    Full Text Available The paper presents an analysis of the Polish financial system, with regard to both the number of financial institutions and their assets over the last two decades. Data on the structure of household assets are also presented. According to the study, banks are the most important institutions in the Polish financial system. Analyzed in order to compare Polish credit institutions with all other members of the European Union were total assets of credit institutions, assets of the 25 largest banks in the European Union, as well as in Central and East Europe, share of the five largest credit institutions in total assets (CR5, asset share of credit institutions with majority foreign equity ownership, number of credit institutions, number of local units (branches, number of residents per credit institution local unit, number of employees of credit institutions, assets of credit institutions per employee and GDP per capita in PPS. The data demonstrate that over the past decade Polish credit institutions have largely strengthened their position within the European Union.

  18. How national institutions mediate the global : Screen translation, institutional interdependencies and the production of national difference in four European countries

    NARCIS (Netherlands)

    Kuipers, G.

    2015-01-01

    How do national institutional contexts mediate the global? This article aims to answer this question by analyzing screen translation—the translation of audiovisual materials like movies and television programs—in four European countries: France, Italy, the Netherlands, and Poland. A cross-national,

  19. Institutional support modernization of public administration in terms of implementation of European integration

    Directory of Open Access Journals (Sweden)

    N. V. Shcherbak

    2016-03-01

    Full Text Available This article highlights main issues of the public administration modernization in the framework of the European integration policy implementation. By analysis of the Ukrainian and European normative acts and other documents, the best national and international practices, the issues on the implementation of the European institution building tools (TWINNING, TAIEX, SIGMA and others are studied. The statistical and other information shows that Ukraine is a leader between EU Initiative «Eastern Partnership» concerning realization of the European institution building tools. It is also defined the main advantages of the mentioned European institution building tools as well as the main results of their realization during 10 last years in Ukraine. The acquired positive experience which is analyzed in the article is undoubtedly useful for ensuring the reform of public administration in Ukraine in accordance to European standards of good governance. Taking into account the priorities of the new Association Agreement between Ukraine and EU, the proposals and the recommendations concerning further implementation of the European institution building tools are prepared (in particular, in the framework of the modernization of the public administration system and ensuring the good goverance standards.

  20. THE JOINT EUROPEAN-UNITED STATES NDEA INSTITUTE FOR ADVANCED STUDY, MANNHEIM-HEIDELBERG.

    Science.gov (United States)

    VAN TESLAAR, A.P.

    THE EUROPEAN COORDINATOR AND RESIDENT CO-DIRECTOR OF THE MANNHEIM-HEIDELBERG BRANCH OF THE SUMMER 1966 LANGUAGE INSTITUTE IN FRANCE AND GERMANY PREPARED THIS EVALUATION OF THE INTERNATIONAL VENTURE. DESIGNED TO ANALYZE THE INNOVATIONAL ASPECTS OF THE 1966 INSTITUTE WITH THE IDEA OF STRENGTHENING THE EFFECTIVENESS OF THIS AND SIMILAR PROGRAMS, THE…

  1. Aptamer Bioinformatics

    OpenAIRE

    Kinghorn, Andrew B.; Fraser, Lewis A.; Liang, Shaolin; Shiu, Simon Chi-Chin; Tanner, Julian A.

    2017-01-01

    Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding. They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment), an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer characterization. As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection. This review will discuss the advancements made in several...

  2. The Threat to Religious Liberties and the European Institutions

    Directory of Open Access Journals (Sweden)

    Roger Kiska

    2011-07-01

    Full Text Available The following article analyzes the 3 chief threats facing religious liberty today in Europe, namely: (1 hate speech legislation; (2 anti-discrimination laws; (3 attacks on parental rights. Concrete examples are given of offenses to religious freedom. Additionally, the black letter law is set out in each section with suggested action points for national governments. The Article also discusses the Lautsi v. Italy judgment of the European Court of Human Rights, explaining its importance and using it as evidence to establish the political nature of the Strasbourg based court.

  3. New Horizons for Innovation in European Higher Education Institutions

    Directory of Open Access Journals (Sweden)

    Gabriela Marchis

    2016-05-01

    Full Text Available In today's European society, the first signs of economic recovery is facing difficulties in recruiting qualified staff with a high level of skills that can adapt quickly to changes that appear, in order to meet our European ambitions: to create a Union of Innovation. The transition to a green, smart and innovative economy, in line with the objectives of “Europe 2020” strategy can only be achieved by decisive actions oriented to labor factor development. Thus, one of the vectors of labor reconstruction starts from the principle of “lifelong learning” and envisages the validation of non-formal and informal education, the orientation towards learning outcomes and last but not the least, it aims to integrate learning and career guidance systems. This paper intends to guide and inspire those people that have the responsibility for management and coordination of HEIs, as well as those engaged in academic activities like professors, students, alumni or other stakeholders, by searching the answers to a simple question: What global society needs and/or desire from HEIs?

  4. The Organization of European Cancer Institute Pathobiology Working Group and its support of European biobanking infrastructures for translational cancer research.

    Science.gov (United States)

    Riegman, Peter H J; de Jong, Bas W D; Llombart-Bosch, Antonio

    2010-04-01

    Today's translational cancer research increasingly depends on international multi-center studies. Biobanking infrastructure or comprehensive sample exchange platforms to enable networking of clinical cancer biobanks are instrumental to facilitate communication, uniform sample quality, and rules for exchange. The Organization of European Cancer Institutes (OECI) Pathobiology Working Group supports European biobanking infrastructure by maintaining the OECI-TuBaFrost exchange platform and organizing regular meetings. This platform originated from a European Commission project and is updated with knowledge from ongoing and new biobanking projects. This overview describes how European biobanking projects that have a large impact on clinical biobanking, including EuroBoNeT, SPIDIA, and BBMRI, contribute to the update of the OECI-TuBaFrost exchange platform. Combining the results of these European projects enabled the creation of an open (upon valid registration only) catalogue view of cancer biobanks and their available samples to initiate research projects. In addition, closed environments supporting active projects could be developed together with the latest views on quality, access rules, ethics, and law. With these contributions, the OECI Pathobiology Working Group contributes to and stimulates a professional attitude within biobanks at the European comprehensive cancer centers. Improving the fundamentals of cancer sample exchange in Europe stimulates the performance of large multi-center studies, resulting in experiments with the desired statistical significance outcome. With this approach, future innovation in cancer patient care can be realized faster and more reliably.

  5. Book Review: Lobbying the European Union: Institutions, Actors and Issues, David Coen and Jeremy Richardson (eds.

    Directory of Open Access Journals (Sweden)

    Alexandra Pop

    2013-03-01

    Full Text Available The volume "Lobbying the European Union: Institutions, Actors and Issues", collects 16 articles on interest group politics at EU level, focusing on the main elements of European lobbying - the existing relations between the EU institutions and the special interests, the main differences between NGO and business lobbying, the specific lobbying strategies adopted in EU's main policy sectors or lobbying regulations. The volume captures the main changes that took place on the European lobbying scene in the last two decades, period in which most EU institutions developed new points of access for lobbyists, while the interest groups became more specialized. The success of an EU lobbying campaign seems to be determined by a combination of various factors such as: a good knowledge of the EU environment, a wise usage of both financial resources and expertise, direct lobbying complemented by an efficient usage of domestic routes and the capability of creating smart alliances.

  6. Labour Market Institutions and Labour Market Performance in the European Union

    OpenAIRE

    Michal, Tvrdon

    2008-01-01

    The presented article deals with labour market institutions and labour market performance in the European Union. The first chapter is devoted to theoretical and methodological background of labour market performance. Theoretical literature has created a set of institutional aspects such as employment protection legislation, structure of wage bargaining, taxation of labour, active labour market policy, the system of unemployment and social benefits. All these aspects determine the institutiona...

  7. The Regina Elena National Cancer Institute process of accreditation according to the standards of the Organisation of European Cancer Institutes.

    Science.gov (United States)

    Canitano, Stefano; Di Turi, Annunziata; Caolo, Giuseppina; Pignatelli, Adriana C; Papa, Elena; Branca, Marta; Cerimele, Marina; De Maria, Ruggero

    2015-01-01

    The accreditation process is, on the one hand, a tool used to homogenize procedures, rendering comparable and standardized processes of care, and on the other, a methodology employed to develop a culture of quality improvement. Although not yet proven by evidence-based studies that health outcomes improve as a result of an accreditation to excellence, it is undeniable that better control of healthcare processes results in better quality and safety of diagnostic and therapeutic pathways. The Regina Elena National Cancer Institute underwent the accreditation process in accordance with the standards criteria set by the Organisation of European Cancer Institutes (OECI), and it has recently completed the process, acquiring its designation as a Comprehensive Cancer Center (CCC). This was an invaluable opportunity for the Regina Elena Institute to create a more cohesive environment, to widely establish a culture of quality, to implement an institutional information system, and to accelerate the process of patient involvement in strategic decisions. The steps of the process allowed us to evaluate the performance and the organization of the institute and put amendments in place designed to be adopted through 26 improvement actions. These actions regarded several aspects of the institute, including quality culture, information communication technology system, care, clinical trials unit, disease management team, nursing, and patient empowerment and involvement. Each area has a timeline. We chose to present the following 3 improvement actions: clinical trial center, computerized ambulatory medical record, and centrality of patient and humanization of clinical pathway.

  8. 25 October 2017 - Meeting on a South-East European International Institute for Sustainable Technologies

    CERN Document Server

    Ordan, Julien Marius

    2017-01-01

    Meeting on a South-East European International Institute for Sustainable Technologies at CERN, organised by the Ministry of Science of Montenegro, followed by a lunch hosted by CERN Director-General F. Gianotti and a site visit to CMS counting room and S'Cool LAB.

  9. Measuring Scale Economies in a Heterogeneous Industry: The Case of European Settlement Institutions

    NARCIS (Netherlands)

    van Cayseele, P.J.G.; Wuyts, C.

    2006-01-01

    We examine whether the European settlement institutions are technically efficient. This is done by means of estimating a translog cost function, and investigating whether scale economies are fully exploited. Since the sample is quite heterogeneous, fixed effects regression is introduced. From the

  10. IR. Theory Meets European Union Law. Constitutional Battles, Sovereign Choices & Institutional Contingencies in the Legacy of the European Integration Process

    DEFF Research Database (Denmark)

    Wind, Marlene

    From the point of departure of international relations theory it is not an easy task to come to grips with the European integration process. We are faced with a situation where some of the world's oldest and traditionally most sovereignty-loving nations have surrendered essential parts of their p......From the point of departure of international relations theory it is not an easy task to come to grips with the European integration process. We are faced with a situation where some of the world's oldest and traditionally most sovereignty-loving nations have surrendered essential parts...... of their power to a supranational institution. In order to make sense of this the book employs a constructivist framework. Empirically it focuses on the way in which the Community has transformed from a traditional international regime, based on classical international law, to a semi-federal polity where...

  11. The European Year of Intercultural Dialogue – an Institutional Representation at the European and National level

    Directory of Open Access Journals (Sweden)

    Ana-Maria Bostan

    2009-11-01

    Full Text Available Humanity has always encapsulated the paradigm of communication within its existence. Thus, interaction has always placed man on a twofold interweaving nature: a partial or even a total exposure through an icon textual signifier and a sort of mystery through a discursive signified. Our paper is a “journey” through the world of icon textual interferences, which guides our steps to one main destination, that of mapping the relationship between the signifier and the signified within non-artistic communication. Having as theoretical background M.A.K. Halliday’s theory on functional grammar (1994 and the social semiotic perspective on colours (Kress, van Leeuwen [1996] 2006, we will analyze the elements that the identity relationship envisages within the logo of the 2008 European Year of Intercultural Dialogue and within the Romanian national campaign PUZZLE.

  12. Institutional pioneers in world politics : regional institution building and the influence of the European Union

    OpenAIRE

    LENZ, Tobias; Burilkov, Alexandr

    2016-01-01

    Published online: 9 November 2016 What drives processes of institution building within regional international organizations? We challenge those established theories of regionalism, and of institutionalized cooperation more broadly, that treat different organizations as independent phenomena whose evolution is conditioned primarily by internal causal factors. Developing the basic premise of ‘diffusion theory’ - meaning that decision-making is interdependent across organizations - we argue t...

  13. European Banking Recovery and Resolution Directive: Potential Impacts on European Systemic Important Financial Institutions

    Directory of Open Access Journals (Sweden)

    Clements Akinsoyinu

    2015-09-01

    Full Text Available The great recession heralded in by the subprime mortgage crisis, took a dramatic turn for worse as a result of collapse of the Lehman Brothers bank in September 2008. The crisis deemed to be the most devastating after the Great Depression of 1929, had a debilitating effect on world economies, developing and advanced alike.  The extent of its devastation which  is still being felt in Europe and many parts of the globe reminds us the interconnectedness of financial institutions, particularly those tagged TBTF or SIFIs. Policy makers scrambled to curtail the ugly effect of the crisis by rescuing the SIFIs within their jurisdiction largely through bailout mechanism and provision of implicit guarantee for the debts of failing/failed institutions. As soon as the tide is stemmed, they cast their gaze on new crisis resolution and recovery measures that could rein in systemic risks associated with SIFIs, prevent future crises and reduce the concomitant moral hazards in the current resolution measures. This paper assesses ex ante the potential impact of implementing the new Banking recovery and resolution directives on Europe’s TBTF banksThe great recession heralded in by the subprime mortgage crisis, took a dramatic turn for worse as a result of collapse of the Lehman Brothers bank in September 2008. The crisis deemed to be the most devastating after the Great Depression of 1929, had a debilitating effect on world economies, developing and advanced alike.  The extent of its devastation which  is still being felt in Europe and many parts of the globe reminds us the interconnectedness of financial institutions, particularly those tagged TBTF or SIFIs. Policy makers scrambled to curtail the ugly effect of the crisis by rescuing the SIFIs within their jurisdiction largely through bailout mechanism and provision of implicit guarantee for the debts of failing/failed institutions. As soon as the tide is stemmed, they cast their gaze on new crisis

  14. Quality assurance systems of higher education - The case of european institutions: origin, evolution and trends

    Directory of Open Access Journals (Sweden)

    Ángela Corengia

    2014-09-01

    Full Text Available The purpose of this research is to analyze the origin, evolution, performance and trends of higher education quality assurance systems in the following European countries: Denmark, Norway, Sweden, Finland, Austria, Italy, Switzerland, Germany, Netherlands, United Kingdom and France. It also studies the performance and impact of the organizations that join the European Quality Assurance Agencies together. The main sources of data collection were in situ semi-structured interviews to members of these agencies. It was found that in higher education institutions there is a strong trend towards the development of ‘internal quality assurance systems' in response to the public policies known as 'quality audits'.

  15. Analysis of the European union’s supranationalism crisis within the political-institutional paradigm

    Directory of Open Access Journals (Sweden)

    O. V. Bashtannyk

    2014-04-01

    So, the same logic of integration policy has caused deferred manifestation of the contradictions that have not been resolved by the development of such a grand united project. It is determined that the investigation of this problem is possible by applying methodological tools of historical institutionalism within political­institutional paradigm of political science. In such kind of analysis it becomes possible to conduct qualitative research and perspective political component of European integration phenomenon’s nature. Economic crisis was the challenge for those unifying international institutions that were considered “post­national polity” and whose institutional framework seemed never shaken. This proves once again that it is impossible to cancel on the willful way the influence of the historical patterns in principle and “path dependence” in particular.

  16. Online Bioinformatics Tutorials | Office of Cancer Genomics

    Science.gov (United States)

    Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.

  17. Economic and labor rights in the European Union after Lisbon: an institutional approach

    Directory of Open Access Journals (Sweden)

    Konstantinos MARGARITIS

    2013-12-01

    Full Text Available Economic and labor rights belong to the core of business action, since they constitute the institutional framework for actors involved in business, employers and workers. Since the European integration is progressing, we may speak of a European environment for business, a common market in European legal terms, which became the main aim for the Communities since 1957. At the end of 2009, with the enforcement of the Lisbon Treaty amendments, important changes were brought in the fundamental rights protection in EU, mainly with the enactment of the EU Charter of Fundamental Rights. For a better understanding of the framework of economic and labor rights in EU, the traditional economic freedoms and provisions of the Charter will be examined in this paper in order to draw conclusions on the level of protection of such rights and the modifications that the Lisbon Treaty have brought in EU legal order with reference to economic and labor rights.

  18. Efficiency of European public higher education institutions: a two-stage multicountry approach.

    Science.gov (United States)

    Wolszczak-Derlacz, Joanna; Parteka, Aleksandra

    2011-12-01

    The purpose of this study is to examine efficiency and its determinants in a set of higher education institutions (HEIs) from several European countries by means of non-parametric frontier techniques. Our analysis is based on a sample of 259 public HEIs from 7 European countries across the time period of 2001-2005. We conduct a two-stage DEA analysis (Simar and Wilson in J Economet 136:31-64, 2007), first evaluating DEA scores and then regressing them on potential covariates with the use of a bootstrapped truncated regression. Results indicate a considerable variability of efficiency scores within and between countries. Unit size (economies of scale), number and composition of faculties, sources of funding and gender staff composition are found to be among the crucial determinants of these units' performance. Specifically, we found evidence that a higher share of funds from external sources and a higher number of women among academic staff improve the efficiency of the institution.

  19. Institutional, Sociological and Spatial Factors Influencing Consumer Protection Perceptions in the European Union

    Directory of Open Access Journals (Sweden)

    Codruţa MARE

    2014-11-01

    Full Text Available The present study assesses through quantitative methods the problems specific to consumer protection. We focused on the factors that influence the number of complaints at national level and the perception of consumers that they are protected by public authorities. Data used for the 27 countries of the European Union were collected by official institutions, such as Heritage Foundations, United Nations Development Programme and the European Commission. Two types of econometric tools were employed: Ordinary Least Squares Multiple Regression and Spatial Econometric methods, such as map analysis, Moran’s I test for spatial autocorrelation and spatial regression. The results are convincing in what regards the institutional factors. Other types of behavior, such as social factors and spatial neighborhood effects, could not be highlighted.

  20. The Aspergillus Mine - publishing bioinformatics

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Rasmussen, Jane Lind Nybo; Theobald, Sebastian

    with the Joint Genome Institute. The Aspergillus Mine is not intended as a genomic data sharing service but instead focuses on creating an environment where the results of bioinformatic analysis is made available for inspection. The data and code is public upon request and figures can be obtained directly from...

  1. Institutional barriers to organic farming in Central and Eastern European countries of the Baltic Sea region

    OpenAIRE

    Larsson, Markus; Morin, Louise; Hahn, Thomas; Sandahl, Johanna

    2013-01-01

    A window of opportunity to promote organic farming is open for the Central andEastern European Countries (CEEC) that joined the EU in 2004. The development oforganic farming has the potential to decrease the amount of nutrient leaching tothe Baltic Sea and could help to stop the environmental degradation of the Sea.However, this requires a diverse set of institutions. This paper explores theinstitutions that are lacking to promote the full development of organic farming inthe CEEC, using Swed...

  2. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

    DEFF Research Database (Denmark)

    Schneider, Maria V.; Walter, Peter; Blatter, Marie-Claude

    2012-01-01

    to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes...... and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review...

  3. OECI accreditation of the European Institute of Oncology of Milan: strengths and weaknesses.

    Science.gov (United States)

    Deriu, Pietro L; Basso, Silvia; Mastrilli, Fabrizio; Orecchia, Roberto

    2015-01-01

    The European Institute of Oncology began the process to reach the accreditation promoted by the Organisation of European Cancer Institutes (OECI) in 2012. This accreditation integrates the quality and safety path started in 2001 with accreditation by the Joint Commission International. Despite the presence of diversified accreditations and certifications and the clear need of time, effort, and commitment, the models are complementary. Each model is not to be considered as an end but as a tool for improvement: e.g., mixing accreditation standards led to an improvement in the quality and safety of processes. The present article details the OECI accreditation experience of the European Institute of Oncology, in particular the following strengths of OECI standards: collaboration among several involved parties (patient, volunteer, patient's general practitioner) in the clinical and quality/safety processes; a larger involvement of support personnel (psycho-oncologists, dieticians, physical therapists); and the development of clinical/translational research and innovation in prevention, diagnosis, and treatment to guarantee the best available practice in diagnosis and treatment. The OECI accreditation is specific to oncology and therefore its standards are tailored to a cancer center, both in terms of language used in the standards manual and in terms of patient needs. The OECI accreditation system puts an auditor team with a standards manual in charge of verifying quality and confirms the definition of IEO as a Comprehensive Cancer Center.

  4. Science on the net: an analysis of the websites of the European public research institutions

    Directory of Open Access Journals (Sweden)

    Laura Massoli

    2007-09-01

    Full Text Available This article introduces a study on the websites of several European public research institutions that aims at identifying the science communication model chosen and implemented online with the purpose of reaching different target publics. The analytical approach takes into account a number of indicators: from the institutional identity to the scientific features, from the interactive services to the internationalisation level, in order to evaluate whether the web provides an added value in the adopted communication model and in building a relation with the users. Lights and shades emerge from this study in which good practices side examples of a much weaker science communication approach, outlining a general context where a public research institution website has been still used as a presentation tool and its interactive opportunities have not been capitalised.

  5. Bioinformatics paper exceeds 500 in citation index

    OpenAIRE

    Whyte, Barry James

    2010-01-01

    A scientific paper that includes contributions from scientists at the Virginia Bioinformatics Institute at Virginia Tech, has exceeded 500 citations in the ISI Web of Knowledge, an online academic database that documents the impact of scientific publications.

  6. The institutional dimension of the European Union’s combat transnational crime, as one of the main threats to European security

    Directory of Open Access Journals (Sweden)

    O. S. Vonsovych

    2016-06-01

    Full Text Available The article investigates the role of the leading institutions of European Union in the fight with transnational crime. It was determined that the problem of transnational crime occupies one of the central places in the field of European security. This is due to the fact that the overall level of crime in Europe in recent years has increased several times compared with the beginning of the XXI century. It was found that today transnational crime is becoming a serious obstacle on the way of building stability and sustainable development. It is nothing less than terrorism, illegal immigration affects the state of European security, creating the new center of a danger in Europe. It is proved that each institution has its own specific of struggle, but the unifying factor is that all of them are working on the same thing – the elimination of the threat in order to increase the level of security in Europe in general and in EU in particular. Substantiated the thesis that it is important to further developing of close and constructive cooperation between the main European institutions, as well as mutual exchange of information and data regarding the recent changes and the manifestations of transnational crime. This will give an opportunity to strengthen the European security system, as well as implement common practical methods of counteraction. It was determined that the actualization of the practical component in the framework of EU institutional dimension in the future will contribute to strengthening European.

  7. The institutional structure and political economy of food distribution systems: A comparative analysis of six Eastern European countries

    DEFF Research Database (Denmark)

    Esbjerg, Lars; Skytte, Hans

    This paper discusses the food distribution systems of six Eastern European countries. It considers the macro and task environments of distribution systems, discussing the constraints and opportunities the environments present to companies. The institutional structure of retailing and wholesaling...

  8. ADJUSTMENT DURING THE CRISIS: INSTITUTIONAL BUFFERS ON THE EASTERN EUROPEAN LABOUR MARKETS

    Directory of Open Access Journals (Sweden)

    Pavol Babos

    2014-05-01

    Full Text Available The economic crisis had profound effects on labour markets of the EU member states in terms of a decline in employment and a rise in unemployment. This paper investigates how the states limited the impact of the change in economic output on the employment and the unemployment. The analysis suggests that there are different labour market institutions influencing the impact of the fall in GDP on the employment decline and unemployment increase. The first part of the paper explores and compares the extent to which the labour market institutions cushioned the impact of the economic crisis on the EU countries. The second part of this paper provides an in-depth comparative analysis of the labour market institutions and the adjustment mechanisms in Central Eastern European countries: Latvia, Slovenia and Slovakia. In the end this paper suggests that the specific institutional setting of a country, according to the Varieties of Capitalism, might shape the form of the government response to the crisis and the effect of particular institutions on the adjustment channels. The study shows that adjustment in Slovenia took place mostly within the firms, while in Latvia the most efficient adjustment channels actuated outside the firms, mostly within the government sponsored training programmes and international migration. In Slovakia, government sponsored adjustment, which focused on maintaining the existing positions, prevailed together with the promotion of self-employment.

  9. The competences of European Union institutions in the trade policy (Lisbon Treaty

    Directory of Open Access Journals (Sweden)

    Margareta Timbur

    2010-12-01

    Full Text Available The European Union is the best known at the world’s leading trade power and the common trade policy is the core of EU external relations. The events of the last years and the extension of the EU to 27 member proved that the functioning system could no longer continue and was requiring a new institutional framework. The Lisbon Treaty was the right solution. It purposes are to bring changes for the citizens, institutions, external relations foe the consolidation of democracy in EU. This paper attempts to provide an overview of the major revisions introduced by the Treaty of Lisbon regarding the trade policy. Also, it analyses the extension and clarification of EU competence, the greater role of the European Parliament and the inclusion of investment policy in trade policy, the voting rules in trade area and the international negotiation of trade agreements. The study describes, as well, the impact of Lisbon Treaty implementation on the MS which are independent nations, but without power of decision in the common trade policy.

  10. A Quick Guide for Building a Successful Bioinformatics Community

    Science.gov (United States)

    Budd, Aidan; Corpas, Manuel; Brazas, Michelle D.; Fuller, Jonathan C.; Goecks, Jeremy; Mulder, Nicola J.; Michaut, Magali; Ouellette, B. F. Francis; Pawlik, Aleksandra; Blomberg, Niklas

    2015-01-01

    “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB). PMID:25654371

  11. Computational Biology and Bioinformatics in Nigeria

    Science.gov (United States)

    Fatumo, Segun A.; Adoga, Moses P.; Ojo, Opeolu O.; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-01-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries. PMID:24763310

  12. Computational biology and bioinformatics in Nigeria.

    Science.gov (United States)

    Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

    2014-04-01

    Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  13. Computational biology and bioinformatics in Nigeria.

    Directory of Open Access Journals (Sweden)

    Segun A Fatumo

    2014-04-01

    Full Text Available Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

  14. Transparency as a Platform for Institutional Politics: The Case of the Council of the European Union

    Directory of Open Access Journals (Sweden)

    Maarten Hillebrandt

    2017-09-01

    Full Text Available The question of transparency is widely regarded as a thermometer of the relation between the Council of the EU and the public at large. Relatively little attention however has been devoted to the implications of transparency (i.e., access for the general public for inter-institutional information politics, even when the limited evidence suggests that the connection is considerable. This article asks how EU actors use Council transparency as a platform and for what reason. It approaches transparency as a policy that is developed in three arenas: the internal, the external political, and the external judicial arena. The article finds strong evidence in support of the view that the Council’s transparency policy played a central role in EU institutions’ attempt to advance their information ambitions. By strongly engaging with the issue of transparency particularly the European Parliament and its members succeeded at expanding their institutional information basis in an area where their political grip was traditionally at its weakest: the Foreign Affairs Council. Acting in turn as a bargaining chip, a political lever, or an alternative to institutional information, the Foreign Affairs Council’s transparency policy was thus clearly used to advance information agendas of oversight and legislative prerogatives.

  15. Institutional Games Rational Actors Play – The empowering of the European Parliament

    Directory of Open Access Journals (Sweden)

    Anders Rasmussen

    2000-01-01

    Full Text Available In the three latest treaty reforms changes have been made to the procedures that regulate the legislative interaction between the European Parliament, the Commission and the Council. Whether the introduction of the co-operation procedure (1987, the co-decision procedure (1994 and the reform of the co-decision procedure (1999 have marked a linear increase in the power of the EP has been the object of debate. However, it has not been disputed that these three procedures vis-à-vis the consultation procedure give the EP a significant legislative role not previously enjoyed. To explain the empowering of the EP, this paper takes its point of departure in the causality between institutional choices and institutional consequences. Using spatial theory and drawing on historical institutionalism it introduces an analytical model that operates on two levels, the level of day-to-day politics and the level of treaty reforms. Two main points are made. First, adapting strategically to the de jure legislative procedures the EP has been able to convert these into de facto procedures that grant it a substantial legislative role. Second, this empowering has enabled the EP and the Commission to pursue a pro-integrationist agenda in a two-level game of legislation and implementation.

  16. Institutional Games Rational Actors Play The empowering of the European Parliament

    Directory of Open Access Journals (Sweden)

    Anders Rasmussen

    2000-01-01

    Full Text Available In the three latest treaty reforms changes have been made to the procedures that regulate the legislative interaction between the European Parliament, the Commission and the Council. Whether the introduction of the co-operation procedure (1987, the co-decision procedure (1994 and the reform of the co-decision procedure (1999 have marked a linear increase in the power of the EP has been the object of debate. However, it has not been disputed that these three procedures vis-à-vis the consultation procedure give the EP a significant legislative role not previously enjoyed. To explain the empowering of the EP, this paper takes its point of departure in the causality between institutional choices and institutional consequences. Using spatial theory and drawing on historical institutionalism it introduces an analytical model that operates on two levels, the level of day-to-day politics and the level of treaty reforms. Two main points are made. First, adapting strategically to the de jure legislative procedures the EP has been able to convert these into de facto procedures that grant it a substantial legislative role. Second, this empowering has enabled the EP and the Commission to pursue a pro-integrationist agenda in a two-level game of legislation and implementation.

  17. Institutional Games Rational Actors Play The empowering of the European Parliament

    Directory of Open Access Journals (Sweden)

    Anders Rasmussen

    2000-01-01

    Full Text Available In the three latest treaty reforms changes have been made to the procedures that regulate the legislative interaction between the European Parliament, the Commission and the Council. Whether the introduction of the co-operation procedure (1987, the co-decision procedure (1994 and the reform of the co-decision procedure (1999 have marked a linear increase in the power of the EP has been the object of debate. However, it has not been disputed that these three procedures vis-à-vis the consultation procedure give the EP a significant legislative role not previously enjoyed. To explain the empowering of the EP, this paper takes its point of departure in the causality between institutional choices and institutional consequences. Using spatial theory and drawing on historical institutionalism it introduces an analytical model that operates on two levels, the level of day-to-day politics and the level of treaty reforms. Two main points are made. First, adapting strategically to the de jure legislative procedures the EP has been able to convert these into de facto procedures that grant it a substantial legislative role. Second, this empowering has enabled the EP and the Commission to pursue a pro-integrationist agenda in a two-level game of legislation and implementation.

  18. Pioneering Quality Assessment in European Cancer Centers: A Data Analysis of the Organization for European Cancer Institutes Accreditation and Designation Program

    NARCIS (Netherlands)

    Saghatchian, Mahasti; Thonon, Frederique; Boomsma, Femke; Hummel, Henk; Koot, Bert; Harrison, Chris; Rajan, Abinaya; de Valeriola, Dominique; Otter, Renee; Pontes, Jose Laranja; Lombardo, Claudio; McGrath, Eoin; Ringborg, Ulrik; Tursz, Thomas; van Harten, Willem H.

    2014-01-01

    Purpose: In order to improve the quality of care in Cancer Centers (CC) and designate Comprehensive Cancer Centers (CCCs), the Organization for European Cancer Institutes (OECI) launched an Accreditation and Designation (A&D) program. The program facilitates the collection of defined data and the

  19. Quality assurance systems of higher education - The case of european institutions: origin, evolution and trends

    Directory of Open Access Journals (Sweden)

    Ángela Corengia

    2014-11-01

    Full Text Available http://dx.doi.org/10.5007/1983-4535.2014v7n3p61 The purpose of this research is to analyze the origin, evolution, performance and trends of higher education quality assurance systems in the following European countries: Denmark, Norway, Sweden, Finland, Austria, Italy, Switzerland, Germany, Netherlands, United Kingdom and France. It also studies the performance and impact of the organizations that join the European Quality Assurance Agencies together. The main sources of data collection were in situ semi-structured interviews to members of these agencies. It was found that in higher education institutions there is a strong trend towards the development of ‘internal quality assurance systems' in response to the public policies known as 'quality audits'. This overview about what is taking place in Europe may provide innovative instruments that could be considered for higher education quality evaluation and accreditation in Latin-American countries: quality audits, disciplinary agencies, evaluation of the quality assurance agencies, among others.

  20. Introduction to structural bioinformatics.

    Science.gov (United States)

    Xu, Qin; Dai, Hao; Zhao, Tangzhen; Wei, Dongqing

    2015-01-01

    Structural Bioinformatics is one of the hot spots of interdisciplinary sciences and obtained amazing advances in recent years. The first chapter overviews the concept of structural bioinformatics, and briefly describe the contents of this book. The interdisciplinary corporations make it difficult to further divide structural bioinformatics, so the chapters in this book are roughly separated according to the different fields of their applications. That is, fundamental developments in methods of structural bioinformatics, tertiary structure prediction and folding mechanism analysis, the binding mechanism and the interactions between biological macromolecules and ligands, structure-based functional analysis of biological macromolecules, as well as the applications in drug design.

  1. Possible Directions for Redefining the Institutional Framework of the Planning Policy Formulation in Serbia in Accordance with European Experiences

    OpenAIRE

    Maksić, Milica

    2012-01-01

    In this paper, in the theoretical framework of neoinstitutional theory, the process of spatial policy formulation in Serbia is discussed and compared with the experience of developed European countries. For the analysis of European experience, three countries with different national administrative tradition are selected: the United Kingdom (market-oriented culture), the Netherlands (the culture of consensus) and Germany (the culture of hierarchy). Various institutional arrangements made in...

  2. The Influence of Institutional Decision Making Mechanism in Russia on the Relations with the European Union

    Directory of Open Access Journals (Sweden)

    Nikita Chernyshev

    2014-05-01

    Full Text Available This article examines the influence of internal factors (such as decision-making processes, political culture, and the connection between government and society on Russia’s foreign policy toward the European Union in the context of neoclassical realism. Excessive personalization and a closed decision-making structure do not encourage effective reactions to emerging challenges and affect the possibility of cooperation in the post-Soviet space. Institutional mechanisms and their impact on a country’s foreign policy are extremely important in the theory of neoclassical realism. This article also analyses EU-Russia relations over major periods and the role of internal factors in Russian policy. Despite an orientation toward long-term cooperation between the EU and Russia, a contradiction remains between Russia’s over-centralized decision-making structure and the EU’s decentralized system. In addition, political leaders and elites play less of a role in the EU, where there is a real separation of powers and competencies. These factors hamper EU-Russia cooperation because Russia prefers to establish bilateral relations with each state. As a result of all these factors, long-term relations may be at risk. However, the decentralization of power, increased efficiency of political institutions and the active participation of civil society will improve the level of mutual trust and overcome the current issues in EU-Russia relations.

  3. The Post-9/11 European Union Counterterrorism Response: Legal-Institutional Framework

    Science.gov (United States)

    2012-12-01

    Madrid bombings , London bombings , effectiveness, legality, measures, Europol, Eurojust. 15. NUMBER OF PAGES 189 16. PRICE CODE 17. SECURITY...European Arrest Warrant EBDS European Bomb Data System ECHR European Court on Human Rights xiv ECJ European Court of Justice ECRIS...groups included: the Club of Berne established in 1971 by national security services of Belgium, Denmark, France, Germany, Switzerland, Great Britain

  4. Bioinformatics meets user-centred design: a perspective.

    Directory of Open Access Journals (Sweden)

    Katrina Pavelin

    Full Text Available Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI, and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.

  5. Challenge: A Multidisciplinary Degree Program in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Mudasser Fraz Wyne

    2006-06-01

    Full Text Available Bioinformatics is a new field that is poorly served by any of the traditional science programs in Biology, Computer science or Biochemistry. Known to be a rapidly evolving discipline, Bioinformatics has emerged from experimental molecular biology and biochemistry as well as from the artificial intelligence, database, pattern recognition, and algorithms disciplines of computer science. While institutions are responding to this increased demand by establishing graduate programs in bioinformatics, entrance barriers for these programs are high, largely due to the significant prerequisite knowledge which is required, both in the fields of biochemistry and computer science. Although many schools currently have or are proposing graduate programs in bioinformatics, few are actually developing new undergraduate programs. In this paper I explore the blend of a multidisciplinary approach, discuss the response of academia and highlight challenges faced by this emerging field.

  6. Students as Stakeholders in the Policy Context of the European Standards and Guidelines for Quality Assurance in Higher Education Institutions

    NARCIS (Netherlands)

    Logermann, Frauke; Leisyte, Liudvika; Curaj, Adrian; Matei, Liviu; Pricopie, Remus; Salmi, Jamil; Scott, Peter

    2015-01-01

    The European Standard and Guidelines for Quality Assurance (ESG) of 2005 can be defined as one of the major Bologna documents aimed at furthering the role of students as stakeholders in internal quality assurance processes at higher education institutions (HEIs). Still little is known about

  7. Parliamentarisation of the CFSP through informal institution-making? The fifth European Parliament and the EU high representative

    NARCIS (Netherlands)

    Crum, B.J.J.

    2006-01-01

    This article examines whether the European Parliament has been able to use the institution of the High Representative as a lever to increase its powers in the EU's common foreign and security policy. Since it is found that the EP's strategy towards the HR has neither brought it any informal powers

  8. INSTITUTIONS IN TRANSITION: IS THE EU INTEGRATION PROCESS RELEVANT FOR INWARD FDI IN TRANSITION EUROPEAN ECONOMIES?

    Directory of Open Access Journals (Sweden)

    Uros Delevic

    2017-02-01

    Full Text Available This research challenges the contemporary view of economic policy makers in transition European economies that the EU integration process will lead to a greater inflow of Foreign Direct Investments (FDI, thereby increasing living standards. With the Brexit referendum, the integration of the EU has been threatened by a distressing existential question: is EU membership valuable for transition countries if even developed countries (like the UK vote to leave or decided not to align like Switzerland and Norway in the past? Our analysis considers the success of several countries in Eastern Europe in attracting and benefiting from FDI on their way to EU membership. Analyzing a 13-year panel data of 16 transition countries, we found no statistically significant positive association between FDI inflow and EU accession. We argue, that it is also important to consider the welfare for domestic economies that can emerge from those investments. We illustrate this through the case study of a successful combination of institutional development and local content policies implementation accompanied by sufficient FDI inflows in a non-EU country - Kazakhstan.

  9. Car driver training and licensing systems in Europe : report prepared by members of Forum of European Road Safety Research Institutes FERSI and supported by European Commission Transport Directorate, DG VII.

    NARCIS (Netherlands)

    Lynam, D. & Twisk, D.A.M.

    1995-01-01

    This report describes a survey of car driver training and licensing systems in European countries, undertaken by the Forum of European Road Safety Research Institutes (FERSI) supported by the Transport Directorate of the European Union. A literature review and collation of general information on

  10. Academic Entrepreneurship vs. Changing Governance and Institutional Management Structures at European Universities

    Science.gov (United States)

    Kwiek, Marek

    2008-01-01

    This article discusses academic entrepreneurship in the context of ongoing changes in university management and governance in European universities. The comparative perspective is provided by the European Union (EU) research project "European Universities for Entrepreneurship: Their Role in the Europe of Knowledge" (EUEREK) comprising…

  11. Bioinformatics and Cancer

    Science.gov (United States)

    Researchers take on challenges and opportunities to mine "Big Data" for answers to complex biological questions. Learn how bioinformatics uses advanced computing, mathematics, and technological platforms to store, manage, analyze, and understand data.

  12. Deep learning in bioinformatics.

    Science.gov (United States)

    Min, Seonwoo; Lee, Byunghan; Yoon, Sungroh

    2017-09-01

    In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e. omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e. deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. RESEARCH ON PROBLEMS WITH PROJECTS AND PARTNERSHIPS THAT PUBLIC INSTITUTIONS IN THE CENTRE REGION FACED IN ACCESSING EUROPEAN FUNDS

    Directory of Open Access Journals (Sweden)

    DUMITRASCU DANUT

    2012-12-01

    Full Text Available European project management is the main filed of the article. Assuming a connection between the degree of absorption of European funds and the degree of maturity of the Romanian society in terms of project management, the article seeks to identify the negative factors on accessing and carrying out European projects. The identified problem is a low degree of absorption of European funds in Romania, and the main objective of the research is to identify the problems faced by the public institutions in the Centre Region in accessing European funds and also the causes that led to the low absorption of European funds. This article’s research is based on a preliminary analysis performed by the authors on the rate of accessing of European funds published in the article called “The current state of European funds absorption through funding programmes – measure of the Romanian performances in the project management practice”. The conclusion of this article was a low rate of absorption of European funds in Romania, a fact that reveals a poor practice of the theory on project management. This article identifies part of the causes of this situation by identifying a part of the problems that stood in the way of beneficiaries of European funds The qualitative and quantitative research methods are used in combination in the research. The investigation has however a highly quantitative character, the purpose of the qualitative research being to provide the prerequisites for achieving the quantitative research. The interview-based qualitative research enabled the researcher to get acquainted with the subjects’ problems related to the theme of investigation, the causes that have generated these problems. This preliminary investigation to the questionnaire-based research aims to provide information that would help the researcher prepare the questionnaire, so that the questions allow getting the most comprehensive information to

  14. Institutional Framework for Analyzing Sustainability in European Agriculture and Rural Areas

    NARCIS (Netherlands)

    Pascucci, S.; Polman, N.B.P.; Slangen, L.H.G.

    2011-01-01

    The aim of this chapter is to develop an institutional framework for analyzing and improving sustainability. More specifically we discuss (i) developing a framework that consists of different institutional levels and a set of indicators for measuring the relevant features of each institutional

  15. Quality assurance systems of higher education - The case of european institutions: origin, evolution and trends

    OpenAIRE

    Ángela Corengia; Juan Carlos Del Bello; María Pita Carranza; Cecilia Adrogué

    2014-01-01

    http://dx.doi.org/10.5007/1983-4535.2014v7n3p61 The purpose of this research is to analyze the origin, evolution, performance and trends of higher education quality assurance systems in the following European countries: Denmark, Norway, Sweden, Finland, Austria, Italy, Switzerland, Germany, Netherlands, United Kingdom and France. It also studies the performance and impact of the organizations that join the European Quality Assurance Agencies together. The main sources of data collection w...

  16. Science on the net: an analysis of the websites of the European public research institutions (Italian original version

    Directory of Open Access Journals (Sweden)

    Laura Massoli

    2007-09-01

    Full Text Available This article introduces a study on the websites of several European public research institutions that aims at identifying the science communication model chosen and implemented online with the purpose of reaching different target publics. The analytical approach takes into account a number of indicators: from the institutional identity to the scientific features, from the interactive services to the internationalisation level, in order to evaluate whether the web provides an added value in the adopted communication model and in building a relation with the users. Lights and shades emerge from this study in which good practices side examples of a much weaker science communication approach, outlining a general context where a public research institution website has been still used as a presentation tool and its interactive opportunities have not been capitalised.

  17. Institutional Quality of the Business Environment: Some European Practices in a Comparative Analysis

    Directory of Open Access Journals (Sweden)

    Cosmin Marinescu

    2013-02-01

    Full Text Available In contemporary economic literature, we can find plenty of theoretical and empirical approaches which seek to highlight the most appropriate factorial variables that are associated with the institutional quality of the business environment. This study presents, in a summarised version, the institutional logic of transaction costs that was substantiated within a scientific research project. In essence, the economic performances of the business environment are circumscribed by the institutions that facilitate or constrain the entrepreneurial initiatives and the economic activity in general. In terms of empirical analysis, the comparative approach of the EU business environments illustrates various exemples of (good or bad practices with respect to the institutional quality of the business environment. By selecting certain relevant institutional variables, the original character of this research resides in developing an indicator – The Institutional Quality of the Business Environment (hereafter IQBE which offers a dynamic perspective upon the business environments that characterise both Romania and other EU countries.

  18. Institutional context effects on managerial practices in a European multinational company

    Directory of Open Access Journals (Sweden)

    Leonardo Liberman

    2010-08-01

    Full Text Available The present study investigates the effect of institutional contexts on managerial practices within a multinational company. Questionnaires measuring actual and ideal managerial practices were completed in four different subsidiaries of the same MNC. Results show that the practices of subsidiaries operating in countries with a higher degree of institutional labor-market regulation were less formalized and directive than in those subsidiaries located in countries with a lower degree of labor-market regulation. It was also found that the degrees of acceptance of these practices differed significantly across institutional contexts: in less restrictive institutional contexts formal and directive practices were more desirable than in more restrictive institutional contexts. It is argued that there is an inverse relationship between the flexibility of subsidiaries’ institutional contexts and the flexibility of their practices (formality and directiveness. Implications and limitations of this study are discussed.

  19. THE TAX POLICY WITHIN THE EUROPEAN UNION: CONCEPTS, INSTITUTIONS, TRENDS AND CHALLENGES

    Directory of Open Access Journals (Sweden)

    CRISTINA COJOCARU (BOROVINA

    2016-06-01

    Full Text Available At the basis of conceiving the tax policy of an European Union member state, one must consider, on the one hand, fulfilling the government's own requirements, and on the other hand, achieving the objectives set by the EC Treaty. At present, the European Union has a quite harmonized and coordinated tax policy in the indirect taxes field, and partially in the direct taxes field, based on the free movement principle of goods, services, capital and labour; thus, although the member states have the freedom to set operation rules of their own national tax systems, this freedom is conditioned by the compliance with the priority objectives of the founding treaties of the European Union. The member states should avoid adopting discriminating tax measures (which could lead to a disadvantageous treatment for the persons, goods and services or capitals coming from other member states. Sometimes, the restrictions regarding free movement on the internal market are generated by the differences between the national tax systems, so that a certain degree of tax harmonization at the European Union level is necessary. The tax harmonization can be achieved either spontaneously (by means of the forces of the market, by means of active actions at the level of the European Union (the implementation of common policies, the coordination of the policies, the harmonization of the legislation, etc. or by means of the passive actions of the European Court of Justice (the interdiction of certain types of conduct of the member states that do not comply with the norms of the European Union. In the absence of the tax harmonization, negative effects can occur, such as: the erosion of the national tax bases, provision of public services and goods at a sub-optimal level, unwanted changes in the structure of the taxes which are levied in the member states, and distortions in assigning resources at the level of the single market.

  20. The European Society of Therapeutic Radiology and Oncology-European Institute of Radiotherapy (ESTRO-EIR) report on 3D CT-based in-room image guidance systems: a practical and technical review and guide

    NARCIS (Netherlands)

    Korreman, Stine; Rasch, Coen; McNair, Helen; Verellen, Dirk; Oelfke, Uwe; Maingon, Philippe; Mijnheer, Ben; Khoo, Vincent

    2010-01-01

    The past decade has provided many technological advances in radiotherapy. The European Institute of Radiotherapy (EIR) was established by the European Society of Therapeutic Radiology and Oncology (ESTRO) to provide current consensus statement with evidence-based and pragmatic guidelines on topics

  1. European practices of providing of efficiency of self-organizations institutions of population in the context of public services

    Directory of Open Access Journals (Sweden)

    T. V. Serohina

    2017-06-01

    Full Text Available The research revealed that European countries devote sufficient attention to ensuring the effectiveness of the institutions of self-organization in the context of their public services. The most common areas where they operate are a system of health, education and assistance during emergencies. The study showed that in the development of public services, there were significant transformations in terms of subject-provider. Historically it was confessional organizations working on a voluntary basis, and linked their activity with the realization of Christian mission. Subsequently, when there had been formation of a «welfare state», the state took over responsibility for the area of public services. In favor of institutions of self-organization has been a change in the system when it became clear that they are best in the provide public services, especially in the social sphere, because they are the demonstrating of social needs. The main mechanisms of cooperation between institutions of self-organization and the public sector are, first, subsidies for statutory activities of the organization. Another mechanism is delegating services or outsourcing and in this case contracts mostly are for one year with possibility of further extension. In addition there is auxiliary element of providing of effectiveness institutions of self-organization, it consists in deprivation of their donors from taxes. Although institutions of self-organization are financed mainly by public authorities, they remain independent, because they have opportunity of funding from other sources. German experience showed that the starting point in the system of public services is the understanding of the necessity of paying taxes as acknowledgment of the rights of all members of society. That is why every taxpayer expects to receive public services at the appropriate level. This unwritten rule contributes to a very high level of provision of public services through an adequate

  2. An Institutional Approach to Bordering in Islands: The Canary Islands on the African-European Migration Routes

    Directory of Open Access Journals (Sweden)

    Dirk Godenau

    2012-05-01

    Full Text Available Islands play a significant role in international irregular maritime migration. Frequently they are part of maritime interstitial spaces between states, and their location, combined with institutional membership, makes them part of international migration routes and subject to border management strategies. In this paper borders are analysed as social institutions used for regulating relative permeability through rules of entry and exit for persons, goods and capital. Borders institutionalize territoriality and are politically implemented by states. They are selective, also in migration, and irregular border transit is not always indicative of an inability to control. The Canary Islands are used as an illustrative example of how border management at the southern edge of the European Union has evolved towards more coercive deterrence and tighter surveillance. The Canary Islands experienced irregular maritime immigration from the west African coasts during the first decade of the 21st century and most of these migrants intended to use the islands as transit space towards the European continent. Increasing surveillance in countries of origin, enforcement of border controls and stricter return policies were used to stop flows. The so-called “cayuco crisis” in 2006 induced institutional change in border management and forced the active involvement of the EU through FRONTEX.

  3. Gender Discrimination and Institutional Frameworks: Evidence from Four European Union Countries

    Directory of Open Access Journals (Sweden)

    Sarah Drakopoulou Dodd

    2008-04-01

    Full Text Available This paper reviews important aspects of gender labour market inequalities in four European Union countries. It shows that individual countries differ in many aspects of gender discrimination. It seems that contributing factors to these differences are the national social and economic structures, the level of economic development, the legislative framework and the effectiveness of anti-discriminatory policies. It also shows that there are notable improvements in many gender gap indicators during the recent years and, at least part of the improvement should be attributed to the European commission’s legislative and policy initiatives.

  4. A desk review on institutional and non-institutional organizations active in the field of migrant's health in the WHO European Region.

    Science.gov (United States)

    Ingrosso, Loredana; Schmidt, Tanja; Sherally, Jamila; Dembech, Matteo; Barragan Montes, Sara; Sa Machado, Rita; Annunziata, Giuseppe; Rezza, Giovanni; Severoni, Santino

    2015-01-01

    Migrants have problematic access to health-care; non-institutional organizations (NGOs), as well as institutional bodies may play a role in facilitating their access to mainstream health care. Our research reviews actions that address the need of migrants in terms of health care in order to understand how, where, and who participates in this effort. Data were from desk or web research, declaration from organisations and their websites, information from WHO Country Offices. 154 NGOs were identified in the WHO European Region. 58% were direct health care providers while the remaining provided either mediation services or were part of a network organization. 173 national institutes (GOVs) were found; less than the 20% were directly or indirectly involved in health care, whereas the majority were involved in research, policy development, international relations and human rights. Some gaps, a certain fragmentation and lack of coordination were identified. WHO can play an overarching role in the exchange of expertise and harmonisation of the efforts in this field.

  5. Territorial change and national identities in Eastern and Western Europe beyond nationalism: three visions of the European Union and their implications for the linguistic regime of its institutions

    NARCIS (Netherlands)

    Mamadouh, V.D.

    1999-01-01

    Samenvatting: The linguistic diversity in the European Union is generally viewed as an essential component of the European identity, but the linguistic regime of the EU institutions (with eleven official and working languages) is not undisputed. In addition, the upcoming enlargements will complicate

  6. Mental health care institutions in nine European countries, 2002 to 2006

    NARCIS (Netherlands)

    Priebe, Stefan; Frottier, Patrick; Gaddini, Andrea; Kilian, Reinhold; Lauber, Christoph; Martinez-Leal, Rafael; Munk-Jorgensen, Povl; Walsh, Dermot; Wiersma, Durk; Wright, Donna

    Objective: Although mental health reforms in the 20th century were characterized by deinstitutionalization, previous research suggested a new era of reinstitutionalization in six European countries between 1990 and 2002. This study aimed to establish whether there has been a trend in Europe toward

  7. New institutional assemblages for borderless customs control in the European Union

    NARCIS (Netherlands)

    Naber, A.C.; Hofman, W.; Enserink, B.; Kotterink, B.

    2013-01-01

    This article is based on a use case proposing a Single Window implementation for borderless customs control in the European Union (EU). This EU e-Customs initiative proposes to combine trade facilitation from a customs perspective with secure trade based on supply chain risk analysis. To achieve

  8. Bioinformatics for Exploration

    Science.gov (United States)

    Johnson, Kathy A.

    2006-01-01

    For the purpose of this paper, bioinformatics is defined as the application of computer technology to the management of biological information. It can be thought of as the science of developing computer databases and algorithms to facilitate and expedite biological research. This is a crosscutting capability that supports nearly all human health areas ranging from computational modeling, to pharmacodynamics research projects, to decision support systems within autonomous medical care. Bioinformatics serves to increase the efficiency and effectiveness of the life sciences research program. It provides data, information, and knowledge capture which further supports management of the bioastronautics research roadmap - identifying gaps that still remain and enabling the determination of which risks have been addressed.

  9. Round robins of solar cells to evaluate measurement systems of different european research institutes

    Energy Technology Data Exchange (ETDEWEB)

    Manshanden, P.; Van der Brog, N.J.C.M. [ECN Solar, Westerduinweg 3, 1755 LE Petten (Netherlands); Bliss, M.; Mihaylov, B.; Gottschlag, R. [CREST, Holywell Park MBG GJ/Gx, Loughborough Univeristy, Leicestershire, LE11 3TU (United Kingdom); Izzi, M.; Tucci, M. [ENEA CASACCIA, Via Anguillarese 301, 00123 Roma (Italy); Roca, F.; Pellegrino, M.; Romano, A.; Graditi, G. [ENEA PORTICI, P. le E. Fermi Localita Granatello, 80055 Portici Napoli (Italy); Hohl-Ebinger, J.; Warta, W. [Fraunhofer ISE, Berliner Allee 30, 79110 Freiburg (Germany); Debucquoy, M.; El Daif, O.; Gordon, I. [IMEC, Kapeldreef 75, B-3001 Heverlee (Belgium); Champliaud, J.; Jouini, A. [INES, 50 avenue du lac Leman, BP 332, 73377, Le Bourget-du-Lac (France); Glatz-Reichenbach, J. [ISC, Rudolf Diesel Str. 15, D-78467 Konstanz (Germany); Bothe, K. [ISFH, Am Ohrberg 1, 31860 Emmerthal (Germany); Herguth, A. [University of Konstanz, Universitaetsstrasse 10, 78457 Konstanz (Germany)

    2013-10-15

    Determination of the solar cell efficiency and internal quantum efficiency are standard characterization methods used by the majority of research institutes. Random errors can be assessed by institutes themselves by repeated measurements, but systematic deviations cannot be assessed without comparisons with other institutes. The comparisons were performed for illuminated IV, spectral response and reflection measurements. The results were split into systematic differences between the partners and random differences within an institute for a single measurement session. The total differences are: J{sub sc}: 0.27 A, V{sub oc}: 8.5 mV, FF: 2.4 %, {eta}: 0.6%, spectral response: 0.14 A/W and reflection: 0.08. For all measurement methods, the systematic differences exceeded the random differences. The major component for the systematic differences is likely the reference device, but also temperature control, contacting scheme and setup differences play a part.

  10. Advance in structural bioinformatics

    CERN Document Server

    Wei, Dongqing; Zhao, Tangzhen; Dai, Hao

    2014-01-01

    This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conform

  11. AXIOMS AND INTERNAL CONTROL REQUIREMENTS MANAGEMENT IN THE PUBLIC INSTITUTIONS. APPLICATION MODE IN ROMANIA AND OTHER EUROPEAN COUNTRIES

    Directory of Open Access Journals (Sweden)

    ENEA CONSTANTIN

    2017-12-01

    Full Text Available The goal of any institution is to have a management that would implement public policies, programs and projects aimed at fulfilling the mission of the institution and the objectives of the government, through the rational use of resources (often limited and at the same time to satisfy stakeholders. Implement a system of internal control has emerged as a necessity from globalization and liberalization of financial markets, free movement of capital, information, people and goods through the application of internationally recognized standards and to be understood in a uniform manner. The research was focused on the one hand, the literature review Romanian and foreign legislation and internal control management system, providing a theoretical and practical approach, but on the other hand, we considered appropriate to perform a research on the application of internal control management system in member states of the European Union.

  12. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  13. Crowdsourcing for bioinformatics.

    Science.gov (United States)

    Good, Benjamin M; Su, Andrew I

    2013-08-15

    Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base population and protein structure determination all benefit from human input. In some cases, people are needed in vast quantities, whereas in others, we need just a few with rare abilities. Crowdsourcing encompasses an emerging collection of approaches for harnessing such distributed human intelligence. Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains. Here, we provide a framework for understanding and applying several different types of crowdsourcing. The framework considers two broad classes: systems for solving large-volume 'microtasks' and systems for solving high-difficulty 'megatasks'. Within these classes, we discuss system types, including volunteer labor, games with a purpose, microtask markets and open innovation contests. We illustrate each system type with successful examples in bioinformatics and conclude with a guide for matching problems to crowdsourcing solutions that highlights the positives and negatives of different approaches.

  14. European Innovation Partnership on Active and Healthy Ageing (EIP on AHA – the opportunities for Polish scientists and institutions

    Directory of Open Access Journals (Sweden)

    Kardas Przemysław

    2016-05-01

    Full Text Available Europe is facing great social and economic challenges now, being a result of the ageing process progressing faster than ever. This, however, might be perceived also as an opportunity for innovation, as well as an additional impulse for the so-called “Silver Economy”. To address these new needs and opportunities, the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA was initiated by the European Commission in 2012. After three years of its activity, it has proved to be a strong movement of European stakeholders committed to innovation, with its overarching target to increase the average healthy lifespan by two years by 2020. The ‘Triple Win’ strategy for Europe is based on the concepts of enabling the EU citizens to lead healthy, active and independent lives while ageing, improving the sustainability and efficiency of social and health care systems, and boosting and improving the competitiveness of markets for innovative products and services. Now, the EIP on AHA opens new calls that enable new stakeholders to become partners of this collaboration. This provides a unique opportunity to Polish institutions, as well as scientists. In order to help them use this opportunity effectively, the history, aims, structure and achievements of the EIP on AHA are shortly described in this paper.

  15. Institutional analysis of incentive schemes for ecosystem service provision - a comparative study across four European countries

    DEFF Research Database (Denmark)

    Prokofieva, Irina; Górriz, Elena; Boon, Tove Enggrob

    2014-01-01

    Incentive schemes and payments for ecosystem services attract increasing attention as a means for aligning the interests of landowners and society by remunerating forest owners for the goods and services their forests produce. As incentive schemes expand around the world, questions related...... and Italy. The analysed schemes are predominantly aimed at enhancing biodiversity and improving recreation. One of the schemes is also related to preserving a variety of forest ecosystem services from forest fires. The incentive schemes are studied following a framework for the institutional analysis of PES...... developed by Prokofieva and Gorriz (Prokofieva, I. and Gorriz, E. 2013: Institutional analysis of incentives for the provision of forest goods and services: an assessment of incentive schemes in Catalonia (North-East Spain), Forest Policy and Economics, 37, 104-114.). We focus on actor and institutional...

  16. «GREEN» LOGISTICS AS A TOOL TO ENSURE ENVIRONMENTAL SECURITY AND INSTITUTIONAL INNOVATION SUBSOIL EUROPEAN ARCTIC

    Directory of Open Access Journals (Sweden)

    M. N. Dudin

    2016-01-01

    Full Text Available This article is an overview of the major logistics and technology solutions to be implemented to streamline the subsoil use in the European Arctic. The theme of this work is very urgent, because Russia, despite the high resource base is underdeveloped institutional framework and resource extraction is characterized by the maximum level of loss of potential gross value of the hydrocarbon potential.The purpose of this article is to study Russian priorities at national and regional level, related to mining, through the use of «green» logistics as an instrument for environmental safety and institutional innovation subsoil of the European Arctic.Methodology. The methodological basis of this article are comparative, economic and statistical analysis methods.The results of this paper have become the solutions to problems, to achieve this goal, in particular: a substantiated conclusion that the Arctic is a world heritage and «climate laboratory» of the planet, so the development of the resource, industrial, transport and logistics potential of the region need to be based on «green» technologies; The article describes four environmentally-oriented direction (creating material and technical base, the formation of a safe icebreaker fleet, the development of new navigation and communication systems, power supply, which will enable to master the industrial, transport and logistics potential of the Arctic with minimal anthropogenic load.Conclusions. The following basic conclusions were as follows: first, subarctic and arctic areas are world heritage, so the development of deposits on them should be in the interest of the world community on a non-discriminatory  basis; secondly, hydrocarbon reserves, concentrated in the European Arctic, currently can not be extracted without environmental impacts, access to these resources is limited due to lack of development of the transport component, therefore, should be used aggressive techniques of extraction of

  17. The European Union as a Minervian Actor in Global Institution Building

    DEFF Research Database (Denmark)

    Manners, Ian

    2013-01-01

    . It introduces constitutive and causal theories, the internal origins of the EU’s norms, EU normative principles, and considers the EU’s external practices in action in order to understand the EU as a Minervan power in global institution building. The chapter illustrates this through the EU notion of “effective...

  18. The distribution of housing wealth in 16 European countries : Accounting for institutional differences

    NARCIS (Netherlands)

    Wind, B.J.; Dewilde, C.L.; Lersch, P.M.

    2017-01-01

    Housing wealth is the largest source of household wealth, but we know little about the distribution of housing wealth and how institutions have shaped this distribution. Subsidies for homeownership, privatisation of social housing and mortgage finance liberalisation are likely to have influenced the

  19. The European Union from Maastricht to Lisbon: institutional and legal unity out of the shadows

    NARCIS (Netherlands)

    Curtin, D.M.; Dekker, I.F.; Craig, P.; de Búrca, G.

    2011-01-01

    The EU was originally established in the Treaty of Maastricht in 1992 as a formal legal construct not entailing legal unity with the pre-existing EC. Almost 20 years later the Treaty of Lisbon explicitly ordains legal unity, thus catching up with legal and institutional practices, social reality and

  20. The European Union from Maastricht to Lisbon. Institutional and Legal Unity out of the Shadows

    NARCIS (Netherlands)

    Curtin, D.; Dekker, I.

    2010-01-01

    The EU was originally established in the Treaty of Maastricht in 1992 as a formal legal construct not entailing legal unity with the pre-existing EC. Almost 20 years later the Treaty of Lisbon explicitly ordains legal unity, thus catching up with legal and institutional practices, social reality and

  1. Institutional challenges caused by the integration of renewable energy sources in the European electricity sector

    NARCIS (Netherlands)

    Verzijlbergh, R.A.; de Vries, L.J.; Dijkema, G.P.J.; Herder, P.M.

    2016-01-01

    The integration of large amounts of variable renewable energy poses fundamental challenges to the operation and governance of the energy system. In this article we address the main institutional challenges that are caused by the integration of variable renewable energy sources like solar and wind

  2. Financial Regulations and the Diversification of Funding Sources in Higher Education Institutions: Selected European Experiences

    Science.gov (United States)

    Stachowiak-Kudla, Monika; Kudla, Janusz

    2017-01-01

    The paper addresses the problem of the financial regulations' impact on the share of private financing in higher education institutions (HEIs). The authors postulate the trade-off between the size and stability of public financing and the regulations fostering stability of HEIs' funds. If the public sources are insufficient then the regulations…

  3. Analysis of the European union’s supranationalism crisis within the political-institutional paradigm

    OpenAIRE

    O. V. Bashtannyk

    2014-01-01

    The effect of integration policies and programs of the foreign policy of the European Union (EU) on the nature of the structural interaction between members and partners of cooperation is examined. It made possible to determine the “initiative” as a practical manifestation of “three­vector” model of the modern EU “drawing” integration strategy, which aims to bring the main state­initiated in cooperation certain group of countries, united mainly on a geographical basis, but conceivably have si...

  4. The Political Economy of the European Union: Institutions, Policy and Economic Growth

    DEFF Research Database (Denmark)

    Svendsen, Gert Tinggaard

    the current institutional set-up of the EU will determine future economic performance and will adversely affect policy outcomes. He looks at whether fundamental EU policies, such as the CAP, are consistent with economic growth or whether these policies will instead distort markets, leading to economic decline....... Focusing in detail on international climate negotiations and wind energy, the author explores the way in which the design of a policy proposal can be affected by the interactions between interest groups and the institutions and bureaucrats of the EU. The case of greenhouse gas emissions trading is a unique......' may be avoided by strengthening the power of the EU Parliament at the expense of the EU Commission. The book also discusses issues surrounding policy design, international negotiations on climate change and renewable energy sources. Using an interdisciplinary framework, the author examines how...

  5. A cooperative effort to exchange age reading experience and protocols between European fish institutes

    DEFF Research Database (Denmark)

    Appelberg, M.; Formigo, N.; Geffen, A.J.

    2005-01-01

    In Europe, research to improve age estimation methods is often limited to small-scale studies and thus it has been difficult to integrate innovations into routine protocols. There has even been a lack of pilot scale studies and implementation of control mechanisms in the age reading process....... This was recognised and addressed by European Fish Ageing Network (EFAN; 1997-2000). EFAN was established as an active, independent and informal network for exchange of ideas and experience for improving age estimation. For the first time, age reading problems were addressed on a common platform across Europe. EFAN...... improved awareness and sensitivity towards the quality of age reading, however, this did not always deliver changes in the routine age reading processes. The present project, Towards Accreditation and Certification of Age Determination of Aquatic Resources (TACADAR); 2002-2006 aims to submit a quality...

  6. Bioinformatics Core Project Management

    Science.gov (United States)

    Vangala, Mahesh; Vincent, James; Driscoll, Heather

    2013-01-01

    Bioinformatics cores that provide fee for service style support encounter a wide variety of projects. The scope of projects varies greatly among investigators. Because of this variety, it is difficult to develop a set of predefined services that fit all project types. While our own core has developed a baseline set of services, we found in practice these often needed significant modification to meet the goals of particular investigator. To overcome this problem we factored common features of all projects and partitioned them into groups: workflow management, data management, user results, and tracking and reporting. We then implemented best practices for each group using commercial and open source software combined with our own management policies. Finally we linked these areas together to produce an overall integrated project management solution that combines workflow management, data management, user results management and reporting capabilities. This system solves the problem of developing well defined services that are trackable and repeatable while simultaneously enabling flexibility that is easily managed. The result improves the effectiveness and efficiency of the bioinformatics core for scientists working within the core, for investigators receiving core support and for external auditors and evaluators.

  7. The Struggle of Benchmarking and Ranking Gender Equality: The Case of the European Institute for Gender Equality

    Directory of Open Access Journals (Sweden)

    Valkovičová Veronika

    2017-03-01

    Full Text Available The aim of this article is to explore the conceptualisation of benchmarking, ranking and good practice sharing tools within European Union gender equality policymaking. In the first part, the article looks at these soft law measures applied within intergovernmental cooperation. Stemming from the extensive body of literature, the study approaches these measures as a form of scientific knowledge, which is diversely applied within policymaking. Next, the article directs various points of criticism at these policymaking tools through different variables that may hinder knowledge use. The second section of this article further focuses on the Open Method of Coordination and the role of the European Institute for Gender Equality (EIGE in relation to gender equality policies. The empirical part of this article is focused on the criticism of EIGE’s External Evaluation Report and the different conceptualisations of scientific knowledge use which are presented within this audit document. As such, this article aims to contribute to a new conceptualisation of the technocratic tools of benchmarking, ranking and good practice sharing within the highly ideological area of gender equality policies.

  8. L’Unione Bancaria Europea. Di nuovo un disegno istituzionale incompleto (The European banking union. An incomplete institutional design, again

    Directory of Open Access Journals (Sweden)

    Mario Tonveronachi

    2013-12-01

    Full Text Available The proposal for a European banking union represents the more recent effort to drive the Eurozone countries towards the effective adoption of a single rulebook and a single supervisory handbook, at the same time endowing them with a centralised mechanism for the resolution of bank crises. The new institutional framework should help to disconnect banking operations from the vicissitudes of sovereign debts, to reverse the recent re-nationalisation of finance and to restore the effectiveness of ECB monetary policy. Although the new framework would mark a significant advancement with respect to the present situation, its predictable incomplete adoption, restricted to the single supervisory mechanism, coupled with the unwillingness to burden it with legacy problems, will most likely produce opposite results from its inception. Although the full implementation of the proposal would not constitute a departure from the political de-centralised design that has so far dominated the European construction, the potential fiscal implications of a centralised resolution mechanism have raised the same barriers that have so far impeded to complete the design initiated with the Maastricht Treaty.

  9. L’Unione Bancaria Europea. Di nuovo un disegno istituzionale incompleto (The European banking union. An incomplete institutional design, again

    Directory of Open Access Journals (Sweden)

    Mario Tonveronachi

    2013-12-01

    Full Text Available The proposal for a European banking union represents the more recent effort to drive the Eurozone countries towards the effective adoption of a single rulebook and a single supervisory handbook, at the same time endowing them with a centralised mechanism for the resolution of bank crises. The new institutional framework should help to disconnect banking operations from the vicissitudes of sovereign debts, to reverse the recent re-nationalisation of finance and to restore the effectiveness of ECB monetary policy. Although the new framework would mark a significant advancement with respect to the present situation, its predictable incomplete adoption, restricted to the single supervisory mechanism, coupled with the unwillingness to burden it with legacy problems, will most likely produce opposite results from its inception. Although the full implementation of the proposal would not constitute a departure from the political de-centralised design that has so far dominated the European construction, the potential fiscal implications of a centralised resolution mechanism have raised the same barriers that have so far impeded to complete the design initiated with the Maastricht Treaty.  JEL Codes: E02, F33, G18 

  10. Implementing a web-based introductory bioinformatics course for non-bioinformaticians that incorporates practical exercises.

    Science.gov (United States)

    Vincent, Antony T; Bourbonnais, Yves; Brouard, Jean-Simon; Deveau, Hélène; Droit, Arnaud; Gagné, Stéphane M; Guertin, Michel; Lemieux, Claude; Rathier, Louis; Charette, Steve J; Lagüe, Patrick

    2017-09-13

    A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become specialized. However, biology students who are not involved in a bioinformatics program also need a solid toolbox of bioinformatics software and skills. Therefore, we have developed a completely online bioinformatics course for non-bioinformaticians, entitled "BIF-1901 Introduction à la bio-informatique et à ses outils (Introduction to bioinformatics and bioinformatics tools)," given by the Department of Biochemistry, Microbiology, and Bioinformatics of Université Laval (Quebec City, Canada). This course requires neither a bioinformatics background nor specific skills in informatics. The underlying main goal was to produce a completely online up-to-date bioinformatics course, including practical exercises, with an intuitive pedagogical framework. The course, BIF-1901, was conceived to cover the three fundamental aspects of bioinformatics: (1) informatics, (2) biological sequence analysis, and (3) structural bioinformatics. This article discusses the content of the modules, the evaluations, the pedagogical framework, and the challenges inherent to a multidisciplinary, fully online course. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  11. Bioinformatics meets parasitology.

    Science.gov (United States)

    Cantacessi, C; Campbell, B E; Jex, A R; Young, N D; Hall, R S; Ranganathan, S; Gasser, R B

    2012-05-01

    The advent and integration of high-throughput '-omics' technologies (e.g. genomics, transcriptomics, proteomics, metabolomics, glycomics and lipidomics) are revolutionizing the way biology is done, allowing the systems biology of organisms to be explored. These technologies are now providing unique opportunities for global, molecular investigations of parasites. For example, studies of a transcriptome (all transcripts in an organism, tissue or cell) have become instrumental in providing insights into aspects of gene expression, regulation and function in a parasite, which is a major step to understanding its biology. The purpose of this article was to review recent applications of next-generation sequencing technologies and bioinformatic tools to large-scale investigations of the transcriptomes of parasitic nematodes of socio-economic significance (particularly key species of the order Strongylida) and to indicate the prospects and implications of these explorations for developing novel methods of parasite intervention. © 2011 Blackwell Publishing Ltd.

  12. Emergent Computation Emphasizing Bioinformatics

    CERN Document Server

    Simon, Matthew

    2005-01-01

    Emergent Computation is concerned with recent applications of Mathematical Linguistics or Automata Theory. This subject has a primary focus upon "Bioinformatics" (the Genome and arising interest in the Proteome), but the closing chapter also examines applications in Biology, Medicine, Anthropology, etc. The book is composed of an organized examination of DNA, RNA, and the assembly of amino acids into proteins. Rather than examine these areas from a purely mathematical viewpoint (that excludes much of the biochemical reality), the author uses scientific papers written mostly by biochemists based upon their laboratory observations. Thus while DNA may exist in its double stranded form, triple stranded forms are not excluded. Similarly, while bases exist in Watson-Crick complements, mismatched bases and abasic pairs are not excluded, nor are Hoogsteen bonds. Just as there are four bases naturally found in DNA, the existence of additional bases is not ignored, nor amino acids in addition to the usual complement of...

  13. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  14. Interdisciplinary Introductory Course in Bioinformatics

    Science.gov (United States)

    Kortsarts, Yana; Morris, Robert W.; Utell, Janine M.

    2010-01-01

    Bioinformatics is a relatively new interdisciplinary field that integrates computer science, mathematics, biology, and information technology to manage, analyze, and understand biological, biochemical and biophysical information. We present our experience in teaching an interdisciplinary course, Introduction to Bioinformatics, which was developed…

  15. Virtual Bioinformatics Distance Learning Suite

    Science.gov (United States)

    Tolvanen, Martti; Vihinen, Mauno

    2004-01-01

    Distance learning as a computer-aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material…

  16. Using institutional theory to analyse hospital responses to external demands for finance and quality in five European countries

    Science.gov (United States)

    Mendel, Peter; Nunes, Francisco; Wiig, Siri; van den Bovenkamp, Hester; Karltun, Anette; Robert, Glenn; Anderson, Janet; Vincent, Charles; Fulop, Naomi

    2015-01-01

    Objectives Given the impact of the global economic crisis, delivering better health care with limited finance grows more challenging. Through the lens of institutional theory, this paper explores pressures experienced by hospital leaders to improve quality and constrain spending, focusing on how they respond to these often competing demands. Methods An in-depth, multilevel analysis of health care quality policies and practices in five European countries including longitudinal case studies in a purposive sample of ten hospitals. Results How hospitals responded to the financial and quality challenges was dependent upon three factors: the coherence of demands from external institutions; managerial competence to align external demands with an overall quality improvement strategy, and managerial stability. Hospital leaders used diverse strategies and practices to manage conflicting external pressures. Conclusions The development of hospital leaders’ skills in translating external requirements into implementation plans with internal support is a complex, but crucial, task, if quality is to remain a priority during times of austerity. Increasing quality improvement skills within a hospital, developing a culture where quality improvement becomes embedded and linking cost reduction measures to improving care are all required. PMID:26683885

  17. Using institutional theory to analyse hospital responses to external demands for finance and quality in five European countries.

    Science.gov (United States)

    Burnett, Susan; Mendel, Peter; Nunes, Francisco; Wiig, Siri; van den Bovenkamp, Hester; Karltun, Anette; Robert, Glenn; Anderson, Janet; Vincent, Charles; Fulop, Naomi

    2016-04-01

    Given the impact of the global economic crisis, delivering better health care with limited finance grows more challenging. Through the lens of institutional theory, this paper explores pressures experienced by hospital leaders to improve quality and constrain spending, focusing on how they respond to these often competing demands. An in-depth, multilevel analysis of health care quality policies and practices in five European countries including longitudinal case studies in a purposive sample of ten hospitals. How hospitals responded to the financial and quality challenges was dependent upon three factors: the coherence of demands from external institutions; managerial competence to align external demands with an overall quality improvement strategy, and managerial stability. Hospital leaders used diverse strategies and practices to manage conflicting external pressures. The development of hospital leaders' skills in translating external requirements into implementation plans with internal support is a complex, but crucial, task, if quality is to remain a priority during times of austerity. Increasing quality improvement skills within a hospital, developing a culture where quality improvement becomes embedded and linking cost reduction measures to improving care are all required. © The Author(s) 2015.

  18. Signature of the Agreement between the University of Liverpool, acting on behalf of the Cockcroft Institute, represented by Inaugural Director of Cockcroft Institute S. Chattopadhyay and the European Organization for Nuclear Research represented by Director-General R. Aymar,concerning collaboration between the Cockcroft Institute and CERN in Accelerator Physics and Technologies.

    CERN Multimedia

    Claudia Marcelloni

    2008-01-01

    Signature of the Agreement between the University of Liverpool, acting on behalf of the Cockcroft Institute, represented by Inaugural Director of Cockcroft Institute S. Chattopadhyay and the European Organization for Nuclear Research represented by Director-General R. Aymar,concerning collaboration between the Cockcroft Institute and CERN in Accelerator Physics and Technologies.

  19. Bioinformatics Education in Pathology Training: Current Scope and Future Direction

    Directory of Open Access Journals (Sweden)

    Michael R Clay

    2017-04-01

    Full Text Available Training anatomic and clinical pathology residents in the principles of bioinformatics is a challenging endeavor. Most residents receive little to no formal exposure to bioinformatics during medical education, and most of the pathology training is spent interpreting histopathology slides using light microscopy or focused on laboratory regulation, management, and interpretation of discrete laboratory data. At a minimum, residents should be familiar with data structure, data pipelines, data manipulation, and data regulations within clinical laboratories. Fellowship-level training should incorporate advanced principles unique to each subspecialty. Barriers to bioinformatics education include the clinical apprenticeship training model, ill-defined educational milestones, inadequate faculty expertise, and limited exposure during medical training. Online educational resources, case-based learning, and incorporation into molecular genomics education could serve as effective educational strategies. Overall, pathology bioinformatics training can be incorporated into pathology resident curricula, provided there is motivation to incorporate, institutional support, educational resources, and adequate faculty expertise.

  20. String Mining in Bioinformatics

    Science.gov (United States)

    Abouelhoda, Mohamed; Ghanem, Moustafa

    Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word "data-mining" is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

  1. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  2. Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software.

    Science.gov (United States)

    Lawlor, Brendan; Walsh, Paul

    2015-01-01

    There is a lack of software engineering skills in bioinformatic contexts. We discuss the consequences of this lack, examine existing explanations and remedies to the problem, point out their shortcomings, and propose alternatives. Previous analyses of the problem have tended to treat the use of software in scientific contexts as categorically different from the general application of software engineering in commercial settings. In contrast, we describe bioinformatic software engineering as a specialization of general software engineering, and examine how it should be practiced. Specifically, we highlight the difference between programming and software engineering, list elements of the latter and present the results of a survey of bioinformatic practitioners which quantifies the extent to which those elements are employed in bioinformatics. We propose that the ideal way to bring engineering values into research projects is to bring engineers themselves. We identify the role of Bioinformatic Engineer and describe how such a role would work within bioinformatic research teams. We conclude by recommending an educational emphasis on cross-training software engineers into life sciences, and propose research on Domain Specific Languages to facilitate collaboration between engineers and bioinformaticians.

  3. Designing XML schemas for bioinformatics.

    Science.gov (United States)

    Bruhn, Russel Elton; Burton, Philip John

    2003-06-01

    Data interchange bioinformatics databases will, in the future, most likely take place using extensible markup language (XML). The document structure will be described by an XML Schema rather than a document type definition (DTD). To ensure flexibility, the XML Schema must incorporate aspects of Object-Oriented Modeling. This impinges on the choice of the data model, which, in turn, is based on the organization of bioinformatics data by biologists. Thus, there is a need for the general bioinformatics community to be aware of the design issues relating to XML Schema. This paper, which is aimed at a general bioinformatics audience, uses examples to describe the differences between a DTD and an XML Schema and indicates how Unified Modeling Language diagrams may be used to incorporate Object-Oriented Modeling in the design of schema.

  4. Genome Exploitation and Bioinformatics Tools

    Science.gov (United States)

    de Jong, Anne; van Heel, Auke J.; Kuipers, Oscar P.

    Bioinformatic tools can greatly improve the efficiency of bacteriocin screening efforts by limiting the amount of strains. Different classes of bacteriocins can be detected in genomes by looking at different features. Finding small bacteriocins can be especially challenging due to low homology and because small open reading frames (ORFs) are often omitted from annotations. In this chapter, several bioinformatic tools/strategies to identify bacteriocins in genomes are discussed.

  5. Implementation and translation: from European standards and guidelines for quality assurance to education quality work in higher education institutions

    NARCIS (Netherlands)

    Westerheijden, Donald F.; Kohoutek, Jan; Eggins, Heather

    2014-01-01

    The Standards and Guidelines for Quality Assurance in the European Higher Education Area (ESG for short) have been part of the regulative infrastructure of the European Higher Education Area (EHEA) since 2005 (European Association for Quality Assurance in Higher Education, 2009).

  6. Bioinformatics in Middle East Program Curricula--A Focus on the Arabian Gulf

    Science.gov (United States)

    Loucif, Samia

    2014-01-01

    The purpose of this paper is to investigate the inclusion of bioinformatics in program curricula in the Middle East, focusing on educational institutions in the Arabian Gulf. Bioinformatics is a multidisciplinary field which has emerged in response to the need for efficient data storage and retrieval, and accurate and fast computational and…

  7. Influenza research database: an integrated bioinformatics resource for influenza virus research

    Science.gov (United States)

    The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics, an...

  8. Implementing a Web-Based Introductory Bioinformatics Course for Non-Bioinformaticians That Incorporates Practical Exercises

    Science.gov (United States)

    Vincent, Antony T.; Bourbonnais, Yves; Brouard, Jean-Simon; Deveau, Hélène; Droit, Arnaud; Gagné, Stéphane M.; Guertin, Michel; Lemieux, Claude; Rathier, Louis; Charette, Steve J.; Lagüe, Patrick

    2018-01-01

    A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become…

  9. A Summer Program Designed to Educate College Students for Careers in Bioinformatics

    Science.gov (United States)

    Krilowicz, Beverly; Johnston, Wendie; Sharp, Sandra B.; Warter-Perez, Nancy; Momand, Jamil

    2007-01-01

    A summer program was created for undergraduates and graduate students that teaches bioinformatics concepts, offers skills in professional development, and provides research opportunities in academic and industrial institutions. We estimate that 34 of 38 graduates (89%) are in a career trajectory that will use bioinformatics. Evidence from…

  10. Application of bioinformatics to optimization of serum proteome in ...

    African Journals Online (AJOL)

    SELDI-TOF-MS technology, Support vector machine, Discriminate Analysis, and CM10 protein chip were applied to study the sera proteomes of 32 healthy ... oral leukoplakia (OLK), ZUCI-PDAS (Zhejiang University Cancer Institute ProteinChip Data Analysis System), bioinformatics technology, discriminate analysis, ...

  11. A BIOINFORMATIC STRATEGY TO RAPIDLY CHARACTERIZE CDNA LIBRARIES

    Science.gov (United States)

    A Bioinformatic Strategy to Rapidly Characterize cDNA LibrariesG. Charles Ostermeier1, David J. Dix2 and Stephen A. Krawetz1.1Departments of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, & Institute for Scientific Computing, Wayne State Univer...

  12. Developing library bioinformatics services in context: the Purdue University Libraries bioinformationist program.

    Science.gov (United States)

    Rein, Diane C

    2006-07-01

    Purdue University is a major agricultural, engineering, biomedical, and applied life science research institution with an increasing focus on bioinformatics research that spans multiple disciplines and campus academic units. The Purdue University Libraries (PUL) hired a molecular biosciences specialist to discover, engage, and support bioinformatics needs across the campus. After an extended period of information needs assessment and environmental scanning, the specialist developed a week of focused bioinformatics instruction (Bioinformatics Week) to launch system-wide, library-based bioinformatics services. The specialist employed a two-tiered approach to assess user information requirements and expectations. The first phase involved careful observation and collection of information needs in-context throughout the campus, attending laboratory meetings, interviewing department chairs and individual researchers, and engaging in strategic planning efforts. Based on the information gathered during the integration phase, several survey instruments were developed to facilitate more critical user assessment and the recovery of quantifiable data prior to planning. Given information gathered while working with clients and through formal needs assessments, as well as the success of instructional approaches used in Bioinformatics Week, the specialist is developing bioinformatics support services for the Purdue community. The specialist is also engaged in training PUL faculty librarians in bioinformatics to provide a sustaining culture of library-based bioinformatics support and understanding of Purdue's bioinformatics-related decision and policy making.

  13. Taking Bioinformatics to Systems Medicine.

    Science.gov (United States)

    van Kampen, Antoine H C; Moerland, Perry D

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically contributes to systems medicine. First, we explain the role of bioinformatics in the management and analysis of data. In particular we show the importance of publicly available biological and clinical repositories to support systems medicine studies. Second, we discuss how the integration and analysis of multiple types of omics data through integrative bioinformatics may facilitate the determination of more predictive and robust disease signatures, lead to a better understanding of (patho)physiological molecular mechanisms, and facilitate personalized medicine. Third, we focus on network analysis and discuss how gene networks can be constructed from omics data and how these networks can be decomposed into smaller modules. We discuss how the resulting modules can be used to generate experimentally testable hypotheses, provide insight into disease mechanisms, and lead to predictive models. Throughout, we provide several examples demonstrating how bioinformatics contributes to systems medicine and discuss future challenges in bioinformatics that need to be addressed to enable the advancement of systems medicine.

  14. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

    . In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http......://www.secondarymetabolites.org) is introduced to provide a one-stop catalog and links to these bioinformatics resources. In addition, an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field....

  15. Training Experimental Biologists in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Pedro Fernandes

    2012-01-01

    Full Text Available Bioinformatics, for its very nature, is devoted to a set of targets that constantly evolve. Training is probably the best response to the constant need for the acquisition of bioinformatics skills. It is interesting to assess the effects of training in the different sets of researchers that make use of it. While training bench experimentalists in the life sciences, we have observed instances of changes in their attitudes in research that, if well exploited, can have beneficial impacts in the dialogue with professional bioinformaticians and influence the conduction of the research itself.

  16. Tools and data services registry: a community effort to document bioinformatics resources

    Science.gov (United States)

    Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; Rydza, Emil; Chmura, Piotr; Anthon, Christian; Beard, Niall; Berka, Karel; Bolser, Dan; Booth, Tim; Bretaudeau, Anthony; Brezovsky, Jan; Casadio, Rita; Cesareni, Gianni; Coppens, Frederik; Cornell, Michael; Cuccuru, Gianmauro; Davidsen, Kristian; Vedova, Gianluca Della; Dogan, Tunca; Doppelt-Azeroual, Olivia; Emery, Laura; Gasteiger, Elisabeth; Gatter, Thomas; Goldberg, Tatyana; Grosjean, Marie; Grüning, Björn; Helmer-Citterich, Manuela; Ienasescu, Hans; Ioannidis, Vassilios; Jespersen, Martin Closter; Jimenez, Rafael; Juty, Nick; Juvan, Peter; Koch, Maximilian; Laibe, Camille; Li, Jing-Woei; Licata, Luana; Mareuil, Fabien; Mičetić, Ivan; Friborg, Rune Møllegaard; Moretti, Sebastien; Morris, Chris; Möller, Steffen; Nenadic, Aleksandra; Peterson, Hedi; Profiti, Giuseppe; Rice, Peter; Romano, Paolo; Roncaglia, Paola; Saidi, Rabie; Schafferhans, Andrea; Schwämmle, Veit; Smith, Callum; Sperotto, Maria Maddalena; Stockinger, Heinz; Vařeková, Radka Svobodová; Tosatto, Silvio C.E.; de la Torre, Victor; Uva, Paolo; Via, Allegra; Yachdav, Guy; Zambelli, Federico; Vriend, Gert; Rost, Burkhard; Parkinson, Helen; Løngreen, Peter; Brunak, Søren

    2016-01-01

    Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools. PMID:26538599

  17. The Country Profiles of the PHARMINE Survey of European Higher Educational Institutions Delivering Pharmacy Education and Training

    Directory of Open Access Journals (Sweden)

    Jeffrey Atkinson

    2017-06-01

    Full Text Available The PHARMINE (Pharmacy Education in Europe consortium surveyed pharmacy education and practice in 2012. Surveys were updated in 2017 for publication. The PHARMINE consortium was especially interested in specialization in pharmacy education and practice (for community, hospital, and industrial pharmacy, and in the impact of the Bologna agreement and the directive of the European Commission on education and training for the sectoral profession of pharmacy on European degree courses. The surveys underline the varying attitudes of the different European countries to these various aspects. The surveys will now be published in Pharmacy. They will be useful to researchers in education, and to staff and students interested in mobility amongst different European and/or non-European countries. In order to assure a full understanding of the country profiles to be published in the journal Pharmacy, this introductory article describes the general format of the survey questionnaire used.

  18. The Country Profiles of the PHARMINE Survey of European Higher Educational Institutions Delivering Pharmacy Education and Training.

    Science.gov (United States)

    Atkinson, Jeffrey

    2017-06-22

    The PHARMINE (Pharmacy Education in Europe) consortium surveyed pharmacy education and practice in 2012. Surveys were updated in 2017 for publication. The PHARMINE consortium was especially interested in specialization in pharmacy education and practice (for community, hospital, and industrial pharmacy), and in the impact of the Bologna agreement and the directive of the European Commission on education and training for the sectoral profession of pharmacy on European degree courses. The surveys underline the varying attitudes of the different European countries to these various aspects. The surveys will now be published in Pharmacy. They will be useful to researchers in education, and to staff and students interested in mobility amongst different European and/or non-European countries. In order to assure a full understanding of the country profiles to be published in the journal Pharmacy, this introductory article describes the general format of the survey questionnaire used.

  19. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    Science.gov (United States)

    Attwood, Teresa K; Atwood, Teresa K; Bongcam-Rudloff, Erik; Brazas, Michelle E; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M; Schneider, Maria Victoria; van Gelder, Celia W G

    2015-04-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

  20. The External Dimension of European Union Marine Governance: Institutional Interplay between the EU and the International Maritime Organization

    NARCIS (Netherlands)

    Leeuwen, van J.; Kern, K.

    2013-01-01

    This article focuses on the emergence of a decentralized institutional complex, interplay management, and the institutional interplay between the International Maritime Organization (IMO) and the EU in the issue area of environmental shipping policies. It shows that the synergistic relationship

  1. Clinical Bioinformatics: challenges and opportunities.

    Science.gov (United States)

    Bellazzi, Riccardo; Masseroli, Marco; Murphy, Shawn; Shabo, Amnon; Romano, Paolo

    2012-01-01

    Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop, held in Pavia, Italy, in October 2011 was aimed at presenting some of the most relevant methods, tools and infrastructures that are nowadays available for Clinical Bioinformatics (CBI), the research field that deals with clinical applications of bioinformatics. In this editorial, the viewpoints and opinions of three world CBI leaders, who have been invited to participate in a panel discussion of the NETTAB workshop on the next challenges and future opportunities of this field, are reported. These include the development of data warehouses and ICT infrastructures for data sharing, the definition of standards for sharing phenotypic data and the implementation of novel tools to implement efficient search computing solutions. Some of the most important design features of a CBI-ICT infrastructure are presented, including data warehousing, modularity and flexibility, open-source development, semantic interoperability, integrated search and retrieval of -omics information. Clinical Bioinformatics goals are ambitious. Many factors, including the availability of high-throughput "-omics" technologies and equipment, the widespread availability of clinical data warehouses and the noteworthy increase in data storage and computational power of the most recent ICT systems, justify research and efforts in this domain, which promises to be a crucial leveraging factor for biomedical research.

  2. Bioinformatics and the Undergraduate Curriculum

    Science.gov (United States)

    Maloney, Mark; Parker, Jeffrey; LeBlanc, Mark; Woodard, Craig T.; Glackin, Mary; Hanrahan, Michael

    2010-01-01

    Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of…

  3. Reproducible Bioinformatics Research for Biologists

    Science.gov (United States)

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  4. Taking Bioinformatics to Systems Medicine

    NARCIS (Netherlands)

    van Kampen, Antoine H. C.; Moerland, Perry D.

    2016-01-01

    Systems medicine promotes a range of approaches and strategies to study human health and disease at a systems level with the aim of improving the overall well-being of (healthy) individuals, and preventing, diagnosing, or curing disease. In this chapter we discuss how bioinformatics critically

  5. Computational intelligence techniques in bioinformatics.

    Science.gov (United States)

    Hassanien, Aboul Ella; Al-Shammari, Eiman Tamah; Ghali, Neveen I

    2013-12-01

    Computational intelligence (CI) is a well-established paradigm with current systems having many of the characteristics of biological computers and capable of performing a variety of tasks that are difficult to do using conventional techniques. It is a methodology involving adaptive mechanisms and/or an ability to learn that facilitate intelligent behavior in complex and changing environments, such that the system is perceived to possess one or more attributes of reason, such as generalization, discovery, association and abstraction. The objective of this article is to present to the CI and bioinformatics research communities some of the state-of-the-art in CI applications to bioinformatics and motivate research in new trend-setting directions. In this article, we present an overview of the CI techniques in bioinformatics. We will show how CI techniques including neural networks, restricted Boltzmann machine, deep belief network, fuzzy logic, rough sets, evolutionary algorithms (EA), genetic algorithms (GA), swarm intelligence, artificial immune systems and support vector machines, could be successfully employed to tackle various problems such as gene expression clustering and classification, protein sequence classification, gene selection, DNA fragment assembly, multiple sequence alignment, and protein function prediction and its structure. We discuss some representative methods to provide inspiring examples to illustrate how CI can be utilized to address these problems and how bioinformatics data can be characterized by CI. Challenges to be addressed and future directions of research are also presented and an extensive bibliography is included. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Challenges in RNA virus bioinformatics.

    Science.gov (United States)

    Marz, Manja; Beerenwinkel, Niko; Drosten, Christian; Fricke, Markus; Frishman, Dmitrij; Hofacker, Ivo L; Hoffmann, Dieter; Middendorf, Martin; Rattei, Thomas; Stadler, Peter F; Töpfer, Armin

    2014-07-01

    Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of >200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses. In contrast to many broad, established and well-organized bioinformatics communities (e.g. structural genomics, ontologies, next-generation sequencing, expression analysis), research groups focusing on viruses can probably be counted on the fingers of two hands. The purpose of this review is to increase awareness among bioinformatics researchers about the pressing needs and unsolved problems of computational virology. We focus primarily on RNA viruses that pose problems to many standard bioinformatics analyses owing to their compact genome organization, fast mutation rate and low evolutionary conservation. We provide an overview of tools and algorithms for handling viral sequencing data, detecting functionally important RNA structures, classifying viral proteins into families and investigating the origin and evolution of viruses. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Peer Mentoring for Bioinformatics presentation

    OpenAIRE

    Budd, Aidan

    2014-01-01

    A handout used in a HUB (Heidelberg Unseminars in Bioinformatics) meeting focused on career development for bioinformaticians. It describes an activity for use to help introduce the idea of peer mentoring, potnetially acting as an opportunity to create peer-mentoring groups.

  8. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

    "The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

  9. Selective Europeanization

    DEFF Research Database (Denmark)

    Hoch Jovanovic, Tamara; Lynggaard, Kennet

    2014-01-01

    political contexts at the European level. We further show how the “translation” of international norms to a domestic context has worked to reinforce the original institutional setup, dating back to the mid-1950s. The translation of European-level minority policy developed in the 1990s and 2000s works most...

  10. The European Society of Therapeutic Radiology and Oncology-European Institute of Radiotherapy (ESTRO-EIR) report on 3D CT-based in-room image guidance systems: a practical and technical review and guide

    DEFF Research Database (Denmark)

    Korreman, Stine; Rasch, Coen; McNair, Helen

    2010-01-01

    The past decade has provided many technological advances in radiotherapy. The European Institute of Radiotherapy (EIR) was established by the European Society of Therapeutic Radiology and Oncology (ESTRO) to provide current consensus statement with evidence-based and pragmatic guidelines on topics...... of practical relevance for radiation oncology. This report focuses primarily on 3D CT-based in-room image guidance (3DCT-IGRT) systems. It will provide an overview and current standing of 3DCT-IGRT systems addressing the rationale, objectives, principles, applications, and process pathways, both clinical...... demonstrates a wide variability based on local practices. This report whilst comprehensive is not exhaustive as this area of development remains a very active field for research and development. However, it should serve as a practical guide and framework for all professional groups within the field, focussed...

  11. The euro and the recent European crisis vis-à-vis the gold standard and the great depression: institutionalities, specificities and interfaces

    Directory of Open Access Journals (Sweden)

    GIULIANO CONTENTO DE OLIVEIRA

    Full Text Available ABSTRACT The paper aims to establish interfaces between the Great Depression of the 1930s under the Gold Standard and the recent European Crisis under the Euro. It is argued that, despite their specificities, both crises revealed the potentially harmful effects, in economic and social terms, of institutional arrangements that considerably reduce the autonomy of monetary, fiscal and exchange rate policies of participating countries, without being accompanied by increased cooperation between them, which should be led by a global (in the case of the Great Depression or regional (in the case of the European Crisis hegemonic power, which is not only capable of, but is also willing to act as a buyer and lender of last resort, especially in circumstances characterized by increased uncertainty, the deterioration of the general state of expectations and increased liquidity preference. In fact, central European countries in the past and peripheral European countries nowadays were effectively pushed toward deflationary adjustments in which a reduction of prices and wages was accompanied by a reduction of output and employment levels. Thus, in the absence of the possibility of restoring the autonomy of economic policy, the overcome of the crisis necessarily requires, both before - under the Gold Standard - and nowadays - under the Euro -, joint actions aimed to assure that the responsibility for the adjustment will be equally distributed among all the economies, in order to avoid that some of them benefit at the expense of the others in this process.

  12. Scientific Fellow of Max Planck Institute of Plasma Physics (IPP) and European Physical Society President Elect F. Wagner at ATLAS experiment with Collaboration Spokesperson P. Jenni on 22 September 2006.

    CERN Multimedia

    Maximilien Brice

    2006-01-01

    Scientific Fellow of Max Planck Institute of Plasma Physics (IPP) and European Physical Society President Elect F. Wagner at ATLAS experiment with Collaboration Spokesperson P. Jenni on 22 September 2006.

  13. The information system of learning quality control in higher education institutions: achievements and problems of European universities

    Directory of Open Access Journals (Sweden)

    Orekhova Elena

    2016-01-01

    Full Text Available The article deals with the main trends in the development of the system of learning quality control connected with the European integration of higher education and the democratization of education. The authors analyze the state of information systems of learning quality control existing in European higher education and identify their strong and weak points. The authors show that in the learning process universities actively use innovative analytic methods as well as modern means of collecting, storing and transferring information that ensure the successful management of such a complex object as the university of the 21st century.

  14. A Bioinformatics Facility for NASA

    Science.gov (United States)

    Schweighofer, Karl; Pohorille, Andrew

    2006-01-01

    Building on an existing prototype, we have fielded a facility with bioinformatics technologies that will help NASA meet its unique requirements for biological research. This facility consists of a cluster of computers capable of performing computationally intensive tasks, software tools, databases and knowledge management systems. Novel computational technologies for analyzing and integrating new biological data and already existing knowledge have been developed. With continued development and support, the facility will fulfill strategic NASA s bioinformatics needs in astrobiology and space exploration. . As a demonstration of these capabilities, we will present a detailed analysis of how spaceflight factors impact gene expression in the liver and kidney for mice flown aboard shuttle flight STS-108. We have found that many genes involved in signal transduction, cell cycle, and development respond to changes in microgravity, but that most metabolic pathways appear unchanged.

  15. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.

  16. Generation IV Reactor Safety and Materials Research by the Institute for Energy and Transport at the European Commission's Joint Research Centre

    Energy Technology Data Exchange (ETDEWEB)

    Tuček, K., E-mail: kamil.tucek@ec.europa.eu; Tsige-Tamirat, H.; Ammirabile, L.; Lázaro, A.; Grah, A.; Carlsson, J.; Döderlein, Ch.; Oettingen, M.; Fütterer, M.A.; D’Agata, E.; Laurie, M.; Turba, K.; Ohms, C.; Nilsson, K.-F.; Hähner, P.

    2013-12-15

    To support the drafting, development, implementation and monitoring of European energy and transport policy, the Institute for Energy and Transport of the European Commissions’ Joint Research Centre conducts pre-competitive research in the areas of experimental qualification of advanced fuels and materials as well as simulation and modelling of reactor safety and material performance. The work covers assessments, design optimisation and improvements to the safety and performance of new, innovative reactor systems, materials and instrumentation, in order to meet the EU's long-term energy needs while respecting enhanced safety, sustainability, and economic aspects. The research is linked, and contributes, to related EURATOM Framework Programme projects, Generation IV International Forum (GIF), International Atomic Energy Agency as well as OECD's Nuclear Energy Agency (OECD NEA) activities. The current paper gives an overview and examples of past, current, and upcoming activities in the areas of reactor safety assessments, advanced fuel irradiation and materials research.

  17. The legal landscape for advanced therapies: material and institutional implementation of European Union rules in France and the United Kingdom.

    Science.gov (United States)

    Mahalatchimy, Aurélie; Rial-Sebbag, Emmanuelle; Tournay, Virginie; Faulkner, Alex

    2012-01-01

    In 2007, the European Union adopted a lex specialis, Regulation (EC) No. 1394/2007 on advanced therapy medicinal products (ATMPs), a new legal category of medical product in regenerative medicine. The regulation applies to ATMPs prepared industrially or manufactured by a method involving an industrial process. It also provides a hospital exemption, which means that medicinal products not regulated by EU law do not benefit from a harmonized regime across the European Union but have to respect national laws. This article describes the recent EU laws, and contrasts two national regimes, asking how France and the United Kingdom regulate ATMPs which do and do not fall under the scope of Regulation (EC) No. 1394/2007. What are the different legal categories and their enforceable regimes, and how does the evolution of these highly complex regimes interact with the material world of regenerative medicine and the regulatory bodies and socioeconomic actors participating in it?

  18. Broad issues to consider for library involvement in bioinformatics.

    Science.gov (United States)

    Geer, Renata C

    2006-07-01

    The information landscape in biological and medical research has grown far beyond literature to include a wide variety of databases generated by research fields such as molecular biology and genomics. The traditional role of libraries to collect, organize, and provide access to information can expand naturally to encompass these new data domains. This paper discusses the current and potential role of libraries in bioinformatics using empirical evidence and experience from eleven years of work in user services at the National Center for Biotechnology Information. Medical and science libraries over the last decade have begun to establish educational and support programs to address the challenges users face in the effective and efficient use of a plethora of molecular biology databases and retrieval and analysis tools. As more libraries begin to establish a role in this area, the issues they face include assessment of user needs and skills, identification of existing services, development of plans for new services, recruitment and training of specialized staff, and establishment of collaborations with bioinformatics centers at their institutions. Increasing library involvement in bioinformatics can help address information needs of a broad range of students, researchers, and clinicians and ultimately help realize the power of bioinformatics resources in making new biological discoveries.

  19. Fuento: functional enrichment for bioinformatics.

    Science.gov (United States)

    Weichselbaum, David; Zagrovic, Bojan; Polyansky, Anton A

    2017-08-15

    The currently available functional enrichment software focuses mostly on gene expression analysis, whereby server- and graphical-user-interface-based tools with specific scope dominate the field. Here we present an efficient, user-friendly, multifunctional command-line-based functional enrichment tool (fu-en-to), tailored for the bioinformatics researcher. Source code and binaries freely available for download at github.com/DavidWeichselbaum/fuento, implemented in C ++ and supported on Linux and OS X. newant@gmail.com or bojan.zagrovic@univie.ac.at.

  20. Political institutions and economic growth reconsidered : Presidential address for the European Public Choice Society conference, Turku, April 2006

    NARCIS (Netherlands)

    de Haan, Jakob

    The debate on the relationship between institutions and economic development is discussed, focusing on two illustrations, i.e., the impact of democracy and political instability on economic growth. Various pitfalls of existing research are identified, like sensitivity of the outcomes to model

  1. Using institutional theory to analyse hospital responses to external demands for finance and quality in five European countries

    NARCIS (Netherlands)

    S. Burnett (Susan); Mendel, P. (Peter); F. Nunes (Francisco); S. Wiig (Siri); van den Bovenkamp, H. (Hester); Karltun, A. (Anette); G. Robert (Glenn); J.E. Anderson (Janet); C. Vincent (Charles); N.J. Fulop (Naomi)

    2016-01-01

    textabstractObjectives: Given the impact of the global economic crisis, delivering better health care with limited finance grows more challenging. Through the lens of institutional theory, this paper explores pressures experienced by hospital leaders to improve quality and constrain spending,

  2. The Socio-Political Construction of a European Census of Higher Education Institutions: Design, Methodological and Comparability Issues

    Science.gov (United States)

    Lepori, Benedetto; Bonaccorsi, Andrea

    2013-01-01

    This paper reports on an experiment concerning the social construction of statistical definitions, where the first census of Higher Education Institutions in Europe has been developed. It conceptualizes the construction of indicators as a social process of definitions and boundaries' negotiation, involving value judgments, social and political…

  3. [Employment of People with Mental Disorders in Terms of the Policies Developed by the European and International Institutions].

    Science.gov (United States)

    Joly, Laurène

    Objectives The aim of this article is to present an overview of the reflections led by various European and international organizations on the employment of people with mental disorders.Methods This study is based on data from websites of international organizations and interviews taken place with a disability specialist at the International Labour Organisation (ILO) and members of the European Commission.Results Unlike the French law of 11 February 2005 which refers expressly to psychic disability, this notion is not explicitly dedicated by various European and international legal rules. However, these standards like the United Nations Convention on the Rights of Persons with Disabilities have adopted the contemporary model which presents disability as the result of an interaction between person and environment. Thus they acknowledge that disabled people include people suffering from mental disorders because in the person's environment, a psychiatric impairment could lead to limitations of activities or restrictions of social participation that constitute a situation of disability of psychiatric origin. Therefore, the legal mechanisms often do not provide appropriate answers to the characteristics of psychiatric disability.Besides, negative attitudes, stereotypes and discrimination towards people with a psychiatric disability are still observed in the workplace, in spite of intensified anti-discrimination legislation.This study inventories the different proposals to remedy to substantial barriers to the employment of people with a psychiatric condition. In the European Union's strategy for increasing the employment of these persons, particular consideration is given to put forward a series of key recommendations to improve practices of reasonable accommodation in the workplace. Nonetheless, it must be emphasized that it is necessary to conceive adequate measures in order to take into account the changeability and the unpredictability of mental disorders. Indeed

  4. Bioinformatics in Africa: The Rise of Ghana?

    Science.gov (United States)

    Karikari, Thomas K.

    2015-01-01

    Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics. PMID:26378921

  5. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Campos, Benito; Barnkob, Mike Stein

    2014-01-01

    therapy target discovery in a bioinformatics analysis pipeline. We describe specialized bioinformatics tools and databases for three main bottlenecks in immunotherapy target discovery: the cataloging of potentially antigenic proteins, the identification of potential HLA binders, and the selection epitopes...... and co-targets for single-epitope and multi-epitope strategies. We provide examples of application to the well-known tumor antigen HER2 and suggest bioinformatics methods to ameliorate therapy resistance and ensure efficient and lasting control of tumors....

  6. Data mining in bioinformatics using Weka

    National Research Council Canada - National Science Library

    Frank, Eibe; Hall, Mark; Trigg, Len; Holmes, Geoffrey; Witten, Ian H

    2004-01-01

    The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research...

  7. A European and Swedish perspective on ICT – policies and strategies in education. National and institutional pathways: crossings, blind alleys and uphill slopes

    Directory of Open Access Journals (Sweden)

    Henrik Hansson

    2004-04-01

    Full Text Available This paper aims at answering the following questions: 1. What general goals do politicians in Europe express in national policy documents for the integration of information and communication technology (ICT in their education systems? To develop that theme further we explored the situation in our own country Sweden as a case. 2. What policies and strategies for ICT in education do leaders of Swedish higher education institutions develop? 3. How do Swedish national priorities and academic institutional interests match? The globalisation of education forces different value systems to meet. There is on the national level highly different political values on what kind of education system to prefer – the Scandinavian model and the American model are two extremes. There are also very different values inherent in higher education institutions, the academia, - compared with the values and visions held by the political leaders. These value differences between and within countries are elaborated and discussed. A Swedish, Scandinavian and European perspective is adopted, but a wider international outlook is also given. It is suggested that the value conflicts, often not explicit, understood or recognised, are one of the major inhibitors for systemic change. The direction of change cannot be taken for granted – the driving forces pull in opposing directions. Different visions of the future struggle to be fulfilled.

  8. How do Labor Market Institutions affect the Link between Growth and Unemployment: the case of the European countries

    Directory of Open Access Journals (Sweden)

    Langot, François

    2010-12-01

    Full Text Available This paper analyzes how the frictions in the labor market simultaneously affect the economic growth and the long run unemployment. To this goal, we develop a schumpeterian model of endogenous growth: agents have the choice between employment and R and D activities. Unemployment is caused by the wage-setting behavior of unions. We show that: (i Increases in the labor costs or in the power of trade unions lead to higher unemployment and lower economic growth. (ii Efficient bargain allows to increase employment, at the price of a lower growth rate. These theoretical predictions are consistent with the insights from our empirical analysis based on 183 European Regions, between 1980-2003

  9. KBWS: an EMBOSS associated package for accessing bioinformatics web services.

    Science.gov (United States)

    Oshita, Kazuki; Arakawa, Kazuharu; Tomita, Masaru

    2011-04-29

    The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded) and http://soap.g-language.org/kbws_dl.wsdl (Document/literal).

  10. KBWS: an EMBOSS associated package for accessing bioinformatics web services

    Directory of Open Access Journals (Sweden)

    Tomita Masaru

    2011-04-01

    Full Text Available Abstract The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS, adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from http://www.g-language.org/kbws/ and GitHub repository http://github.com/cory-ko/KBWS. Users can utilize the SOAP services implemented in Perl directly via WSDL file at http://soap.g-language.org/kbws.wsdl (RPC Encoded and http://soap.g-language.org/kbws_dl.wsdl (Document/literal.

  11. A European and Swedish perspective on ICT – policies and strategies in education. National and institutional pathways: crossings, blind alleys and uphill slopes

    Directory of Open Access Journals (Sweden)

    Henrik Hansson

    2004-04-01

    The globalisation of education forces different value systems to meet. There is on the national level highly different political values on what kind of education system to prefer – the Scandinavian model and the American model are two extremes. There are also very different values inherent in higher education institutions, the academia, - compared with the values and visions held by the political leaders. These value differences between and within countries are elaborated and discussed. A Swedish, Scandinavian and European perspective is adopted, but a wider international outlook is also given. It is suggested that the value conflicts, often not explicit, understood or recognised, are one of the major inhibitors for systemic change. The direction of change cannot be taken for granted – the driving forces pull in opposing directions. Different visions of the future struggle to be fulfilled.

  12. Biomarkers of immunity and inflammation for use in nutrition interventions: International Life Sciences Institute European Branch work on selection criteria and interpretation.

    Science.gov (United States)

    Calder, Philip C

    2014-01-01

    In order to gain better insight into meaningful effects of nutrition on immune function, there is a need for guidance on the assessment and interpretation of immune markers. However, there is no consensus as to which markers best represent the various aspects of immunity, including acute, chronic or low-grade inflammation. International Life Sciences Institute European Branch has commissioned several expert groups comprising individuals from different backgrounds including academia, government and the food industry to prepare descriptive and guidance documents on this topic. Two of these considered the markers of the immune response mainly in the context of host defence against pathogens, two considered general markers of inflammation, and one focussed on chronic low-grade inflammation in relation to overweight and obesity. This article describes the background to these documents and will summarise the work, findings and recommendations of the expert groups.

  13. Using "Arabidopsis" Genetic Sequences to Teach Bioinformatics

    Science.gov (United States)

    Zhang, Xiaorong

    2009-01-01

    This article describes a new approach to teaching bioinformatics using "Arabidopsis" genetic sequences. Several open-ended and inquiry-based laboratory exercises have been designed to help students grasp key concepts and gain practical skills in bioinformatics, using "Arabidopsis" leucine-rich repeat receptor-like kinase (LRR…

  14. A Mathematical Optimization Problem in Bioinformatics

    Science.gov (United States)

    Heyer, Laurie J.

    2008-01-01

    This article describes the sequence alignment problem in bioinformatics. Through examples, we formulate sequence alignment as an optimization problem and show how to compute the optimal alignment with dynamic programming. The examples and sample exercises have been used by the author in a specialized course in bioinformatics, but could be adapted…

  15. Bioinformatics clouds for big data manipulation

    Directory of Open Access Journals (Sweden)

    Dai Lin

    2012-11-01

    Full Text Available Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS, Software as a Service (SaaS, Platform as a Service (PaaS, and Infrastructure as a Service (IaaS, and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor.

  16. Bioinformatics clouds for big data manipulation

    Science.gov (United States)

    2012-01-01

    Abstract As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics. Reviewers This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. PMID:23190475

  17. Bioinformatics clouds for big data manipulation

    KAUST Repository

    Dai, Lin

    2012-11-28

    As advances in life sciences and information technology bring profound influences on bioinformatics due to its interdisciplinary nature, bioinformatics is experiencing a new leap-forward from in-house computing infrastructure into utility-supplied cloud computing delivered over the Internet, in order to handle the vast quantities of biological data generated by high-throughput experimental technologies. Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.This article was reviewed by Frank Eisenhaber, Igor Zhulin, and Sandor Pongor. 2012 Dai et al.; licensee BioMed Central Ltd.

  18. The 2016 Bioinformatics Open Source Conference (BOSC).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

    2016-01-01

    Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

  19. The 2017 Bioinformatics Open Source Conference (BOSC).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

    2017-01-01

    The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

  20. The 2017 Bioinformatics Open Source Conference (BOSC)

    Science.gov (United States)

    Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

    2017-01-01

    The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

  1. GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

    Science.gov (United States)

    Atwood, Teresa K.; Bongcam-Rudloff, Erik; Brazas, Michelle E.; Corpas, Manuel; Gaudet, Pascale; Lewitter, Fran; Mulder, Nicola; Palagi, Patricia M.; Schneider, Maria Victoria; van Gelder, Celia W. G.

    2015-01-01

    In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy—paradoxically, many are actually closing “niche” bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all. PMID:25856076

  2. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

    Directory of Open Access Journals (Sweden)

    Teresa K Attwood

    2015-04-01

    Full Text Available In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

  3. When cloud computing meets bioinformatics: a review.

    Science.gov (United States)

    Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

    2013-10-01

    In the past decades, with the rapid development of high-throughput technologies, biology research has generated an unprecedented amount of data. In order to store and process such a great amount of data, cloud computing and MapReduce were applied to many fields of bioinformatics. In this paper, we first introduce the basic concepts of cloud computing and MapReduce, and their applications in bioinformatics. We then highlight some problems challenging the applications of cloud computing and MapReduce to bioinformatics. Finally, we give a brief guideline for using cloud computing in biology research.

  4. BIRCH: A user-oriented, locally-customizable, bioinformatics system

    Directory of Open Access Journals (Sweden)

    Fristensky Brian

    2007-02-01

    Full Text Available Abstract Background Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. Results BIRCH (Biological Research Computing Hierarchy is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. Conclusion BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere.

  5. Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory.

    Science.gov (United States)

    Brazas, Michelle D; Yamada, Joseph Tadashi; Ouellette, B F Francis

    2009-07-01

    All of the life science research web servers published in this and previous issues of Nucleic Acids Research, together with other useful tools, databases and resources for bioinformatics and molecular biology research are freely accessible online through the Bioinformatics Links Directory, http://bioinformatics.ca/links_directory/. Entirely dependent on user feedback and community input, the Bioinformatics Links Directory exemplifies an open access research tool and resource. With 112 websites featured in the July 2009 Web Server Issue of Nucleic Acids Research, the 2009 update brings the total number of servers listed in the Bioinformatics Links Directory close to an impressive 1400 links. A complete list of all links listed in this Nucleic Acids Research 2009 Web Server Issue can be accessed online at http://bioinfomatics.ca/links_directory/narweb2009/. The 2009 update of the Bioinformatics Links Directory, which includes the Web Server list and summaries, is also available online at the Nucleic Acids Research website, http://nar.oxfordjournals.org/.

  6. Concepts and introduction to RNA bioinformatics

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Hofacker, Ivo L.; Ruzzo, Walter L.

    2014-01-01

    RNA bioinformatics and computational RNA biology have emerged from implementing methods for predicting the secondary structure of single sequences. The field has evolved to exploit multiple sequences to take evolutionary information into account, such as compensating (and structure preserving) base...

  7. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...

  8. [What is the subject of science "bioinformatics"?].

    Science.gov (United States)

    Chaĭlakhian, L M

    2005-01-01

    The paper is concerned with some problems of terminology, in particular the term "bioinformatics". In the last few years, the term "bioinformatics" has been intensively used among molecular biologists to indicate a subject that is only a constituent of genomics and is considered to involve a computer-assisted analysis of all data on nucleotide sequences of DNA. However, a wide circle of scientists, including biologists, physicists, mathematicians, and specialists in the field of cybernetics, informatics, and other disciplines have accepted and accept, as a rule, the "bioinformatics" as a synonym of science cybernetics and as a successor of this science. In this case, the subject of science "bioinformatics" should embrace not only genomics but practically all sections of the biological science. It should involve a study of information processes (storage, transfer, and processing of information, etc.) participating in the regulation and control at all levels of living systems, from macromolecules to the brain of higher animals and human.

  9. ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR

    Science.gov (United States)

    Larcombe, L.; Hendricusdottir, R.; Attwood, T.K.; Bacall, F.; Beard, N.; Bellis, L.J.; Dunn, W.B.; Hancock, J.M.; Nenadic, A.; Orengo, C.; Overduin, B.; Sansone, S-A; Thurston, M.; Viant, M.R.; Winder, C.L.; Goble, C.A.; Ponting, C.P.; Rustici, G.

    2017-01-01

    ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform’s coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR’s flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project – a coordinated effort to drive engagement with training in statistics. PMID:28781748

  10. Coronavirus Genomics and Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Kwok-Yung Yuen

    2010-08-01

    Full Text Available The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002, with estimated substitution rate of 4´10-4 to 2´10-2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV, between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1. Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.

  11. Deciphering psoriasis. A bioinformatic approach.

    Science.gov (United States)

    Melero, Juan L; Andrades, Sergi; Arola, Lluís; Romeu, Antoni

    2018-02-01

    Psoriasis is an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. The cause of psoriasis is still unknown. The fundamental feature of the disease is the hyperproliferation of keratinocytes and the recruitment of cells from the immune system in the region of the affected skin, which leads to deregulation of many well-known gene expressions. Based on data mining and bioinformatic scripting, here we show a new dimension of the effect of psoriasis at the genomic level. Using our own pipeline of scripts in Perl and MySql and based on the freely available NCBI Gene Expression Omnibus (GEO) database: DataSet Record GDS4602 (Series GSE13355), we explore the extent of the effect of psoriasis on gene expression in the affected tissue. We give greater insight into the effects of psoriasis on the up-regulation of some genes in the cell cycle (CCNB1, CCNA2, CCNE2, CDK1) or the dynamin system (GBPs, MXs, MFN1), as well as the down-regulation of typical antioxidant genes (catalase, CAT; superoxide dismutases, SOD1-3; and glutathione reductase, GSR). We also provide a complete list of the human genes and how they respond in a state of psoriasis. Our results show that psoriasis affects all chromosomes and many biological functions. If we further consider the stable and mitotically inheritable character of the psoriasis phenotype, and the influence of environmental factors, then it seems that psoriasis has an epigenetic origin. This fit well with the strong hereditary character of the disease as well as its complex genetic background. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

  12. Methodology for Constructing Problem Definitions in Bioinformatics

    OpenAIRE

    Hauth, Amy M.; Burger, Gertraud

    2008-01-01

    Motivation: A recurrent criticism is that certain bioinformatics tools do not account for crucial biology and therefore fail answering the targeted biological question. We posit that the single most important reason for such shortcomings is an inaccurate formulation of the computational problem. Results: Our paper describes how to define a bioinformatics problem so that it captures both the underlying biology and the computational constraints for a particular problem. The proposed model delin...

  13. Institutional Investors

    DEFF Research Database (Denmark)

    Birkmose, Hanne Søndergaard; Strand, Therese

    Research Question/Issue: Institutional investors are facing increased pressure and threats of legislation from the European Union to abandon passive ownership strategies. This study investigates the prerequisites for – and potential dissimilarities in the practice of, active ownership among....../Policy Implications: Regulators should be aware of the impact by local governance mechanisms, and how shareholders react under different legal and practical prerequisites. The paper also highlights legal elements that differ between Denmark and Sweden, and which might affect institutional activism....

  14. Bioinformatics advances in saliva diagnostics.

    Science.gov (United States)

    Ai, Ji-Ye; Smith, Barry; Wong, David T W

    2012-06-01

    There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval,integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart.

  15. Diagnostic biases in translational bioinformatics.

    Science.gov (United States)

    Han, Henry

    2015-08-01

    With the surge of translational medicine and computational omics research, complex disease diagnosis is more and more relying on massive omics data-driven molecular signature detection. However, how to detect and prevent possible diagnostic biases in translational bioinformatics remains an unsolved problem despite its importance in the coming era of personalized medicine. In this study, we comprehensively investigate the diagnostic bias problem by analyzing benchmark gene array, protein array, RNA-Seq and miRNA-Seq data under the framework of support vector machines for different model selection methods. We further categorize the diagnostic biases into different types by conducting rigorous kernel matrix analysis and provide effective machine learning methods to conquer the diagnostic biases. In this study, we comprehensively investigate the diagnostic bias problem by analyzing benchmark gene array, protein array, RNA-Seq and miRNA-Seq data under the framework of support vector machines. We have found that the diagnostic biases happen for data with different distributions and SVM with different kernels. Moreover, we identify total three types of diagnostic biases: overfitting bias, label skewness bias, and underfitting bias in SVM diagnostics, and present corresponding reasons through rigorous analysis. Compared with the overfitting and underfitting biases, the label skewness bias is more challenging to detect and conquer because it can be easily confused as a normal diagnostic case from its deceptive accuracy. To tackle this problem, we propose a derivative component analysis based support vector machines to conquer the label skewness bias by achieving the rivaling clinical diagnostic results. Our studies demonstrate that the diagnostic biases are mainly caused by the three major factors, i.e. kernel selection, signal amplification mechanism in high-throughput profiling, and training data label distribution. Moreover, the proposed DCA-SVM diagnosis provides a

  16. Unix interfaces, Kleisli, bucandin structure, etc. -- the heroic beginning of bioinformatics in Singapore.

    Science.gov (United States)

    Eisenhaber, Frank

    2014-06-01

    Remarkably, Singapore as one of today's hotspots for bioinformatics and computational biology research appeared de novo out of pioneering efforts of engaged local individuals in the early 90-s that, supported with increasing public funds from 1996 on, morphed into the present vibrant research community. This article brings to mind the pioneers, their first successes and early institutional developments.

  17. Incorporating a New Bioinformatics Component into Genetics at a Historically Black College: Outcomes and Lessons

    Science.gov (United States)

    Holtzclaw, J. David; Eisen, Arri; Whitney, Erika M.; Penumetcha, Meera; Hoey, J. Joseph; Kimbro, K. Sean

    2006-01-01

    Many students at minority-serving institutions are underexposed to Internet resources such as the human genome project, PubMed, NCBI databases, and other Web-based technologies because of a lack of financial resources. To change this, we designed and implemented a new bioinformatics component to supplement the undergraduate Genetics course at…

  18. Regulatory bioinformatics for food and drug safety.

    Science.gov (United States)

    Healy, Marion J; Tong, Weida; Ostroff, Stephen; Eichler, Hans-Georg; Patak, Alex; Neuspiel, Margaret; Deluyker, Hubert; Slikker, William

    2016-10-01

    "Regulatory Bioinformatics" strives to develop and implement a standardized and transparent bioinformatic framework to support the implementation of existing and emerging technologies in regulatory decision-making. It has great potential to improve public health through the development and use of clinically important medical products and tools to manage the safety of the food supply. However, the application of regulatory bioinformatics also poses new challenges and requires new knowledge and skill sets. In the latest Global Coalition on Regulatory Science Research (GCRSR) governed conference, Global Summit on Regulatory Science (GSRS2015), regulatory bioinformatics principles were presented with respect to global trends, initiatives and case studies. The discussion revealed that datasets, analytical tools, skills and expertise are rapidly developing, in many cases via large international collaborative consortia. It also revealed that significant research is still required to realize the potential applications of regulatory bioinformatics. While there is significant excitement in the possibilities offered by precision medicine to enhance treatments of serious and/or complex diseases, there is a clear need for further development of mechanisms to securely store, curate and share data, integrate databases, and standardized quality control and data analysis procedures. A greater understanding of the biological significance of the data is also required to fully exploit vast datasets that are becoming available. The application of bioinformatics in the microbiological risk analysis paradigm is delivering clear benefits both for the investigation of food borne pathogens and for decision making on clinically important treatments. It is recognized that regulatory bioinformatics will have many beneficial applications by ensuring high quality data, validated tools and standardized processes, which will help inform the regulatory science community of the requirements

  19. Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory.

    Science.gov (United States)

    Brazas, Michelle D; Yamada, Joseph T; Ouellette, B F Francis

    2010-07-01

    The Links Directory at Bioinformatics.ca continues its collaboration with Nucleic Acids Research to jointly publish and compile a freely accessible, online collection of tools, databases and resource materials for bioinformatics and molecular biology research. The July 2010 Web Server issue of Nucleic Acids Research adds an additional 115 web server tools and 7 updates to the directory at http://bioinformatics.ca/links_directory/, bringing the total number of servers listed close to an impressive 1500 links. The Bioinformatics Links Directory represents an excellent community resource for locating bioinformatic tools and databases to aid one's research, and in this context bioinformatic education needs and initiatives are discussed. A complete list of all links featured in this Nucleic Acids Research 2010 Web Server issue can be accessed online at http://bioinformatics.ca/links_directory/narweb2010/. The 2010 update of the Bioinformatics Links Directory, which includes the Web Server list and summaries, is also available online at the Nucleic Acids Research website, http://nar.oxfordjournals.org/.

  20. Protecting innovation in bioinformatics and in-silico biology.

    Science.gov (United States)

    Harrison, Robert

    2003-01-01

    Commercial success or failure of innovation in bioinformatics and in-silico biology requires the appropriate use of legal tools for protecting and exploiting intellectual property. These tools include patents, copyrights, trademarks, design rights, and limiting information in the form of 'trade secrets'. Potentially patentable components of bioinformatics programmes include lines of code, algorithms, data content, data structure and user interfaces. In both the US and the European Union, copyright protection is granted for software as a literary work, and most other major industrial countries have adopted similar rules. Nonetheless, the grant of software patents remains controversial and is being challenged in some countries. Current debate extends to aspects such as whether patents can claim not only the apparatus and methods but also the data signals and/or products, such as a CD-ROM, on which the programme is stored. The patentability of substances discovered using in-silico methods is a separate debate that is unlikely to be resolved in the near future.

  1. The GMOD Drupal bioinformatic server framework.

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G

    2010-12-15

    Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS). We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community. Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished. Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com.

  2. Bioinformatics for discovery of microbiome variation

    DEFF Research Database (Denmark)

    Brejnrod, Asker Daniel

    in both the environment and human hosts that are not accessible through traditional means, and genome bioinformatics have allowed interrogation of their metabolic capabilities through novel tools of reconstructing genomes from short DNA sequencing reads. These new approaches to studying bacterial taxonomy...... particularly for considerations there was no space for in the papers. The main focus is on the bioinformatics, the processing of the data after it has been generated by the sequencing machines. However, some topics such as DNA extraction is touched upon as it have a big impact on downstream results. Manuscript...

  3. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

    Science.gov (United States)

    Mulder, Nicola J.; Adebiyi, Ezekiel; Alami, Raouf; Benkahla, Alia; Brandful, James; Doumbia, Seydou; Everett, Dean; Fadlelmola, Faisal M.; Gaboun, Fatima; Gaseitsiwe, Simani; Ghazal, Hassan; Hazelhurst, Scott; Hide, Winston; Ibrahimi, Azeddine; Jaufeerally Fakim, Yasmina; Jongeneel, C. Victor; Joubert, Fourie; Kassim, Samar; Kayondo, Jonathan; Kumuthini, Judit; Lyantagaye, Sylvester; Makani, Julie; Mansour Alzohairy, Ahmed; Masiga, Daniel; Moussa, Ahmed; Nash, Oyekanmi; Ouwe Missi Oukem-Boyer, Odile; Owusu-Dabo, Ellis; Panji, Sumir; Patterton, Hugh; Radouani, Fouzia; Sadki, Khalid; Seghrouchni, Fouad; Tastan Bishop, Özlem; Tiffin, Nicki; Ulenga, Nzovu

    2016-01-01

    The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet. PMID:26627985

  4. Applying instructional design theories to bioinformatics education in microarray analysis and primer design workshops.

    Science.gov (United States)

    Shachak, Aviv; Ophir, Ron; Rubin, Eitan

    2005-01-01

    The need to support bioinformatics training has been widely recognized by scientists, industry, and government institutions. However, the discussion of instructional methods for teaching bioinformatics is only beginning. Here we report on a systematic attempt to design two bioinformatics workshops for graduate biology students on the basis of Gagne's Conditions of Learning instructional design theory. This theory, although first published in the early 1970s, is still fundamental in instructional design and instructional technology. First, top-level as well as prerequisite learning objectives for a microarray analysis workshop and a primer design workshop were defined. Then a hierarchy of objectives for each workshop was created. Hands-on tutorials were designed to meet these objectives. Finally, events of learning proposed by Gagne's theory were incorporated into the hands-on tutorials. The resultant manuals were tested on a small number of trainees, revised, and applied in 1-day bioinformatics workshops. Based on this experience and on observations made during the workshops, we conclude that Gagne's Conditions of Learning instructional design theory provides a useful framework for developing bioinformatics training, but may not be optimal as a method for teaching it.

  5. Bioinformatics applications in proteomics data analysis

    NARCIS (Netherlands)

    Peng, M.

    2015-01-01

    In this thesis, I detail my 4-year efforts in developing bioinformatics tools and algorithms to address the growing demands of current proteomics endeavors, covering a range of facets such as large-scale protein expression profiling, charting post-translation modifications as well as

  6. KDE Bioscience: platform for bioinformatics analysis workflows.

    Science.gov (United States)

    Lu, Qiang; Hao, Pei; Curcin, Vasa; He, Weizhong; Li, Yuan-Yuan; Luo, Qing-Ming; Guo, Yi-Ke; Li, Yi-Xue

    2006-08-01

    Bioinformatics is a dynamic research area in which a large number of algorithms and programs have been developed rapidly and independently without much consideration so far of the need for standardization. The lack of such common standards combined with unfriendly interfaces make it difficult for biologists to learn how to use these tools and to translate the data formats from one to another. Consequently, the construction of an integrative bioinformatics platform to facilitate biologists' research is an urgent and challenging task. KDE Bioscience is a java-based software platform that collects a variety of bioinformatics tools and provides a workflow mechanism to integrate them. Nucleotide and protein sequences from local flat files, web sites, and relational databases can be entered, annotated, and aligned. Several home-made or 3rd-party viewers are built-in to provide visualization of annotations or alignments. KDE Bioscience can also be deployed in client-server mode where simultaneous execution of the same workflow is supported for multiple users. Moreover, workflows can be published as web pages that can be executed from a web browser. The power of KDE Bioscience comes from the integrated algorithms and data sources. With its generic workflow mechanism other novel calculations and simulations can be integrated to augment the current sequence analysis functions. Because of this flexible and extensible architecture, KDE Bioscience makes an ideal integrated informatics environment for future bioinformatics or systems biology research.

  7. An integrative bioinformatics pipeline for the genomewide ...

    Indian Academy of Sciences (India)

    2013-12-06

    Dec 6, 2013 ... [Fang W., Zhou N., Li D., Chen Z., Jiang P. and Zhang D. 2013 An integrative bioinformatics pipeline for the genomewide identification of novel porcine microRNA genes. J. Genet. 92, 587–593]. Introduction. MicroRNA (miRNA) is a pivotal type of noncoding RNA gene in posttranscriptional gene regulation ...

  8. Protein raftophilicity. How bioinformatics can help membranologists

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Sperotto, Maria Maddalena

    )-based bioinformatics approach. The ANN was trained to recognize feature-based patterns in proteins that are considered to be associated with lipid rafts. The trained ANN was then used to predict protein raftophilicity. We found that, in the case of α-helical membrane proteins, their hydrophobic length does not affect...

  9. Novel bioinformatic developments for exome sequencing

    NARCIS (Netherlands)

    Lelieveld, S.H.; Veltman, J.A.; Gilissen, C.F.

    2016-01-01

    With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers

  10. Bioinformatics: A History of Evolution "In Silico"

    Science.gov (United States)

    Ondrej, Vladan; Dvorak, Petr

    2012-01-01

    Bioinformatics, biological databases, and the worldwide use of computers have accelerated biological research in many fields, such as evolutionary biology. Here, we describe a primer of nucleotide sequence management and the construction of a phylogenetic tree with two examples; the two selected are from completely different groups of organisms:…

  11. Bioinformatics in Undergraduate Education: Practical Examples

    Science.gov (United States)

    Boyle, John A.

    2004-01-01

    Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a…

  12. Privacy Preserving PCA on Distributed Bioinformatics Datasets

    Science.gov (United States)

    Li, Xin

    2011-01-01

    In recent years, new bioinformatics technologies, such as gene expression microarray, genome-wide association study, proteomics, and metabolomics, have been widely used to simultaneously identify a huge number of human genomic/genetic biomarkers, generate a tremendously large amount of data, and dramatically increase the knowledge on human…

  13. "Extreme Programming" in a Bioinformatics Class

    Science.gov (United States)

    Kelley, Scott; Alger, Christianna; Deutschman, Douglas

    2009-01-01

    The importance of Bioinformatics tools and methodology in modern biological research underscores the need for robust and effective courses at the college level. This paper describes such a course designed on the principles of cooperative learning based on a computer software industry production model called "Extreme Programming" (EP).…

  14. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  15. Development and implementation of a bioinformatics online ...

    African Journals Online (AJOL)

    Thus, there is the need for appropriate strategies of introducing the basic components of this emerging scientific field to part of the African populace through the development of an online distance education learning tool. This study involved the design of a bioinformatics online distance educative tool an implementation of ...

  16. MOWServ: a web client for integration of bioinformatic resources

    Science.gov (United States)

    Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J.; Claros, M. Gonzalo; Trelles, Oswaldo

    2010-01-01

    The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794

  17. Agile parallel bioinformatics workflow management using Pwrake

    Directory of Open Access Journals (Sweden)

    Tanaka Masahiro

    2011-09-01

    Full Text Available Abstract Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows

  18. Agile parallel bioinformatics workflow management using Pwrake.

    Science.gov (United States)

    Mishima, Hiroyuki; Sasaki, Kensaku; Tanaka, Masahiro; Tatebe, Osamu; Yoshiura, Koh-Ichiro

    2011-09-08

    In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles

  19. Promoting synergistic research and education in genomics and bioinformatics

    Science.gov (United States)

    2008-01-01

    Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology. High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine (http://www.isibm.org) and its official journals, the International Journal of Functional Informatics and Personalized Medicine (http://www.inderscience.com/ijfipm) and the International Journal of Computational Biology and Drug Design (http://www.inderscience.com/ijcbdd) in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and

  20. Promoting synergistic research and education in genomics and bioinformatics.

    Science.gov (United States)

    Yang, Jack Y; Yang, Mary Qu; Zhu, Mengxia Michelle; Arabnia, Hamid R; Deng, Youping

    2008-01-01

    Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine (http://www.isibm.org) and its official journals, the International Journal of Functional Informatics and Personalized Medicine (http://www.inderscience.com/ijfipm) and the International Journal of Computational Biology and Drug Design (http://www.inderscience.com/ijcbdd) in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and

  1. Navigating the changing learning landscape: perspective from bioinformatics.ca.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2013-09-01

    With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.

  2. The Bioinformatics of Integrative Medical Insights: Proposals for an International Psycho-Social and Cultural Bioinformatics Project

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

    Full Text Available We propose the formation of an International Psycho-Social and Cultural Bioinformatics Project (IPCBP to explore the research foundations of Integrative Medical Insights (IMI on all levels from the molecular-genomic to the psychological, cultural, social, and spiritual. Just as The Human Genome Project identified the molecular foundations of modern medicine with the new technology of sequencing DNA during the past decade, the IPCBP would extend and integrate this neuroscience knowledge base with the technology of gene expression via DNA/proteomic microarray research and brain imaging in development, stress, healing, rehabilitation, and the psychotherapeutic facilitation of existentional wellness. We anticipate that the IPCBP will require a unique international collaboration of, academic institutions, researchers, and clinical practioners for the creation of a new neuroscience of mind-body communication, brain plasticity, memory, learning, and creative processing during optimal experiential states of art, beauty, and truth. We illustrate this emerging integration of bioinformatics with medicine with a videotape of the classical 4-stage creative process in a neuroscience approach to psychotherapy.

  3. The Bioinformatics of Integrative Medical Insights: Proposals for an International PsychoSocial and Cultural Bioinformatics Project

    Directory of Open Access Journals (Sweden)

    Ernest Rossi

    2006-01-01

    Full Text Available We propose the formation of an International PsychoSocial and Cultural Bioinformatics Project (IPCBP to explore the research foundations of Integrative Medical Insights (IMI on all levels from the molecular-genomic to the psychological, cultural, social, and spiritual. Just as The Human Genome Project identified the molecular foundations of modern medicine with the new technology of sequencing DNA during the past decade, the IPCBP would extend and integrate this neuroscience knowledge base with the technology of gene expression via DNA/proteomic microarray research and brain imaging in development, stress, healing, rehabilitation, and the psychotherapeutic facilitation of existentional wellness. We anticipate that the IPCBP will require a unique international collaboration of, academic institutions, researchers, and clinical practioners for the creation of a new neuroscience of mind-body communication, brain plasticity, memory, learning, and creative processing during optimal experiential states of art, beauty, and truth. We illustrate this emerging integration of bioinformatics with medicine with a videotape of the classical 4-stage creative process in a neuroscience approach to psychotherapy.

  4. BCNTB bioinformatics: the next evolutionary step in the bioinformatics of breast cancer tissue banking.

    Science.gov (United States)

    Gadaleta, Emanuela; Pirrò, Stefano; Dayem Ullah, Abu Zafer; Marzec, Jacek; Chelala, Claude

    2017-10-09

    Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to query findings from publicly available, in-house and experimental data generated using samples supplied from the Breast Cancer Now Tissue Bank. This in silico environment aims to help researchers use breast cancer data to their full potential, irrespective of any bioinformatics barriers. For this new release, a complete overhaul of the IT and bioinformatic infrastructure underlying the portal has been conducted and a host of novel analytical modules established. We developed and adopted an automated data selection and prioritisation system, expanded the data content and included tissue and cell line data generated from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia, designed a host of novel analytical modalities and enhanced the query building process. Furthermore, the results are presented in an interactive format, providing researchers with greater control over the information on which they want to focus. Breast Cancer Now Tissue Bank bioinformatics can be accessed at http://bioinformatics.breastcancertissuebank.org/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. A Bioinformatics Reference Model: Towards a Framework for Developing and Organising Bioinformatic Resources

    Science.gov (United States)

    Hiew, Hong Liang; Bellgard, Matthew

    2007-11-01

    Life Science research faces the constant challenge of how to effectively handle an ever-growing body of bioinformatics software and online resources. The users and developers of bioinformatics resources have a diverse set of competing demands on how these resources need to be developed and organised. Unfortunately, there does not exist an adequate community-wide framework to integrate such competing demands. The problems that arise from this include unstructured standards development, the emergence of tools that do not meet specific needs of researchers, and often times a communications gap between those who use the tools and those who supply them. This paper presents an overview of the different functions and needs of bioinformatics stakeholders to determine what may be required in a community-wide framework. A Bioinformatics Reference Model is proposed as a basis for such a framework. The reference model outlines the functional relationship between research usage and technical aspects of bioinformatics resources. It separates important functions into multiple structured layers, clarifies how they relate to each other, and highlights the gaps that need to be addressed for progress towards a diverse, manageable, and sustainable body of resources. The relevance of this reference model to the bioscience research community, and its implications in progress for organising our bioinformatics resources, are discussed.

  6. Recent developments in life sciences research: Role of bioinformatics

    African Journals Online (AJOL)

    SERVER

    2008-03-04

    Mar 4, 2008 ... discovery, biological databases, bioinformatic tools, bioinformatic tasks and its application in life sciences research. Key words: ... Bioinformatics and computational biology are rooted in life sciences as well as computer and ... Several updates are publishing to support this draft version to understand the ...

  7. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik

    2013-01-01

    to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse...... organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists....

  8. Component-Based Approach for Educating Students in Bioinformatics

    Science.gov (United States)

    Poe, D.; Venkatraman, N.; Hansen, C.; Singh, G.

    2009-01-01

    There is an increasing need for an effective method of teaching bioinformatics. Increased progress and availability of computer-based tools for educating students have led to the implementation of a computer-based system for teaching bioinformatics as described in this paper. Bioinformatics is a recent, hybrid field of study combining elements of…

  9. Translational Bioinformatics: Linking the Molecular World to the Clinical World

    OpenAIRE

    Altman, RB

    2012-01-01

    Translational bioinformatics represents the union of translational medicine and bioinformatics. Translational medicine moves basic biological discoveries from the research bench into the patient-care setting and uses clinical observations to inform basic biology. It focuses on patient care, including the creation of new diagnostics, prognostics, prevention strategies, and therapies based on biological discoveries. Bioinformatics involves algorithms to represent, store, and analyze basic biolo...

  10. Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

    Science.gov (United States)

    Schönbach, Christian; Verma, Chandra; Bond, Peter J; Ranganathan, Shoba

    2016-12-22

    The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics and BMC Systems Biology, 24 articles with a bioinformatics or systems biology focus are reviewed in this editorial. InCoB2017 is scheduled to be held in Shenzen, China, September 20-22, 2017.

  11. The 2011 Bioinformatics Links Directory update: more resources, tools and databases and features to empower the bioinformatics community.

    Science.gov (United States)

    Brazas, Michelle D; Yim, David S; Yamada, Joseph T; Ouellette, B F Francis

    2011-07-01

    The Bioinformatics Links Directory continues its collaboration with Nucleic Acids Research to collaboratively publish and compile a freely accessible, online collection of tools, databases and resource materials for bioinformatics and molecular biology research. The July 2011 Web Server issue of Nucleic Acids Research adds an additional 78 web server tools and 14 updates to the directory at http://bioinformatics.ca/links_directory/.

  12. Bioinformatics Approaches for Human Gut Microbiome Research

    Directory of Open Access Journals (Sweden)

    Zhijun Zheng

    2016-07-01

    Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.

  13. Bioinformatics in New Generation Flavivirus Vaccines

    Directory of Open Access Journals (Sweden)

    Penelope Koraka

    2010-01-01

    Full Text Available Flavivirus infections are the most prevalent arthropod-borne infections world wide, often causing severe disease especially among children, the elderly, and the immunocompromised. In the absence of effective antiviral treatment, prevention through vaccination would greatly reduce morbidity and mortality associated with flavivirus infections. Despite the success of the empirically developed vaccines against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus, there is an increasing need for a more rational design and development of safe and effective vaccines. Several bioinformatic tools are available to support such rational vaccine design. In doing so, several parameters have to be taken into account, such as safety for the target population, overall immunogenicity of the candidate vaccine, and efficacy and longevity of the immune responses triggered. Examples of how bio-informatics is applied to assist in the rational design and improvements of vaccines, particularly flavivirus vaccines, are presented and discussed.

  14. Bioinformatics approaches to single-cell analysis in developmental biology.

    Science.gov (United States)

    Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

    2016-03-01

    Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. © The Author 2015. Published by Oxford University Press on behalf of the European

  15. The roots of bioinformatics in theoretical biology.

    Directory of Open Access Journals (Sweden)

    Paulien Hogeweg

    2011-03-01

    Full Text Available From the late 1980s onward, the term "bioinformatics" mostly has been used to refer to computational methods for comparative analysis of genome data. However, the term was originally more widely defined as the study of informatic processes in biotic systems. In this essay, I will trace this early history (from a personal point of view and I will argue that the original meaning of the term is re-emerging.

  16. The growing need for microservices in bioinformatics

    Directory of Open Access Journals (Sweden)

    Christopher L Williams

    2016-01-01

    Full Text Available Objective: Within the information technology (IT industry, best practices and standards are constantly evolving and being refined. In contrast, computer technology utilized within the healthcare industry often evolves at a glacial pace, with reduced opportunities for justified innovation. Although the use of timely technology refreshes within an enterprise′s overall technology stack can be costly, thoughtful adoption of select technologies with a demonstrated return on investment can be very effective in increasing productivity and at the same time, reducing the burden of maintenance often associated with older and legacy systems. In this brief technical communication, we introduce the concept of microservices as applied to the ecosystem of data analysis pipelines. Microservice architecture is a framework for dividing complex systems into easily managed parts. Each individual service is limited in functional scope, thereby conferring a higher measure of functional isolation and reliability to the collective solution. Moreover, maintenance challenges are greatly simplified by virtue of the reduced architectural complexity of each constitutive module. This fact notwithstanding, rendered overall solutions utilizing a microservices-based approach provide equal or greater levels of functionality as compared to conventional programming approaches. Bioinformatics, with its ever-increasing demand for performance and new testing algorithms, is the perfect use-case for such a solution. Moreover, if promulgated within the greater development community as an open-source solution, such an approach holds potential to be transformative to current bioinformatics software development. Context: Bioinformatics relies on nimble IT framework which can adapt to changing requirements. Aims: To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics Conclusions: Use of the microservices framework

  17. VLSI Microsystem for Rapid Bioinformatic Pattern Recognition

    Science.gov (United States)

    Fang, Wai-Chi; Lue, Jaw-Chyng

    2009-01-01

    A system comprising very-large-scale integrated (VLSI) circuits is being developed as a means of bioinformatics-oriented analysis and recognition of patterns of fluorescence generated in a microarray in an advanced, highly miniaturized, portable genetic-expression-assay instrument. Such an instrument implements an on-chip combination of polymerase chain reactions and electrochemical transduction for amplification and detection of deoxyribonucleic acid (DNA).

  18. Comprehensive decision tree models in bioinformatics.

    Science.gov (United States)

    Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

    2012-01-01

    Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly

  19. A review of bioinformatic pipeline frameworks

    Science.gov (United States)

    2017-01-01

    Abstract High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base. PMID:27013646

  20. Improving bioinformatic pipelines for exome variant calling

    OpenAIRE

    Ji, Hanlee P.

    2012-01-01

    Exome sequencing analysis is a cost-effective approach for identifying variants in coding regions. However, recognizing the relevant single nucleotide variants, small insertions and deletions remains a challenge for many researchers and diagnostic laboratories typically do not have access to the bioinformatic analysis pipelines necessary for clinical application. The Atlas2 suite, recently released by Baylor Genome Center, is designed to be widely accessible, runs on desktop computers but is ...

  1. An active registry for bioinformatics web services.

    Science.gov (United States)

    Pettifer, S; Thorne, D; McDermott, P; Attwood, T; Baran, J; Bryne, J C; Hupponen, T; Mowbray, D; Vriend, G

    2009-08-15

    The EMBRACE Registry is a web portal that collects and monitors web services according to test scripts provided by the their administrators. Users are able to search for, rank and annotate services, enabling them to select the most appropriate working service for inclusion in their bioinformatics analysis tasks. Web site implemented with PHP, Python, MySQL and Apache, with all major browsers supported. (www.embraceregistry.net).

  2. Introduction: European climate leadership

    NARCIS (Netherlands)

    Wurzel, R.K.W.; Liefferink, J.D.; Connelly, J.

    2017-01-01

    There is no shortage of would-be leaders in EU climate change politics. The EU institutions (e.g. European Council, Council of the EU, Commission and the European Parliament (EP)), member states and societal actors have all, though to varying degrees and at different time periods, tried to offer

  3. Bioinformatics Training: A Review of Challenges, Actions and Support Requirements

    DEFF Research Database (Denmark)

    Schneider, M.V.; Watson, J.; Attwood, T.

    2010-01-01

    As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics...... services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article derive from the first...

  4. Translational bioinformatics in psychoneuroimmunology: methods and applications.

    Science.gov (United States)

    Yan, Qing

    2012-01-01

    Translational bioinformatics plays an indispensable role in transforming psychoneuroimmunology (PNI) into personalized medicine. It provides a powerful method to bridge the gaps between various knowledge domains in PNI and systems biology. Translational bioinformatics methods at various systems levels can facilitate pattern recognition, and expedite and validate the discovery of systemic biomarkers to allow their incorporation into clinical trials and outcome assessments. Analysis of the correlations between genotypes and phenotypes including the behavioral-based profiles will contribute to the transition from the disease-based medicine to human-centered medicine. Translational bioinformatics would also enable the establishment of predictive models for patient responses to diseases, vaccines, and drugs. In PNI research, the development of systems biology models such as those of the neurons would play a critical role. Methods based on data integration, data mining, and knowledge representation are essential elements in building health information systems such as electronic health records and computerized decision support systems. Data integration of genes, pathophysiology, and behaviors are needed for a broad range of PNI studies. Knowledge discovery approaches such as network-based systems biology methods are valuable in studying the cross-talks among pathways in various brain regions involved in disorders such as Alzheimer's disease.

  5. Bioinformatics on the cloud computing platform Azure.

    Directory of Open Access Journals (Sweden)

    Hugh P Shanahan

    Full Text Available We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development.

  6. Bioinformatics on the cloud computing platform Azure.

    Science.gov (United States)

    Shanahan, Hugh P; Owen, Anne M; Harrison, Andrew P

    2014-01-01

    We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development.

  7. Bringing Web 2.0 to bioinformatics.

    Science.gov (United States)

    Zhang, Zhang; Cheung, Kei-Hoi; Townsend, Jeffrey P

    2009-01-01

    Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.

  8. Adapting bioinformatics curricula for big data

    Science.gov (United States)

    Greene, Anna C.; Giffin, Kristine A.; Greene, Casey S.

    2016-01-01

    Modern technologies are capable of generating enormous amounts of data that measure complex biological systems. Computational biologists and bioinformatics scientists are increasingly being asked to use these data to reveal key systems-level properties. We review the extent to which curricula are changing in the era of big data. We identify key competencies that scientists dealing with big data are expected to possess across fields, and we use this information to propose courses to meet these growing needs. While bioinformatics programs have traditionally trained students in data-intensive science, we identify areas of particular biological, computational and statistical emphasis important for this era that can be incorporated into existing curricula. For each area, we propose a course structured around these topics, which can be adapted in whole or in parts into existing curricula. In summary, specific challenges associated with big data provide an important opportunity to update existing curricula, but we do not foresee a wholesale redesign of bioinformatics training programs. PMID:25829469

  9. Bioinformatic pipelines in Python with Leaf

    Science.gov (United States)

    2013-01-01

    Background An incremental, loosely planned development approach is often used in bioinformatic studies when dealing with custom data analysis in a rapidly changing environment. Unfortunately, the lack of a rigorous software structuring can undermine the maintainability, communicability and replicability of the process. To ameliorate this problem we propose the Leaf system, the aim of which is to seamlessly introduce the pipeline formality on top of a dynamical development process with minimum overhead for the programmer, thus providing a simple layer of software structuring. Results Leaf includes a formal language for the definition of pipelines with code that can be transparently inserted into the user’s Python code. Its syntax is designed to visually highlight dependencies in the pipeline structure it defines. While encouraging the developer to think in terms of bioinformatic pipelines, Leaf supports a number of automated features including data and session persistence, consistency checks between steps of the analysis, processing optimization and publication of the analytic protocol in the form of a hypertext. Conclusions Leaf offers a powerful balance between plan-driven and change-driven development environments in the design, management and communication of bioinformatic pipelines. Its unique features make it a valuable alternative to other related tools. PMID:23786315

  10. Chapter 16: text mining for translational bioinformatics.

    Science.gov (United States)

    Cohen, K Bretonnel; Hunter, Lawrence E

    2013-04-01

    Text mining for translational bioinformatics is a new field with tremendous research potential. It is a subfield of biomedical natural language processing that concerns itself directly with the problem of relating basic biomedical research to clinical practice, and vice versa. Applications of text mining fall both into the category of T1 translational research-translating basic science results into new interventions-and T2 translational research, or translational research for public health. Potential use cases include better phenotyping of research subjects, and pharmacogenomic research. A variety of methods for evaluating text mining applications exist, including corpora, structured test suites, and post hoc judging. Two basic principles of linguistic structure are relevant for building text mining applications. One is that linguistic structure consists of multiple levels. The other is that every level of linguistic structure is characterized by ambiguity. There are two basic approaches to text mining: rule-based, also known as knowledge-based; and machine-learning-based, also known as statistical. Many systems are hybrids of the two approaches. Shared tasks have had a strong effect on the direction of the field. Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing.

  11. Bioinformatics tools for analysing viral genomic data.

    Science.gov (United States)

    Orton, R J; Gu, Q; Hughes, J; Maabar, M; Modha, S; Vattipally, S B; Wilkie, G S; Davison, A J

    2016-04-01

    The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing.

  12. Strengthening of the Blood Safety System in the National Blood Transfusion Service - Implementation of the European Union IPA Project - at the Institute for Transfusion Medicine of the Republic of Macedonia

    Directory of Open Access Journals (Sweden)

    Rada M. Grubovic

    2014-09-01

    Full Text Available The Safety of the Blood Supply in any country is of utmost importance to safeguard patients from serious adverse events of blood transfusion. Implementation of a Quality System in the Blood Transfusion Service, with support of Government and Ministry of Health is a key element to guarantee safe blood. The IPA TAIB 2009 project - Strengthening of the Blood Safety System executed in 2013/14 provided the means to start implementing a Quality System in the Institute for Transfusion Medicine of the Republic of Macedonia. This project aimed to ultimately bring the Blood Transfusion Service to European Union standards, allowing the exchange of blood components and all other types of collaboration with other European Union countries in future. The project put the basis for unification of blood transfusion standards and operating procedures in the whole country as well as set up essential education of blood transfusion personnel.

  13. Surgery for complications of trans-catheter closure of atrial septal defects : a multi-institutional study from the European Congenital Heart Surgeons Association

    NARCIS (Netherlands)

    Sarris, George E.; Kirvassilis, George; Zavaropoulos, Prodromos; Belli, Emre; Berggren, Hakan; Carrel, Thierry; Comas, Juan V.; Corno, Antonio F.; Daenen, Willem; Di Carlo, Duccio; Ebels, Tjark; Fragata, Jose; Hamilton, Leslie; Hraska, Viktor; Jacobs, Jeffrey; Lazarov, Stojan; Mavroudis, Constantine; Metras, Dominique; Rubay, Jean; Schreiber, Christian; Stellin, Giovanni

    Objective: This study aims to analyse the collective experience of participating European Congenital Heart Surgeons Association centres in the surgical management of complications resulting from trans-catheter closure of atrial septal defects (ASDs). Methods: The records of all (n = 56) patients,

  14. Pakistan's Textile and Clothing Sector and its Future in the European Union (Evaluation Report published by Sustainable Development Policy Institute, Islamabad)

    NARCIS (Netherlands)

    K.A. Siegmann (Karin Astrid)

    2008-01-01

    textabstract[Introduction:] EU-Pakistan Trade in Textiles and Clothing: A Love – Hate Relationship? European nights are intimately linked to Pakistan. A large number of the community’s citizens spend their nights on Pakistani bed-sheets. In 2005, the South Asian economy was the largest supplier of

  15. Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package.

    Science.gov (United States)

    El-Kalioby, Mohamed; Abouelhoda, Mohamed; Krüger, Jan; Giegerich, Robert; Sczyrba, Alexander; Wall, Dennis P; Tonellato, Peter

    2012-01-01

    Bioinformatics services have been traditionally provided in the form of a web-server that is hosted at institutional infrastructure and serves multiple users. This model, however, is not flexible enough to cope with the increasing number of users, increasing data size, and new requirements in terms of speed and availability of service. The advent of cloud computing suggests a new service model that provides an efficient solution to these problems, based on the concepts of "resources-on-demand" and "pay-as-you-go". However, cloud computing has not yet been introduced within bioinformatics servers due to the lack of usage scenarios and software layers that address the requirements of the bioinformatics domain. In this paper, we provide different use case scenarios for providing cloud computing based services, considering both the technical and financial aspects of the cloud computing service model. These scenarios are for individual users seeking computational power as well as bioinformatics service providers aiming at provision of personalized bioinformatics services to their users. We also present elasticHPC, a software package and a library that facilitates the use of high performance cloud computing resources in general and the implementation of the suggested bioinformatics scenarios in particular. Concrete examples that demonstrate the suggested use case scenarios with whole bioinformatics servers and major sequence analysis tools like BLAST are presented. Experimental results with large datasets are also included to show the advantages of the cloud model. Our use case scenarios and the elasticHPC package are steps towards the provision of cloud based bioinformatics services, which would help in overcoming the data challenge of recent biological research. All resources related to elasticHPC and its web-interface are available at http://www.elasticHPC.org.

  16. Marine microbial biodiversity, bioinformatics and biotechnology (M2B3) data reporting and service standards.

    Science.gov (United States)

    Ten Hoopen, Petra; Pesant, Stéphane; Kottmann, Renzo; Kopf, Anna; Bicak, Mesude; Claus, Simon; Deneudt, Klaas; Borremans, Catherine; Thijsse, Peter; Dekeyzer, Stefanie; Schaap, Dick Ma; Bowler, Chris; Glöckner, Frank Oliver; Cochrane, Guy

    2015-01-01

    Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7(th) Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.

  17. Financijske institucije i trzista Europske unije - regulacija i supervizija/Financial institutions and markets in the European Union - regulation and supervision

    National Research Council Canada - National Science Library

    Ana Grdovic Gnip

    2016-01-01

    .... Since the regulation of financial institutions and markets combines the study of regulatory theories from law and from economics, the author first of all relates these two fields by explaining...

  18. Causality in Europeanization Research

    DEFF Research Database (Denmark)

    Lynggaard, Kennet

    2012-01-01

    to develop discursive institutional analytical frameworks and something that comes close to the formulation of hypothesis on the effects of European Union (EU) policies and institutions on domestic change. Even if these efforts so far do not necessarily amount to substantive theories or claims of causality...

  19. European Psychology Map

    Directory of Open Access Journals (Sweden)

    DANA SCHÖN

    2009-06-01

    Full Text Available The Institute for Psychology Information (ZPID compiled an extensive list of European psycho-logical organizations, comprised of university departments, research institutions, professional associa-tions and publishing houses. The list is available on the ZPID website, together with a web mapping applet that indicates the exact geographical location of the organizations.

  20. Allergen cross-reactivity in allergic rhinitis and oral-allergy syndrome: a bioinformatic protein sequence analysis.

    Science.gov (United States)

    Platt, Michael; Howell, Sara; Sachdeva, Ricky; Dumont, Charles

    2014-07-01

    Clinical allergy cross-reactivity that is seen with related inhalant allergens or between unrelated inhalant allergens and foods in oral allergy syndrome (OAS) remains poorly understood. The goal of this study is to determine whether clinical cross-reactivity can be identified from primary protein sequences in allergy epitopes and food proteins. High-throughput analysis was performed by assembling all known allergy epitopes within the Immune Epitope Database (IEDB; http://www.iedb.org) for 5 common species from 5 inhalant allergen subclasses and comparing their protein sequences to each other, as well as to sequences of intact proteins from known cross-reactive foods in the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) protein database (http://www.uniprot.org) that have been implicated in OAS. Computational methods were employed to allow for exact matching, gaps, and similar amino acids using multiple algorithms. A phylogenetic tree was created to determine evolutionary relationships between cross-reactive epitopes in OAS. Twenty-three common inhalant allergens had 4429 unique epitopes; the 19 foods implicated in OAS had 9497 protein sequences. The Basic Local Alignment Search Tool (BLAST) algorithm identified interclass and intraclass sequence similarities for the 5 inhalant allergy classes with high similarity for mites, grasses, and trees. Analysis of OAS proteins identified 104 matches to inhalant allergy epitopes that are known to cross-react. The phylogenetic tree displayed relationships that mostly followed organism phylogeny. Use of primary protein sequences was successful in explaining clinical allergy cross-reactivity. Clinical correlation is needed for use of these epitopes as diagnostic or therapeutic entities for patients with cross-reactive allergic disease. © 2014 ARS-AAOA, LLC.

  1. Introducing bioinformatics, the biosciences' genomic revolution

    CERN Document Server

    Zanella, Paolo

    1999-01-01

    The general audience for these lectures is mainly physicists, computer scientists, engineers or the general public wanting to know more about what’s going on in the biosciences. What’s bioinformatics and why is all this fuss being made about it ? What’s this revolution triggered by the human genome project ? Are there any results yet ? What are the problems ? What new avenues of research have been opened up ? What about the technology ? These new developments will be compared with what happened at CERN earlier in its evolution, and it is hoped that the similiraties and contrasts will stimulate new curiosity and provoke new thoughts.

  2. Databases and bioinformatics tools for rice research

    Directory of Open Access Journals (Sweden)

    Priyanka Garg

    2016-11-01

    Full Text Available Rice is one of the most important agricultural crop in the world and widely studied model plant. The completion of whole genome sequence of rice (Oryza sativa and high-throughput experimental platforms have led to the generation of the tremendous amount of data, and development of the specialized databases and bioinformatics tools for data processing, efficient organization, analysis, and visualization. In this article, we discuss a collection of biological databases that host genomics data on sequence, gene expression, genetic variation, gene-interactomes, and pathways, and facilitate data analysis and visualization.

  3. Robust Bioinformatics Recognition with VLSI Biochip Microsystem

    Science.gov (United States)

    Lue, Jaw-Chyng L.; Fang, Wai-Chi

    2006-01-01

    A microsystem architecture for real-time, on-site, robust bioinformatic patterns recognition and analysis has been proposed. This system is compatible with on-chip DNA analysis means such as polymerase chain reaction (PCR)amplification. A corresponding novel artificial neural network (ANN) learning algorithm using new sigmoid-logarithmic transfer function based on error backpropagation (EBP) algorithm is invented. Our results show the trained new ANN can recognize low fluorescence patterns better than the conventional sigmoidal ANN does. A differential logarithmic imaging chip is designed for calculating logarithm of relative intensities of fluorescence signals. The single-rail logarithmic circuit and a prototype ANN chip are designed, fabricated and characterized.

  4. A model of differentiation in quantum bioinformatics.

    Science.gov (United States)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Yamato, Ichiro

    2017-11-01

    Differentiation is a universal process found in various phenomena of nature. As seen in the example of cell differentiation, the creation diversity on individual's character is caused by environmental interactions. In this paper, we try to explain its mechanism, which has been discussed mainly in Biology, by using the formalism of quantum physics. Our approach known as quantum bioinformatics shows that the temporal change of statistical state called decoherence fits to describe non-local phenomena like differentiation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. STUDY ON THE PROBLEMS IN THE STAGES OF FILLING OUT THE APPLICATION FORM AND TECHNICAL-FINANCIAL REPORTING ENCOUNTERED BY THE PUBLIC INSTITUTIONS IN THE CENTRE REGION IN ACCESSING EUROPEAN FUNDS

    Directory of Open Access Journals (Sweden)

    DUMITRASCU DANUT

    2012-07-01

    Full Text Available The article has as main field the project management, specifically, identifying the negative factors on European projects. The article assumes that there is a connection between the absorption of European funds and the maturity of the Romanian society in terms of project management. The main objective of the research is to identify the problems faced by public institutions from Centre Region in accessing European funds. The purpose of the research is to identify the causes that led to the low absorption of European funds, with devastating effects on the current economic situation. The present research is based on a preliminary analysis performed by the author on the rate of accessing European funds published in an article entitled “The current state of European funds absorption through funding programmes – measure of the Romanian performances in the project management practice”. The small degree of absorption of European funds resulting from the analysis shows a poor practice of the theory on project management. To identify the causes of this problem, a research was carried out to recognise the issues that led to this situation. The investigation included two successive surveys, the first one qualitative, exploratory type, interview-based, meant to demonstrate the qualitative aspects of the investigated phenomena and the other one, quantitative, based on a questionnaire in the form of occasional surveys. The qualitative and quantitative research methods are used in combination; this approach has become necessary especially due to the very complex reality whose trueness cannot be captured through one method. The investigation has however a highly quantitative character, the purpose of the qualitative research being to provide the prerequisites for achieving the quantitative research. The qualitative research revealed the existence of some problems faced by institutions in relation to accessing and developing projects that focus

  6. A Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

    Science.gov (United States)

    Magana, Alejandra J.; Taleyarkhan, Manaz; Alvarado, Daniela Rivera; Kane, Michael; Springer, John; Clase, Kari

    2014-01-01

    Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the…

  7. State budget transfers to Health Insurance Funds for universal health coverage: institutional design patterns and challenges of covering those outside the formal sector in Eastern European high-income countries.

    Science.gov (United States)

    Vilcu, Ileana; Mathauer, Inke

    2016-01-15

    Many countries from the European region, which moved from a government financed and provided health system to social health insurance, would have had the risk of moving away from universal health coverage if they had followed a "traditional" approach. The Eastern European high-income countries studied in this paper managed to avoid this potential pitfall by using state budget revenues to explicitly pay health insurance contributions on behalf of certain (vulnerable) population groups who have difficulties to pay these contributions themselves. The institutional design aspects of their government revenue transfer arrangements are analysed, as well as their impact on universal health coverage progress. This regional study is based on literature review and review of databases for the performance assessment. The analytical framework focuses on the following institutional design features: rules on eligibility for contribution exemption, financing and pooling arrangements, and purchasing arrangements and benefit package design. More commonalities than differences can be identified across countries: a broad range of groups eligible for exemption from payment of health insurance contributions, full state contributions on behalf of the exempted groups, mostly mandatory participation, integrated pools for both the exempted and contributors, and relatively comprehensive benefit packages. In terms of performance, all countries have high total population coverage rates, but there are still challenges regarding financial protection and access to and utilization of health care services, especially for low income people. Overall, government revenue transfer arrangements to exempt vulnerable groups from contributions are one option to progress towards universal health coverage.

  8. Bioinformatics tools for predicting GPCR gene functions.

    Science.gov (United States)

    Suwa, Makiko

    2014-01-01

    The automatic classification of GPCRs by bioinformatics methodology can provide functional information for new GPCRs in the whole 'GPCR proteome' and this information is important for the development of novel drugs. Since GPCR proteome is classified hierarchically, general ways for GPCR function prediction are based on hierarchical classification. Various computational tools have been developed to predict GPCR functions; those tools use not simple sequence searches but more powerful methods, such as alignment-free methods, statistical model methods, and machine learning methods used in protein sequence analysis, based on learning datasets. The first stage of hierarchical function prediction involves the discrimination of GPCRs from non-GPCRs and the second stage involves the classification of the predicted GPCR candidates into family, subfamily, and sub-subfamily levels. Then, further classification is performed according to their protein-protein interaction type: binding G-protein type, oligomerized partner type, etc. Those methods have achieved predictive accuracies of around 90 %. Finally, I described the future subject of research of the bioinformatics technique about functional prediction of GPCR.

  9. Conveyor: a workflow engine for bioinformatic analyses.

    Science.gov (United States)

    Linke, Burkhard; Giegerich, Robert; Goesmann, Alexander

    2011-04-01

    The rapidly increasing amounts of data available from new high-throughput methods have made data processing without automated pipelines infeasible. As was pointed out in several publications, integration of data and analytic resources into workflow systems provides a solution to this problem, simplifying the task of data analysis. Various applications for defining and running workflows in the field of bioinformatics have been proposed and published, e.g. Galaxy, Mobyle, Taverna, Pegasus or Kepler. One of the main aims of such workflow systems is to enable scientists to focus on analysing their datasets instead of taking care for data management, job management or monitoring the execution of computational tasks. The currently available workflow systems achieve this goal, but fundamentally differ in their way of executing workflows. We have developed the Conveyor software library, a multitiered generic workflow engine for composition, execution and monitoring of complex workflows. It features an open, extensible system architecture and concurrent program execution to exploit resources available on modern multicore CPU hardware. It offers the ability to build complex workflows with branches, loops and other control structures. Two example use cases illustrate the application of the versatile Conveyor engine to common bioinformatics problems. The Conveyor application including client and server are available at http://conveyor.cebitec.uni-bielefeld.de.

  10. Bioinformatics Analyst | Center for Cancer Research

    Science.gov (United States)

    PROGRAM DESCRIPTION The Advanced Biomedical Computing Center (ABCC) is a part of the Data Science and Information Technology Program at Leidos Biomedical Research, Inc. The ABCC provides technology development, scientific consultation, collaboration and training, and high-performance computing support to the NCI and NIH scientists and staff. The Single Cell Analysis Facility (SCAF) is established to utilize a mix of existing and new resources aimed at providing state-of-the-art single-cell technologies to support the cancer research at NCI. KEY ROLES/RESPONSIBILITIES Bioinformatics Analyst Responsible for providing bioinformatics support including project consultation, experimental design, data management and analysis of high throughput sequencing data from next-generation sequencing and single cell technologies Perform single-cell genetic and transcriptional analysis to determine tumor heterogeneity, clonal evolution, immune signatures, and mechanism of resistance Design, develop and maintain robust analysis workflows and software pipelines, as well as custom scripts, to support the analysis of high-throughput sequencing data Provide biological interpretation of analysis results and present analysis results in a clear and concise manner, to scientific audiences Work effectively as a member of a team; coordinate activities among groups located at the Bethesda, Frederick, and Rockville NCI campuses; follow sound scientific practices and maintain effective documentation of activities and analyses This position is in support of the Center for Cancer Research (CCR).

  11. Higher Education Institutions and International Students' Hindrances: A Case of Students from the African Portuguese-Speaking Countries at Two European Portuguese Universities

    Science.gov (United States)

    Ambrósio, Susana; Marques, João Filipe; Santos, Lucília; Doutor, Catarina

    2017-01-01

    We present a study to comprehend if the support given by higher education institution (HEI) to international students coming from the Portuguese-Speaking African Countries meets their academic and social hindrances. Our starting point was a set of semi-structured interviews focused on the perspectives of these students, their Professors and Course…

  12. Controlling new knowledge: Genomic science, governance and the politics of bioinformatics.

    Science.gov (United States)

    Salter, Brian; Salter, Charlotte

    2017-04-01

    The rise of bioinformatics is a direct response to the political difficulties faced by genomics in its quest to be a new biomedical innovation, and the value of bioinformatics lies in its role as the bridge between the promise of genomics and its realization in the form of health benefits. Western scientific elites are able to use their close relationship with the state to control and facilitate the emergence of new domains compatible with the existing distribution of epistemic power - all within the embrace of public trust. The incorporation of bioinformatics as the saviour of genomics had to be integrated with the operation of two key aspects of governance in this field: the definition and ownership of the new knowledge. This was achieved mainly by the development of common standards and by the promotion of the values of communality, open access and the public ownership of data to legitimize and maintain the governance power of publicly funded genomic science. Opposition from industry advocating the private ownership of knowledge has been largely neutered through the institutions supporting the science-state concordat. However, in order for translation into health benefits to occur and public trust to be assured, genomic and clinical data have to be integrated and knowledge ownership agreed upon across the separate and distinct governance territories of scientist, clinical medicine and society. Tensions abound as science seeks ways of maintaining its control of knowledge production through the negotiation of new forms of governance with the institutions and values of clinicians and patients.

  13. Controlling new knowledge: Genomic science, governance and the politics of bioinformatics

    Science.gov (United States)

    Salter, Brian; Salter, Charlotte

    2017-01-01

    The rise of bioinformatics is a direct response to the political difficulties faced by genomics in its quest to be a new biomedical innovation, and the value of bioinformatics lies in its role as the bridge between the promise of genomics and its realization in the form of health benefits. Western scientific elites are able to use their close relationship with the state to control and facilitate the emergence of new domains compatible with the existing distribution of epistemic power – all within the embrace of public trust. The incorporation of bioinformatics as the saviour of genomics had to be integrated with the operation of two key aspects of governance in this field: the definition and ownership of the new knowledge. This was achieved mainly by the development of common standards and by the promotion of the values of communality, open access and the public ownership of data to legitimize and maintain the governance power of publicly funded genomic science. Opposition from industry advocating the private ownership of knowledge has been largely neutered through the institutions supporting the science-state concordat. However, in order for translation into health benefits to occur and public trust to be assured, genomic and clinical data have to be integrated and knowledge ownership agreed upon across the separate and distinct governance territories of scientist, clinical medicine and society. Tensions abound as science seeks ways of maintaining its control of knowledge production through the negotiation of new forms of governance with the institutions and values of clinicians and patients. PMID:28056721

  14. Highlighting computations in bioscience and bioinformatics: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB07).

    Science.gov (United States)

    Lu, Guoqing; Ni, Jun

    2008-05-28

    The Second Symposium on Computations in Bioinformatics and Bioscience (SCBB07) was held in Iowa City, Iowa, USA, on August 13-15, 2007. This annual event attracted dozens of bioinformatics professionals and students, who are interested in solving emerging computational problems in bioscience, from China, Japan, Taiwan and the United States. The Scientific Committee of the symposium selected 18 peer-reviewed papers for publication in this supplemental issue of BMC Bioinformatics. These papers cover a broad spectrum of topics in computational biology and bioinformatics, including DNA, protein and genome sequence analysis, gene expression and microarray analysis, computational proteomics and protein structure classification, systems biology and machine learning.

  15. Study protocol for the development of a European measure of best practice for people with long term mental health problems in institutional care (DEMoBinc

    Directory of Open Access Journals (Sweden)

    Killaspy Helen

    2009-06-01

    Full Text Available Abstract Background This study aims to build a measure for assessing and reviewing the living conditions, care and human rights of people with longer term mental health problems in psychiatric and social care institutions. Protection of their human rights is imperative since impaired mental capacity secondary to mental illness can make them vulnerable to abuse and exploitation from others. They also constitute a major resource pressure for mental health services, social services, informal carers and society as a whole. Methods/Design This study uses an iterative methodology to develop a toolkit to assess internationally agreed domains of care that are considered most important for recovery. These domains are identified by collating results from: i a systematic review of the literature on institutional care for this service user group; ii a review of the relevant care standards in each participating country; iii Delphi exercises in partner countries with mental health professionals, service users, carers and advocates. Common domains and cross-cutting themes are agreed by the principal researchers and an international expert panel. Items are developed to assess these domains and incorporated into the toolkit which is designed to be administered through a face to face interview with the institution's manager. The toolkit is refined in response to inter-rater reliability testing, feedback from interviewers and interviewees regarding its utility, and feedback from key stakeholders in each country about its ability to deliver information that can be used within each country's established systems for quality assessment and review. Cross-validation of the toolkit ratings against service users' quality of life, autonomy and markers of recovery tests whether it can deliver a proxy-measure of the service users' experiences of care and the institution's promotion of their human rights and recovery. The ability of the toolkit to assess the "value for money

  16. Mobyle: a new full web bioinformatics framework.

    Science.gov (United States)

    Néron, Bertrand; Ménager, Hervé; Maufrais, Corinne; Joly, Nicolas; Maupetit, Julien; Letort, Sébastien; Carrere, Sébastien; Tuffery, Pierre; Letondal, Catherine

    2009-11-15

    For the biologist, running bioinformatics analyses involves a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally, given that scientific tools can be difficult to install, it is particularly helpful for biologists to be able to use these tools through a web user interface. However, providing a web interface for a set of tools raises the problem that a single web portal cannot offer all the existing and possible services: it is the user, again, who has to cope with data copy among a number of different services. A framework enabling portal administrators to build a network of cooperating services would therefore clearly be beneficial. We have designed a system, Mobyle, to provide a flexible and usable Web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using a hierarchical typing system. Mobyle offers invocation of services distributed over remote Mobyle servers, thus enabling a federated network of curated bioinformatics portals without the user having to learn complex concepts or to install sophisticated software. While being focused on the end user, the Mobyle system also addresses the need, for the bioinfomatician, to automate remote services execution: PlayMOBY is a companion tool that automates the publication of BioMOBY web services, using Mobyle program definitions. The Mobyle system is distributed under the terms of the GNU GPLv2 on the project web site (http://bioweb2.pasteur.fr/projects/mobyle/). It is already deployed on three servers: http://mobyle.pasteur.fr, http://mobyle.rpbs.univ-paris-diderot.fr and http://lipm-bioinfo.toulouse.inra.fr/Mobyle. The PlayMOBY companion is distributed under the terms of the CeCILL license, and is

  17. INSTITUTIONAL ASPECTS OF THE CAUSES AND CONSEQUENCES VIOLATION OF FINANCIAL STABILITY: HISTORICAL RETROSPECTIVE AND CURRENT UKRAINIAN REALITIES IN THE CONTEXT OF CHALLENGES OF EUROPEAN INTEGRATION

    Directory of Open Access Journals (Sweden)

    I. Novikova

    2016-06-01

    Full Text Available The article analyzes the institutional aspect of the causes and consequences of violations of financial stability. Done analysis of famous historical examples of the emergence of inflationary bursts, as well as ways of establishing a financial equilibrium. In particular, states that often main cause of violations of financial stability becomes inflationary boom, which arose by wars, socio-economic and political contradictions. It was considered role of institutional instability in the context of the emergence of contemporary geopolitical challenges and socio-economic changes in Ukraine. The paper examines the impact of modern social and economic challenges on growth in inflation and on the deterioration of other macroeconomic indicators in Ukraine. At the end, was provided of the recommendations to overcome the financial problems in the national economy. Emphasized importance of the exchange rate stability of the currency.

  18. Circadian regulation of myocardial sarcomeric Titin-cap (Tcap, telethonin: identification of cardiac clock-controlled genes using open access bioinformatics data.

    Directory of Open Access Journals (Sweden)

    Peter S Podobed

    Full Text Available Circadian rhythms are important for healthy cardiovascular physiology and are regulated at the molecular level by a circadian clock mechanism. We and others previously demonstrated that 9-13% of the cardiac transcriptome is rhythmic over 24 h daily cycles; the heart is genetically a different organ day versus night. However, which rhythmic mRNAs are regulated by the circadian mechanism is not known. Here, we used open access bioinformatics databases to identify 94 transcripts with expression profiles characteristic of CLOCK and BMAL1 targeted genes, using the CircaDB website and JTK_Cycle. Moreover, 22 were highly expressed in the heart as determined by the BioGPS website. Furthermore, 5 heart-enriched genes had human/mouse conserved CLOCK:BMAL1 promoter binding sites (E-boxes, as determined by UCSC table browser, circadian mammalian promoter/enhancer database PEDB, and the European Bioinformatics Institute alignment tool (EMBOSS. Lastly, we validated findings by demonstrating that Titin cap (Tcap, telethonin was targeted by transcriptional activators CLOCK and BMAL1 by showing 1 Tcap mRNA and TCAP protein had a diurnal rhythm in murine heart; 2 cardiac Tcap mRNA was rhythmic in animals kept in constant darkness; 3 Tcap and control Per2 mRNA expression and cyclic amplitude were blunted in Clock(Δ19/Δ19 hearts; 4 BMAL1 bound to the Tcap promoter by ChIP assay; 5 BMAL1 bound to Tcap promoter E-boxes by biotinylated oligonucleotide assay; and 6 CLOCK and BMAL1 induced tcap expression by luciferase reporter assay. Thus this study identifies circadian regulated genes in silico, with validation of Tcap, a critical regulator of cardiac Z-disc sarcomeric structure and function.

  19. Data mining in bioinformatics using Weka.

    Science.gov (United States)

    Frank, Eibe; Hall, Mark; Trigg, Len; Holmes, Geoffrey; Witten, Ian H

    2004-10-12

    The Weka machine learning workbench provides a general-purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data pre-processing methods complemented by graphical user interfaces for data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it. http://www.cs.waikato.ac.nz/ml/weka.

  20. Bioinformatics and molecular modeling in glycobiology

    Science.gov (United States)

    Schloissnig, Siegfried

    2010-01-01

    The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed. PMID:20364395

  1. Bioinformatic Analysis of Strawberry GSTF12 Gene

    Science.gov (United States)

    Wang, Xiran; Jiang, Leiyu; Tang, Haoru

    2018-01-01

    GSTF12 has always been known as a key factor of proanthocyanins accumulate in plant testa. Through bioinformatics analysis of the nucleotide and encoded protein sequence of GSTF12, it is more advantageous to the study of genes related to anthocyanin biosynthesis accumulation pathway. Therefore, we chosen GSTF12 gene of 11 kinds species, downloaded their nucleotide and protein sequence from NCBI as the research object, found strawberry GSTF12 gene via bioinformation analyse, constructed phylogenetic tree. At the same time, we analysed the strawberry GSTF12 gene of physical and chemical properties and its protein structure and so on. The phylogenetic tree showed that Strawberry and petunia were closest relative. By the protein prediction, we found that the protein owed one proper signal peptide without obvious transmembrane regions.

  2. Spectral clustering and its use in bioinformatics

    Science.gov (United States)

    Higham, Desmond J.; Kalna, Gabriela; Kibble, Milla

    2007-07-01

    We formulate a discrete optimization problem that leads to a simple and informative derivation of a widely used class of spectral clustering algorithms. Regarding the algorithms as attempting to bi-partition a weighted graph with N vertices, our derivation indicates that they are inherently tuned to tolerate all partitions into two non-empty sets, independently of the cardinality of the two sets. This approach also helps to explain the difference in behaviour observed between methods based on the unnormalized and normalized graph Laplacian. We also give a direct explanation of why Laplacian eigenvectors beyond the Fiedler vector may contain fine-detail information of relevance to clustering. We show numerical results on synthetic data to support the analysis. Further, we provide examples where normalized and unnormalized spectral clustering is applied to microarray data--here the graph summarizes similarity of gene activity across different tissue samples, and accurate clustering of samples is a key task in bioinformatics.

  3. Bioinformatic and Biometric Methods in Plant Morphology

    Directory of Open Access Journals (Sweden)

    Surangi W. Punyasena

    2014-08-01

    Full Text Available Recent advances in microscopy, imaging, and data analyses have permitted both the greater application of quantitative methods and the collection of large data sets that can be used to investigate plant morphology. This special issue, the first for Applications in Plant Sciences, presents a collection of papers highlighting recent methods in the quantitative study of plant form. These emerging biometric and bioinformatic approaches to plant sciences are critical for better understanding how morphology relates to ecology, physiology, genotype, and evolutionary and phylogenetic history. From microscopic pollen grains and charcoal particles, to macroscopic leaves and whole root systems, the methods presented include automated classification and identification, geometric morphometrics, and skeleton networks, as well as tests of the limits of human assessment. All demonstrate a clear need for these computational and morphometric approaches in order to increase the consistency, objectivity, and throughput of plant morphological studies.

  4. Bioinformatics methods for identifying candidate disease genes

    Directory of Open Access Journals (Sweden)

    van Driel Marc A

    2006-06-01

    Full Text Available Abstract With the explosion in genomic and functional genomics information, methods for disease gene identification are rapidly evolving. Databases are now essential to the process of selecting candidate disease genes. Combining positional information with disease characteristics and functional information is the usual strategy by which candidate disease genes are selected. Enrichment for candidate disease genes, however, depends on the skills of the operating researcher. Over the past few years, a number of bioinformatics methods that enrich for the most likely candidate disease genes have been developed. Such in silico prioritisation methods may further improve by completion of datasets, by development of standardised ontologies across databases and species and, ultimately, by the integration of different strategies.

  5. Academic Training - Bioinformatics: Decoding the Genome

    CERN Multimedia

    Chris Jones

    2006-01-01

    ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...

  6. HARMONIZED EUROPE OR EUROPEAN HARMONY?

    Directory of Open Access Journals (Sweden)

    Cosmin Marinescu

    2007-07-01

    Full Text Available Recent evolutions in Europe raise questions on the viability of the present economic and social model that defines the European construction project. In this paper, the author will try to explain the viability of institutional European model that sticks between free market mechanisms and protectionism. The main challenge for the EU is about the possibility to bring together the institutional convergence and the welfare for all Europeans. This is the result of the view, still dominant, of European politics elite, according to which institutional harmonization is the solution of a more dynamic and prosper Europe. But, economic realities convince us that, more and more, a harmonized, standardized Europe is not necessarily identical with a Europe of harmony and social cooperation. If „development through integration” seems to be harmonization through „institutional transplant”, how could then be the European model one sufficiently wide open to market, which creates the prosperity so long waited for by new member countries?

  7. Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience

    Science.gov (United States)

    Panji, Sumir; Fernandes, Pedro L.; Judge, David P.; Ghouila, Amel; Salifu, Samson P.; Ahmed, Rehab; Kayondo, Jonathan; Ssemwanga, Deogratius

    2017-01-01

    Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge “Introduction to Bioinformatics” course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery–mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online “question and discussion” forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings. PMID:28981516

  8. The 2015 Bioinformatics Open Source Conference (BOSC 2015.

    Directory of Open Access Journals (Sweden)

    Nomi L Harris

    2016-02-01

    Full Text Available The Bioinformatics Open Source Conference (BOSC is organized by the Open Bioinformatics Foundation (OBF, a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG before the annual Intelligent Systems in Molecular Biology (ISMB conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  9. Recent developments in life sciences research: Role of bioinformatics

    African Journals Online (AJOL)

    Life sciences research and development has opened up new challenges and opportunities for bioinformatics. The contribution of bioinformatics advances made possible the mapping of the entire human genome and genomes of many other organisms in just over a decade. These discoveries, along with current efforts to ...

  10. Current status and future perspectives of bioinformatics in Tanzania ...

    African Journals Online (AJOL)

    The main bottleneck in advancing genomics in present times is the lack of expertise in using bioinformatics tools and approaches for data mining in raw DNA sequences generated by modern high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and ...

  11. Bioinformatics and its application in animal health: a review | Soetan ...

    African Journals Online (AJOL)

    Bioinformatics is an interdisciplinary subject, which uses computer application, statistics, mathematics and engineering for the analysis and management of biological information. It has become an important tool for basic and applied research in veterinary sciences. Bioinformatics has brought about advancements into ...

  12. Web-based bioinformatic resources for protein and nucleic acids ...

    African Journals Online (AJOL)

    Bioinformatics can be broadly defined as the creation and development of advanced information and computational techniques for problems in biology. More narrowly, bioinformatics is the set of computing techniques used to manage and extract useful information from the DNA/RNA/protein sequence data being generated ...

  13. Bioinformatic analysis to discover putative drug targets against ...

    African Journals Online (AJOL)

    /

    2012-01-26

    Jan 26, 2012 ... Bioinformatic analysis to discover putative drug targets against diarrheal causative agents. Muhammad Shakil Khan, Sana Zahra and Hamid Rashid*. Department of Bioinformatics, Mohammad Ali Jinnah University, Islamabad, Pakistan. Accepted 23 September, 2011. Availability of genome sequences of ...

  14. Generative Topic Modeling in Image Data Mining and Bioinformatics Studies

    Science.gov (United States)

    Chen, Xin

    2012-01-01

    Probabilistic topic models have been developed for applications in various domains such as text mining, information retrieval and computer vision and bioinformatics domain. In this thesis, we focus on developing novel probabilistic topic models for image mining and bioinformatics studies. Specifically, a probabilistic topic-connection (PTC) model…

  15. Assessment of a Bioinformatics across Life Science Curricula Initiative

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.; Grunwald, Sandra K.; Abler, Michael L.

    2007-01-01

    At the University of Wisconsin-La Crosse, we have undertaken a program to integrate the study of bioinformatics across the undergraduate life science curricula. Our efforts have included incorporating bioinformatics exercises into courses in the biology, microbiology, and chemistry departments, as well as coordinating the efforts of faculty within…

  16. Rust-Bio: a fast and safe bioinformatics library

    NARCIS (Netherlands)

    J. Köster (Johannes)

    2015-01-01

    textabstractWe present Rust-Bio, the first general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to provide a fast and safe set of bioinformatics algorithms and data

  17. The 2015 Bioinformatics Open Source Conference (BOSC 2015).

    Science.gov (United States)

    Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

    2016-02-01

    The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

  18. Concepts Of Bioinformatics And Its Application In Veterinary ...

    African Journals Online (AJOL)

    Bioinformatics has advanced the course of research and future veterinary vaccines development because it has provided new tools for identification of vaccine targets from sequenced biological data of organisms. In Nigeria, there is lack of bioinformatics training in the universities, expect for short training courses in which ...

  19. Report from the 2012 European Gender Summit

    CERN Document Server

    European Gender Summit, 2012

    2012-01-01

    Report from the 2012 European Gender Summit to the European Parliament and the Council, the European Commission, the Council of Europe, EU Member and Associate States, Science Institutions. Developing Systematic Implementation Strategy to Advance EU Policy on Gender Equality in Science, as part of HORIZON 2020, European Research Area and Innovation Union.

  20. European Physical Society awards

    CERN Multimedia

    2004-01-01

    The winners of the 2004 Accelerator Prizes, awarded by the European Physical Society's Interdivisional Group on Accelerators (EPS-IGA), have been announced. Vladmir Shiltsev (Fermilab) and Igor Meshkov (JINR, Joint Institute of Nuclear Research, Dubna) will be presented with their awards during the 9th European Particle Accelerator Conference, EPAC'04, on 8 July 2004 in Lucerne. Both physicists will also give a talk about their work. More details on: http://epac.web.cern.ch/

  1. LXtoo: an integrated live Linux distribution for the bioinformatics community.

    Science.gov (United States)

    Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

    2012-07-19

    Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

  2. 4273π: bioinformatics education on low cost ARM hardware.

    Science.gov (United States)

    Barker, Daniel; Ferrier, David Ek; Holland, Peter Wh; Mitchell, John Bo; Plaisier, Heleen; Ritchie, Michael G; Smart, Steven D

    2013-08-12

    Teaching bioinformatics at universities is complicated by typical computer classroom settings. As well as running software locally and online, students should gain experience of systems administration. For a future career in biology or bioinformatics, the installation of software is a useful skill. We propose that this may be taught by running the course on GNU/Linux running on inexpensive Raspberry Pi computer hardware, for which students may be granted full administrator access. We release 4273π, an operating system image for Raspberry Pi based on Raspbian Linux. This includes minor customisations for classroom use and includes our Open Access bioinformatics course, 4273π Bioinformatics for Biologists. This is based on the final-year undergraduate module BL4273, run on Raspberry Pi computers at the University of St Andrews, Semester 1, academic year 2012-2013. 4273π is a means to teach bioinformatics, including systems administration tasks, to undergraduates at low cost.

  3. LXtoo: an integrated live Linux distribution for the bioinformatics community

    Directory of Open Access Journals (Sweden)

    Yu Guangchuang

    2012-07-01

    Full Text Available Abstract Background Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Findings Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. Conclusions LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

  4. The development and application of bioinformatics core competencies to improve bioinformatics training and education

    Science.gov (United States)

    Brooksbank, Cath; Morgan, Sarah L.; Rosenwald, Anne; Warnow, Tandy; Welch, Lonnie

    2018-01-01

    Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans. PMID:29390004

  5. The Citizen, the Culture and European Union

    National Research Council Canada - National Science Library

    Marine Imberechts

    2009-01-01

    From the beginning of its work (1988), the European Centre of Culture tried to attract theattention of the European institutions on the urgent need to bring in the greatest number of citizens asense of belonging to a new space...

  6. Bioinformatic landscapes for plant transcription factor system research.

    Science.gov (United States)

    Wang, Yijun; Lu, Wenjie; Deng, Dexiang

    2016-02-01

    Diverse bioinformatic resources have been developed for plant transcription factor (TF) research. This review presents the bioinformatic resources and methodologies for the elucidation of plant TF-mediated biological events. Such information is helpful to dissect the transcriptional regulatory systems in the three reference plants Arabidopsis , rice, and maize and translation to other plants. Transcription factors (TFs) orchestrate diverse biological programs by the modulation of spatiotemporal patterns of gene expression via binding cis-regulatory elements. Advanced sequencing platforms accompanied by emerging bioinformatic tools revolutionize the scope and extent of TF research. The system-level integration of bioinformatic resources is beneficial to the decoding of TF-involved networks. Herein, we first briefly introduce general and specialized databases for TF research in three reference plants Arabidopsis, rice, and maize. Then, as proof of concept, we identified and characterized heat shock transcription factor (HSF) members through the TF databases. Finally, we present how the integration of bioinformatic resources at -omics layers can aid the dissection of TF-mediated pathways. We also suggest ways forward to improve the bioinformatic resources of plant TFs. Leveraging these bioinformatic resources and methodologies opens new avenues for the elucidation of transcriptional regulatory systems in the three model systems and translation to other plants.

  7. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

    Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.

  8. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.

    Science.gov (United States)

    Taboada, Eduardo N; Graham, Morag R; Carriço, João A; Van Domselaar, Gary

    2017-01-01

    Public health labs and food regulatory agencies globally are embracing whole genome sequencing (WGS) as a revolutionary new method that is positioned to replace numerous existing diagnostic and microbial typing technologies with a single new target: the microbial draft genome. The ability to cheaply generate large amounts of microbial genome sequence data, combined with emerging policies of food regulatory and public health institutions making their microbial sequences increasingly available and public, has served to open up the field to the general scientific community. This open data access policy shift has resulted in a proliferation of data being deposited into sequence repositories and of novel bioinformatics software designed to analyze these vast datasets. There also has been a more recent drive for improved data sharing to achieve more effective global surveillance, public health and food safety. Such developments have heightened the need for enhanced analytical systems in order to process and interpret this new type of data in a timely fashion. In this review we outline the emergence of genomics, bioinformatics and open data in the context of food safety. We also survey major efforts to translate genomics and bioinformatics technologies out of the research lab and into routine use in modern food safety labs. We conclude by discussing the challenges and opportunities that remain, including those expected to play a major role in the future of food safety science.

  9. Multimodal monitoring and neurocritical care bioinformatics.

    Science.gov (United States)

    Hemphill, J Claude; Andrews, Peter; De Georgia, Michael

    2011-07-12

    Neurocritical care bioinformatics is a new field that focuses on the acquisition, storage and analysis of physiological and other data relevant to the bedside care of patients with acute neurological conditions such as traumatic brain injury or stroke. The main focus of neurocritical care for these conditions relates to prevention, detection and management of secondary brain injury, which relies heavily on monitoring of systemic and cerebral parameters (such as blood-pressure level and intracranial pressure). Advanced neuromonitoring tools also exist that enable measurement of brain tissue oxygen tension, cerebral oxygen utilization, and aerobic metabolism. The ability to analyze these advanced data for real-time clinical care, however, remains intuitive and primitive. Advanced statistical and mathematical tools are now being applied to the large volume of clinical physiological data routinely monitored in neurocritical care with the goal of identifying better markers of brain injury and providing clinicians with improved ability to target specific goals in the management of these patients. This Review provides an introduction to the concepts of multimodal monitoring for secondary brain injury in neurocritical care and outlines initial and future approaches using informatics tools for understanding and applying these data to clinical care.

  10. Bioinformatics study of the mangrove actin genes

    Science.gov (United States)

    Basyuni, M.; Wasilah, M.; Sumardi

    2017-01-01

    This study describes the bioinformatics methods to analyze eight actin genes from mangrove plants on DDBJ/EMBL/GenBank as well as predicted the structure, composition, subcellular localization, similarity, and phylogenetic. The physical and chemical properties of eight mangroves showed variation among the genes. The percentage of the secondary structure of eight mangrove actin genes followed the order of a helix > random coil > extended chain structure for BgActl, KcActl, RsActl, and A. corniculatum Act. In contrast to this observation, the remaining actin genes were random coil > extended chain structure > a helix. This study, therefore, shown the prediction of secondary structure was performed for necessary structural information. The values of chloroplast or signal peptide or mitochondrial target were too small, indicated that no chloroplast or mitochondrial transit peptide or signal peptide of secretion pathway in mangrove actin genes. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove actin genes. To clarify the relationship among the mangrove actin gene, a phylogenetic tree was constructed. Three groups of mangrove actin genes were formed, the first group contains B. gymnorrhiza BgAct and R. stylosa RsActl. The second cluster which consists of 5 actin genes the largest group, and the last branch consist of one gene, B. sexagula Act. The present study, therefore, supported the previous results that plant actin genes form distinct clusters in the tree.

  11. Bioinformatic tools for microRNA dissection.

    Science.gov (United States)

    Akhtar, Most Mauluda; Micolucci, Luigina; Islam, Md Soriful; Olivieri, Fabiola; Procopio, Antonio Domenico

    2016-01-08

    Recently, microRNAs (miRNAs) have emerged as important elements of gene regulatory networks. MiRNAs are endogenous single-stranded non-coding RNAs (~22-nt long) that regulate gene expression at the post-transcriptional level. Through pairing with mRNA, miRNAs can down-regulate gene expression by inhibiting translation or stimulating mRNA degradation. In some cases they can also up-regulate the expression of a target gene. MiRNAs influence a variety of cellular pathways that range from development to carcinogenesis. The involvement of miRNAs in several human diseases, particularly cancer, makes them potential diagnostic and prognostic biomarkers. Recent technological advances, especially high-throughput sequencing, have led to an exponential growth in the generation of miRNA-related data. A number of bioinformatic tools and databases have been devised to manage this growing body of data. We analyze 129 miRNA tools that are being used in diverse areas of miRNA research, to assist investigators in choosing the most appropriate tools for their needs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Systems Biology: The Next Frontier for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Vladimir A. Likić

    2010-01-01

    Full Text Available Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i mathematical and computational modeling; (ii the application of traditional engineering practices in the analysis of biochemical systems; and in the past decade increasingly (iii the use of near-comprehensive data sets derived from ‘omics platform technologies, in particular “downstream” technologies relative to genome sequencing, including transcriptomics, proteomics and metabolomics. The future progress in understanding biological principles will increasingly depend on the development of temporal and spatial analytical techniques that will provide high-resolution data for systems analyses. To date, particularly successful were strategies involving (a quantitative measurements of cellular components at the mRNA, protein and metabolite levels, as well as in vivo metabolic reaction rates, (b development of mathematical models that integrate biochemical knowledge with the information generated by high-throughput experiments, and (c applications to microbial organisms. The inevitable role bioinformatics plays in modern systems biology puts mathematical and computational sciences as an equal partner to analytical and experimental biology. Furthermore, mathematical and computational models are expected to become increasingly prevalent representations of our knowledge about specific biochemical systems.

  13. Bioinformatics Tools for Extracellular Vesicles Research.

    Science.gov (United States)

    Keerthikumar, Shivakumar; Gangoda, Lahiru; Gho, Yong Song; Mathivanan, Suresh

    2017-01-01

    Extracellular vesicles (EVs) are a class of membranous vesicles that are released by multiple cell types into the extracellular environment. This unique class of extracellular organelles which play pivotal role in intercellular communication are conserved across prokaryotes and eukaryotes. Depending upon the cell origin and the functional state, the molecular cargo including proteins, lipids, and RNA within the EVs are modulated. Owing to this, EVs are considered as a subrepertoire of the host cell and are rich reservoirs of disease biomarkers. In addition, the availability of EVs in multiple bodily fluids including blood has created significant interest in biomarker and signaling research. With the advancement in high-throughput techniques, multiple EV studies have embarked on profiling the molecular cargo. To benefit the scientific community, existing free Web-based resources including ExoCarta, EVpedia, and Vesiclepedia catalog multiple datasets. These resources aid in elucidating molecular mechanism and pathophysiology underlying different disease conditions from which EVs are isolated. Here, the existing bioinformatics tools to perform integrated analysis to identify key functional components in the EV datasets are discussed.

  14. Bioconductor: open software development for computational biology and bioinformatics

    DEFF Research Database (Denmark)

    Gentleman, R.C.; Carey, V.J.; Bates, D.M.

    2004-01-01

    The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisci......The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry...... into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples....

  15. ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

    Science.gov (United States)

    Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

    2004-03-22

    ClusterControl is a web interface to simplify distributing and monitoring bioinformatics applications on Linux cluster systems. We have developed a modular concept that enables integration of command line oriented program into the application framework of ClusterControl. The systems facilitate integration of different applications accessed through one interface and executed on a distributed cluster system. The package is based on freely available technologies like Apache as web server, PHP as server-side scripting language and OpenPBS as queuing system and is available free of charge for academic and non-profit institutions. http://genome.tugraz.at/Software/ClusterControl

  16. Scalable pattern recognition algorithms applications in computational biology and bioinformatics

    CERN Document Server

    Maji, Pradipta

    2014-01-01

    Reviews the development of scalable pattern recognition algorithms for computational biology and bioinformatics Includes numerous examples and experimental results to support the theoretical concepts described Concludes each chapter with directions for future research and a comprehensive bibliography

  17. Survey of Natural Language Processing Techniques in Bioinformatics

    Science.gov (United States)

    Zeng, Zhiqiang; Shi, Hua; Wu, Yun; Hong, Zhiling

    2015-01-01

    Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we aim to search for knowledge on biology, retrieve references using text mining methods, and reconstruct databases. For example, protein-protein interactions and gene-disease relationship can be mined from PubMed. Then, we analyze the applications of text mining and natural language processing techniques in bioinformatics, including predicting protein structure and function, detecting noncoding RNA. Finally, numerous methods and applications, as well as their contributions to bioinformatics, are discussed for future use by text mining and natural language processing researchers. PMID:26525745

  18. Pokemon expression in malignant glioma: an application of bioinformatics methods.

    Science.gov (United States)

    Rovin, Richard A; Winn, Robert

    2005-10-15

    In this report the authors review the role of bioinformatics in the design of a research project in which the molecular genetics of malignant glioma were studied. A project to characterize Pokemon expression in malignant glioma was developed, refined, and implemented using bioinformatics methods. Using the resources available from the National Center for Biotechnology Information, the messenger RNA (mRNA) sequence for Pokemon was determined. With this information and online primer design tools, novel primers were designed that would specifically amplify Pokemon mRNA by using reverse transcription-polymerase chain reaction assays. The promise of bioinformatics is in the rapid and widespread dissemination and analysis of genomic information. This information is then used in research investigating the genetic basis of disease. In this paper the authors review the bioinformatics methods used in their study of Pokemon expression in malignant glioma.

  19. The potential of translational bioinformatics approaches for pharmacology research.

    Science.gov (United States)

    Li, Lang

    2015-10-01

    The field of bioinformatics has allowed the interpretation of massive amounts of biological data, ushering in the era of 'omics' to biomedical research. Its potential impact on pharmacology research is enormous and it has shown some emerging successes. A full realization of this potential, however, requires standardized data annotation for large health record databases and molecular data resources. Improved standardization will further stimulate the development of system pharmacology models, using translational bioinformatics methods. This new translational bioinformatics paradigm is highly complementary to current pharmacological research fields, such as personalized medicine, pharmacoepidemiology and drug discovery. In this review, I illustrate the application of transformational bioinformatics to research in numerous pharmacology subdisciplines. © 2015 The British Pharmacological Society.

  20. Probabilistic models and machine learning in structural bioinformatics

    DEFF Research Database (Denmark)

    Hamelryck, Thomas

    2009-01-01

    Structural bioinformatics is concerned with the molecular structure of biomacromolecules on a genomic scale, using computational methods. Classic problems in structural bioinformatics include the prediction of protein and RNA structure from sequence, the design of artificial proteins or enzymes......, and the automated analysis and comparison of biomacromolecules in atomic detail. The determination of macromolecular structure from experimental data (for example coming from nuclear magnetic resonance, X-ray crystallography or small angle X-ray scattering) has close ties with the field of structural bioinformatics...... methods that are based on inference. Although this review is not exhaustive, I believe the selected topics give a good impression of the exciting new, probabilistic road the field of structural bioinformatics is taking....

  1. clubber: removing the bioinformatics bottleneck in big data analyses

    National Research Council Canada - National Science Library

    Maximilian Miller; Chengsheng Zhu; Yana Bromberg

    2017-01-01

    .... is our automated cluster-load balancing system developed for optimizing these “big data” analyses. Its plug-and-play framework encourages re-use of existing solutions for bioinformatics problems...

  2. In silico cloning and bioinformatic analysis of PEPCK gene in ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-03-29

    Mar 29, 2010 ... Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. According to the relative conservation of homologous gene, a bioinformatics strategy was applied to.

  3. In silico cloning and bioinformatic analysis of PEPCK gene in ...

    African Journals Online (AJOL)

    Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. According to the relative conservation of homologous gene, a bioinformatics strategy was applied to clone Fusarium ...

  4. The potential of translational bioinformatics approaches for pharmacology research

    Science.gov (United States)

    Li, Lang

    2015-01-01

    The field of bioinformatics has allowed the interpretation of massive amounts of biological data, ushering in the era of ‘omics’ to biomedical research. Its potential impact on pharmacology research is enormous and it has shown some emerging successes. A full realization of this potential, however, requires standardized data annotation for large health record databases and molecular data resources. Improved standardization will further stimulate the development of system pharmacology models, using translational bioinformatics methods. This new translational bioinformatics paradigm is highly complementary to current pharmacological research fields, such as personalized medicine, pharmacoepidemiology and drug discovery. In this review, I illustrate the application of transformational bioinformatics to research in numerous pharmacology subdisciplines. PMID:25753093

  5. ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR [version 1; referees: 2 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    L. Larcombe

    2017-06-01

    Full Text Available ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform’s coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR’s flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project – a coordinated effort to drive engagement with training in statistics.

  6. Bioinformatics Analyst | Center for Cancer Research

    Science.gov (United States)

    BASIC QUALIFICATIONS To be considered for this position, you must minimally meet the knowledge, skills, and abilities listed below: Bachelor’s degree in life science/bioinformatics/math/physics/computer related field from an accredited college or university according to the Council for Higher Education Accreditation (CHEA). (Additional qualifying experience may be substituted for the required education). Foreign degrees must be evaluated for U.S. equivalency. In addition to the educational requirements, a minimum of five (5) years of progressively responsible relevant experience. Must be able to obtain and maintain a security clearance. PREFERRED QUALIFICATIONS Candidates with these desired skills will be given preferential consideration: A Masters’ or PhD degree in any quantitative science is preferred. Commitment to solving biological problems and communicating these solutions. Ability to multi-task across projects. Experience in submitting data sets to public repositories. Management of large genomic data sets including integration with data available from public sources. Prior customer-facing role. Record of scientific achievements including journal publications and conference presentations. Expected Competencies: Deep understanding of and experience in processing high throughput biomedical data: data cleaning, normalization, analysis, interpretation and visualization. Ability to understand and analyze data from complex experimental designs. Proficiency in at least two of the following programming languages: Perl, Python, R, Java and C/C++. Experience in at least two of the following areas: metagenomics, ChIPSeq, RNASeq, ExomeSeq, DHS-Seq, microarray analysis. Familiarity with public databases: NCBI, Ensembl, TCGA, cBioPortal, Broad FireHose. Knowledge of working in a cluster environment.

  7. Hidden in the middle: culture, value and reward in bioinformatics

    OpenAIRE

    Lewis, Jamie Thornton; Bartlett, Andrew; Atkinson, Paul

    2016-01-01

    Bioinformatics – the so-called shotgun marriage between biology and computer science – is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised ‘outputs’ in academia are often defined and rewarded by discipline. Bioinformatics, as an interdisciplinary bricolage, incorporates experts from various disciplinar...

  8. An innovative approach for testing bioinformatics programs using metamorphic testing

    Directory of Open Access Journals (Sweden)

    Liu Huai

    2009-01-01

    Full Text Available Abstract Background Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered. Results We propose to use a novel software testing technique, metamorphic testing (MT, to test a range of bioinformatics programs. Instead of requiring a mechanism to verify whether an individual test output is correct, the MT technique verifies whether a pair of test outputs conform to a set of domain specific properties, called metamorphic relations (MRs, thus greatly increases the number and variety of test cases that can be applied. To demonstrate how MT is used in practice, we applied MT to test two open-source bioinformatics programs, namely GNLab and SeqMap. In particular we show that MT is simple to implement, and is effective in detecting faults in a real-life program and some artificially fault-seeded programs. Further, we discuss how MT can be applied to test programs from various domains of bioinformatics. Conclusion This paper describes the application of a simple, effective and automated technique to systematically test a range of bioinformatics programs. We show how MT can be implemented in practice through two real-life case studies. Since many bioinformatics programs, particularly those for large scale simulation and data analysis, are hard to test systematically, their developers may benefit from using MT as part of the testing strategy. Therefore our work

  9. BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services.

    Science.gov (United States)

    Velloso, Henrique; Vialle, Ricardo A; Ortega, J Miguel

    2015-06-02

    Bioinformaticians face a range of difficulties to get locally-installed tools running and producing results; they would greatly benefit from a system that could centralize most of the tools, using an easy interface for input and output. Web services, due to their universal nature and widely known interface, constitute a very good option to achieve this goal. Bioinformatics open web services (BOWS) is a system based on generic web services produced to allow programmatic access to applications running on high-performance computing (HPC) clusters. BOWS intermediates the access to registered tools by providing front-end and back-end web services. Programmers can install applications in HPC clusters in any programming language and use the back-end service to check for new jobs and their parameters, and then to send the results to BOWS. Programs running in simple computers consume the BOWS front-end service to submit new processes and read results. BOWS compiles Java clients, which encapsulate the front-end web service requisitions, and automatically creates a web page that disposes the registered applications and clients. Bioinformatics open web services registered applications can be accessed from virtually any programming language through web services, or using standard java clients. The back-end can run in HPC clusters, allowing bioinformaticians to remotely run high-processing demand applications directly from their machines.

  10. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

    Science.gov (United States)

    Krampis, Konstantinos; Booth, Tim; Chapman, Brad; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E

    2012-03-19

    A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly

  11. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

    Directory of Open Access Journals (Sweden)

    Krampis Konstantinos

    2012-03-01

    Full Text Available Abstract Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds

  12. Assessment of Data Reliability of Wireless Sensor Network for Bioinformatics

    Directory of Open Access Journals (Sweden)

    Ting Dong

    2017-09-01

    Full Text Available As a focal point of biotechnology, bioinformatics integrates knowledge from biology, mathematics, physics, chemistry, computer science and information science. It generally deals with genome informatics, protein structure and drug design. However, the data or information thus acquired from the main areas of bioinformatics may not be effective. Some researchers combined bioinformatics with wireless sensor network (WSN into biosensor and other tools, and applied them to such areas as fermentation, environmental monitoring, food engineering, clinical medicine and military. In the combination, the WSN is used to collect data and information. The reliability of the WSN in bioinformatics is the prerequisite to effective utilization of information. It is greatly influenced by factors like quality, benefits, service, timeliness and stability, some of them are qualitative and some are quantitative. Hence, it is necessary to develop a method that can handle both qualitative and quantitative assessment of information. A viable option is the fuzzy linguistic method, especially 2-tuple linguistic model, which has been extensively used to cope with such issues. As a result, this paper introduces 2-tuple linguistic representation to assist experts in giving their opinions on different WSNs in bioinformatics that involve multiple factors. Moreover, the author proposes a novel way to determine attribute weights and uses the method to weigh the relative importance of different influencing factors which can be considered as attributes in the assessment of the WSN in bioinformatics. Finally, an illustrative example is given to provide a reasonable solution for the assessment.

  13. PineappleDB: An online pineapple bioinformatics resource

    Science.gov (United States)

    Moyle, Richard L; Crowe, Mark L; Ripi-Koia, Jonni; Fairbairn, David J; Botella, José R

    2005-01-01

    Background A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences. Description PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST) data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information. Conclusion The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants. PMID:16202174

  14. PineappleDB: an online pineapple bioinformatics resource.

    Science.gov (United States)

    Moyle, Richard L; Crowe, Mark L; Ripi-Koia, Jonni; Fairbairn, David J; Botella, José R

    2005-10-05

    A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences. PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST) data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information. The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.

  15. Public Accountability in the European Union: Is the European Parliament able to hold the European Council accountable?

    Directory of Open Access Journals (Sweden)

    Marianne van de Steeg

    2009-08-01

    Full Text Available The European Council occupies a central role in European politics. Yet it is not officially accountable to any public or parliamentary body for the decisions it makes on behalf of European citizens. National parliaments are only entitled to exert control over their own Heads of Government or State. The European Parliament, as a supranational institution, is the only parliamentary body that regularly discusses European politics with the European Council as a collective, namely via the European Council Presidency. As such, it alone has the possibility to hold the Council accountable for the agreements made at European Summits. However, the European Parliament has limited rights to impose pressure on the European Council Presidency. Nonetheless, despite the lack of a formal accountability arrangement, the European Council Presidency is more forthcoming than could have been expected.

  16. ECLIPSE, an Emerging Standardized Modular, Secure and Affordable Software Toolset in Support of Product Assurance, Quality Assurance and Project Management for the Entire European Space Industry (from Innovative SMEs to Primes and Institutions)

    Science.gov (United States)

    Bennetti, Andrea; Ansari, Salim; Dewhirst, Tori; Catanese, Giuseppe

    2010-08-01

    The development of satellites and ground systems (and the technologies that support them) is complex and demands a great deal of rigor in the management of both the information it relies upon and the information it generates via the performance of well established processes. To this extent for the past fifteen years Sapienza Consulting has been supporting the European Space Agency (ESA) in the management of this information and provided ESA with ECSS (European Cooperation for Space Standardization) Standards based Project Management (PM), Product Assurance (PA) and Quality Assurance (QA) software applications. In 2009 Sapienza recognised the need to modernize, standardizing and integrate its core ECSS-based software tools into a single yet modularised suite of applications named ECLIPSE aimed at: • Fulfilling a wider range of historical and emerging requirements, • Providing a better experience for users, • Increasing the value of the information it collects and manages • Lowering the cost of ownership and operation • Increasing collaboration within and between space sector organizations • Aiding in the performance of several PM, PA, QA, and configuration management tasks in adherence to ECSS standards. In this paper, Sapienza will first present the toolset, and a rationale for its development, describing and justifying its architecture, and basic modules composition. Having defined the toolset architecture, this paper will address the current status of the individual applications. A compliance assessment will be presented for each module in the toolset with respect to the ECSS standard it addresses. Lastly experience from early industry and Institutional users will be presented.

  17. European Patterns of Participation

    DEFF Research Database (Denmark)

    Harrebye, Silas Fehmerling; Ejrnæs, Anders

    2015-01-01

    Social Survey (ESS) Round 4 (2008), the article finds that satisfaction/dissatisfaction with the government is an important predictor alongside the institutional macro-level variable. The article combines a critical tradition, which suggests that political participation is motivated by a feeling...... of dissatisfaction with the government and feelings of being member of a discriminated group affect the level of extra-parliamentary participation, and second, how different welfare regimes condition the extend to which these groups chose to act. In a comparative multilevel design, using data from the European...... of dissatisfaction with an institutional perspective in which certain institutional conditions are seen as enablers for citizens to actively participate in political life. Our results show that the overall level of extra-parliamentary activity in the Scandinavian countries is higher than in the other European...

  18. An integrative bioinformatics pipeline for the genomewide ...

    Indian Academy of Sciences (India)

    Center for Bioinformation, College of Life Science, Northwest A and F University, Yangling 712100, Shaanxi, People's Republic of China; Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A and F University, Yangling 712100, Shaanxi, People's Republic of China; Institute of ...

  19. How do the ASTRO consensus statement guidelines for the application of accelerated partial breast irradiation fit intraoperative radiotherapy? A retrospective analysis of patients treated at the European Institute of Oncology.

    Science.gov (United States)

    Leonardi, Maria Cristina; Maisonneuve, Patrick; Mastropasqua, Mauro Giuseppe; Morra, Anna; Lazzari, Roberta; Rotmensz, Nicole; Sangalli, Claudia; Luini, Alberto; Veronesi, Umberto; Orecchia, Roberto

    2012-07-01

    To verify how the classification according to the American Society for Therapeutic Radiation Oncology (ASTRO) consensus statement (CS) for the application of accelerated partial breast irradiation (APBI) fits patients treated with intraoperative radiotherapy with electrons (ELIOT) at a single institution. The study included 1,822 patients treated with ELIOT as the sole radiation modality outside of a clinical trial at the European Institute of Oncology after breast-conserving surgery for invasive breast cancer, who were classified into CS groups of suitable, cautionary, and unsuitable. The outcome in terms of ipsilateral breast recurrence, regional node relapse, distant metastases, progression free-survival, cause-specific survival, and overall survival were assessed. All the 1,822 cases except for 25 could be classified according to ASTRO CS: 294 patients met the criteria for inclusion into the suitable group, 691 patients into the cautionary group, and 812 patients into the unsuitable group. The 5-year rate of ipsilateral breast recurrence for suitable, cautionary, and unsuitable groups were 1.5%, 4.4%, and 8.8%, respectively (p = 0.0003). Whereas the regional node relapse showed no difference, the rate of distant metastases was significantly different in the unsuitable group compared with the suitable and cautionary groups, having a significant impact on survival. In the context of patients treated with ELIOT, the ASTRO guidelines identify well the groups for whom APBI might be considered as an effective alternative to whole breast radiotherapy and also identify groups for whom APBI is not indicated. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. How Do the ASTRO Consensus Statement Guidelines for the Application of Accelerated Partial Breast Irradiation Fit Intraoperative Radiotherapy? A Retrospective Analysis of Patients Treated at the European Institute of Oncology

    Energy Technology Data Exchange (ETDEWEB)

    Leonardi, Maria Cristina, E-mail: cristina.leonardi@ieo.it [Division of Radiation Oncology, European Institute of Oncology, Milan (Italy); Maisonneuve, Patrick [Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan (Italy); Mastropasqua, Mauro Giuseppe [Division of Pathology, European Institute of Oncology, Milan (Italy); Morra, Anna; Lazzari, Roberta [Division of Radiation Oncology, European Institute of Oncology, Milan (Italy); Rotmensz, Nicole [Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan (Italy); Sangalli, Claudia; Luini, Alberto [Division of Breast Surgery, European Institute of Oncology, Milan (Italy); Veronesi, Umberto [Scientific Directorate, European Institute of Oncology, Milan (Italy); Orecchia, Roberto [Division of Radiation Oncology, European Institute of Oncology, Milan (Italy); University of Milan (Italy)

    2012-07-01

    Purpose: To verify how the classification according to the American Society for Therapeutic Radiation Oncology (ASTRO) consensus statement (CS) for the application of accelerated partial breast irradiation (APBI) fits patients treated with intraoperative radiotherapy with electrons (ELIOT) at a single institution. Methods and Materials: The study included 1,822 patients treated with ELIOT as the sole radiation modality outside of a clinical trial at the European Institute of Oncology after breast-conserving surgery for invasive breast cancer, who were classified into CS groups of suitable, cautionary, and unsuitable. The outcome in terms of ipsilateral breast recurrence, regional node relapse, distant metastases, progression free-survival, cause-specific survival, and overall survival were assessed. Results: All the 1,822 cases except for 25 could be classified according to ASTRO CS: 294 patients met the criteria for inclusion into the suitable group, 691 patients into the cautionary group, and 812 patients into the unsuitable group. The 5-year rate of ipsilateral breast recurrence for suitable, cautionary, and unsuitable groups were 1.5%, 4.4%, and 8.8%, respectively (p = 0.0003). Whereas the regional node relapse showed no difference, the rate of distant metastases was significantly different in the unsuitable group compared with the suitable and cautionary groups, having a significant impact on survival. Conclusion: In the context of patients treated with ELIOT, the ASTRO guidelines identify well the groups for whom APBI might be considered as an effective alternative to whole breast radiotherapy and also identify groups for whom APBI is not indicated.

  1. 1st European Biomedical Engineering Conference for Young Investigators

    CERN Document Server

    2015-01-01

     This volume presents the proceedings of the first European Biomedical Engineering Conference for Young Investigators ENCY2015. It was in Budapest, from 28th to 30th May, 2015. The papers were assembled under the motto "Understanding complex living systems” and cover the topics sensors, image processing, bioinformatics, biomechanics, and modeling.

  2. Bioinformatics analysis of circulating cell-free DNA sequencing data.

    Science.gov (United States)

    Chan, Landon L; Jiang, Peiyong

    2015-10-01

    The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  3. "A bare outpost of learned European culture on the edge of the jungles of Java": Johan Maurits Mohr (1716-1775) and the emergence of instrumental and institutional science in Dutch Colonial Indonesia

    Science.gov (United States)

    Zuidervaart, Huib J.; van Gent, Robert H.

    2004-03-01

    The transits of Venus in 1761 and 1769 appear to mark the starting point of instrumental science in the Dutch East Indies (now Indonesia). This essay examines the conditions that triggered and constituted instrumental and institutional science on Indonesian soil in the late eighteenth century. In 1765 the Reverend J. M. Mohr, whose wife had received a large inheritance, undertook to build a fully equipped private observatory in Batavia (now Jakarta). There he made several major astronomical and meteorological observations. Mohr's initiative inspired other Europeans living on Java around 1770 to start a scientific movement. Because of the lack of governmental and other support, it was not until 1778 that this offspring of the Dutch-Indonesian Enlightenment became a reality. The Bataviaasch Genootschap van Kunsten en Wetenschappen tried from the beginning to put into effect the program Mohr had outlined. The members even bought his instruments from his widow, intending to continue his measurements. For a number of reasons, however, this instrumental program was more than the society could support. Around 1790 instrumental science in the former Dutch East Indies came to a standstill, not to be resumed for several decades.

  4. "A bare outpost of learned European culture on the edge of the jungles of Java": Johan Maurits Mohr (1716-1775) and the emergence of instrumental and institutional science in Dutch colonial Indonesia.

    Science.gov (United States)

    Zuidervaart, Huib J; Van Gent, Rob H

    2004-03-01

    The transits of Venus in 1761 and 1769 appear to mark the starting point of instrumental science in the Dutch East Indies (now Indonesia). This essay examines the conditions that triggered and constituted instrumental and institutional science on Indonesian soil in the late eighteenth century. In 1765 the Reverend J. M. Mohr, whose wife had received a large inheritance, undertook to build a fully equipped private observatory in Batavia (now Jakarta). There he made several major astronomical and meteorological observations. Mohr's initiative inspired other Europeans living on Java around 1770 to start a scientific movement. Because of the lack of governmental and other support, it was not until 1778 that this offspring of the Dutch-Indonesian Enlightenment became a reality. The Bataviaasch Genootschap van Kunsten en Wetenschappen tried from the beginning to put into effect the program Mohr had outlined. The members even bought his instruments from his widow, intending to continue his measurements. For a number of reasons, however, this instrumental program was more than the society could support. Around 1790 instrumental science in the former Dutch East Indies came to a standstill, not to be resumed for several decades.

  5. International Electronical Committee (IEC 61850 Mapping with Constrained Application Protocol (CoAP in Smart Grids Based European Telecommunications Standard Institute Machine-to-Machine (M2M Environment

    Directory of Open Access Journals (Sweden)

    In-Jae Shin

    2017-03-01

    Full Text Available As power systems develop rapidly into smarter and more flexible configurations, so too must the communication technologies that support them. Machine-to-machine (M2M communication in power systems enables information collection by combining sensors and communication protocols. In doing so, M2M technology supports communication between machines to improve power quality and protection coordination. When functioning in a “smart grid” environment, M2M has been labelled by the European Telecommunications Standard Institute (ETSI. International Electronical Committee (IEC 61850 as the most important standard in power network systems. As evidence, this communication platform has been used for device data collection/control in substation automation systems and distribution automation systems. If the IEC 61850 information model were to be combined with a set of contemporary web protocols, the potential benefits would be enormous. Therefore, a constrained application protocol (CoAP has been adopted to create an ETSI M2M communication architecture. CoAP is compared with other protocols (MQTT, SOAP to demonstrate the validity of using it. This M2M communication technology is applied in an IEC61850, and use the OPNET Modeler 17.1 to demonstrate intercompatibility of CoAP Gateway. The proposed IEC 61850 and CoAP mapping scheme reduces the mapping time and improves throughput. CoAP is useful in the ETSI M2M environment where device capability is able to be limited.

  6. Comparison between National Institute for Health and Care Excellence (NICE) and European Society of Cardiology (ESC) guidelines for the diagnosis and management of stable angina: implications for clinical practice.

    Science.gov (United States)

    Archbold, R Andrew

    2016-01-01

    Cardiologists in the UK use clinical practice guidelines from the National Institute for Health and Care Excellence (NICE) and from the European Society of Cardiology (ESC) to aid clinical decision-making. This review compares their recommendations regarding stable angina. NICE's diagnostic algorithm changed clinical practice in the UK, with most cardiologists moving from the exercise ECG towards newer, more accurate imaging modalities such as CT and MRI for diagnostic testing in patients with a low or medium probability of coronary artery disease (CAD), and directly to invasive coronary angiography in patients with a high probability of CAD. ESC guidelines are based around stress imaging for most patient groups. Both guidelines stress the importance of optimal medical therapy for patients with stable angina. NICE recommends coronary artery bypass graft surgery to improve prognosis for patients with left main stem and/or proximal 3-vessel disease, whereas the ESC also includes proximal left anterior descending artery disease among its indications for revascularisation to improve prognosis, particularly if there is evidence of myocardial ischaemia. The relation between disease complexity and 5-year clinical outcomes after revascularisation in patients with left main stem and/or 3-vessel CAD has been integrated into ESC guidance through the use of the SYNTAX score to aid treatment selection in this group of patients. Patients with stable angina who have disease involving the proximal left anterior descending artery are less likely to undergo myocardial revascularisation if they are managed according to NICE's guidance compared with the ESC's guidance.

  7. International institutional law

    CERN Document Server

    Schermers, Henry G

    1972-01-01

    In several respects the present study is an enlargement of a former analysis about the specialized agencies of the United Nations to more organisations and into further detail. In particular the creation of the European Communities, adding new aspects to international institutional law, have received attention.

  8. European Union Financial Crisis: A Marxist Analysis

    NARCIS (Netherlands)

    Petrus Kanisius Farneubun, P.

    European financial crisis poses a serious challenge to the fundamental structure of the European Union, political and financial institutions, as well as the values that bind European together. Different factors have been suggested as the causes of the crisis notably the failure of national

  9. Is there a European way of war?

    DEFF Research Database (Denmark)

    Vennesson, P.; Breuer, F.; de Franco, Chiara

    2009-01-01

    Europe is the region of the world where the network of security institutions is the densest. Yet, these institutions did not erase differences about conceptions of force employment among European countries and between European countries and the United States. Why have concepts of military power a...

  10. The accession of the European Union to the European Convention on Human Rights

    OpenAIRE

    Callewaert, Johan

    2014-01-01

    Provided for under the Treaty of Lisbon, the accession of the European Union to the European Convention on Human Rights is destined to be a landmark in European legal history because it will finally make it possible for individuals and undertakings to apply to the European Court of Human Rights for review of the acts of European Union institutions, which unquestionably play an increasingly important role in our daily lives. After nearly three years of negotiations, a draft agreement on Europe...

  11. European communion

    DEFF Research Database (Denmark)

    Manners, Ian James

    2013-01-01

    Political theory of European union, through an engagement between political concepts and theoretical understandings, provides a means of identifying the EU as a political object. It is argued that understanding the projects, processes and products of European union, based on ‘sharing’ or ‘communion......’, provides a better means of perceiving the EU as a political object rather than terms such as ‘integration’ or ‘co-operation’. The concept of ‘European communion’ is defined as the ‘subjective sharing of relationships’, understood as the extent to which individuals or groups believe themselves to be sharing...... relations (or not), and the consequences of these beliefs for European political projects, processes and products. By exploring European communion through an engagement with contemporary political theory, using very brief illustrations from the Treaty of Lisbon, the article also suggests that European...

  12. Corporate Communication in European Financial Institutions

    NARCIS (Netherlands)

    C.B.M. van Riel (Cees)

    1992-01-01

    textabstractIn 1988 the Rotterdam School of Management and Fairfield University conducted jointly a survey in twenty-one banks and twenty insurance companies in Europe and the U.S. The purpose was to examine corporate communication practices in comparable service industries on two

  13. Training and mobility: a priority for the Organisation of the European Cancer Institutes. How a national mobility initiative could enhance EU cooperation in cancer research contributing to the development of an European Research Area: the example of The Italian Comprehensive Cancer Centers' Network "Alleanza Contro il Cancro".

    Science.gov (United States)

    Lombardo, Claudio; Albanese, Daniela; Belardelli, Filippo; d'Alessandro, Francesca; Giacomini, Mauro; Rondanina, Tania; Spagnoli, Luigi G

    2008-01-01

    It is widely recognized that productivity gains, sustained economic growth and employment are largely determined by technological progress, innovation and human capital. The 2000 Lisbon strategy to make Europe a competitive knowledge-based economy by 2010 and, more specifically, the Barcelona objectives agreed upon in 2002 to increase R&D investment in the EU to approach 3% of GDP, ensuring that there are sufficient human resources for research, are a preliminary step in this direction. If we want to reach this goal we have to succeed in retaining the best researchers, creating the right environment where they can perform their activities and develop their careers. To this aim the Organization of European Cancer Institutes (OECI) has set up a working group on Education and Training with the mandate to encourage continuing education in cancer research and applications and to verify the feasibility to promote mobility programs inside the network and in association with industries. Until now only few OECI training programs have been launched and a full mobility program has not been developed yet due to limited budget resources. The Italian Network of Comprehensive Cancer Centers, Alleanza Contro il Cancro, has planned the launch of a mobility program awarding 70 annual fellowships over a period of 36 months. This program, which will be open to the world research community, could represent a first interaction through mobility among the members of the OECI network also involving industries. The program is a tangible approach to sustain the translational process needed for the development of an European Research Area in the field of cancer and its related biomedical disciplines, thus providing a practical answer to the 2005 renewed Lisbon Strategy.

  14. Survey of MapReduce frame operation in bioinformatics.

    Science.gov (United States)

    Zou, Quan; Li, Xu-Bin; Jiang, Wen-Rui; Lin, Zi-Yu; Li, Gui-Lin; Chen, Ke

    2014-07-01

    Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  15. Embracing the Future: Bioinformatics for High School Women

    Science.gov (United States)

    Zales, Charlotte Rappe; Cronin, Susan J.

    Sixteen high school women participated in a 5-week residential summer program designed to encourage female and minority students to choose careers in scientific fields. Students gained expertise in bioinformatics through problem-based learning in a complex learning environment of content instruction, speakers, labs, and trips. Innovative hands-on activities filled the program. Students learned biological principles in context and sophisticated bioinformatics tools for processing data. Students additionally mastered a variety of information-searching techniques. Students completed creative individual and group projects, demonstrating the successful integration of biology, information technology, and bioinformatics. Discussions with female scientists allowed students to see themselves in similar roles. Summer residential aspects fostered an atmosphere in which students matured in interacting with others and in their views of diversity.

  16. Omics-bioinformatics in the context of clinical data

    DEFF Research Database (Denmark)

    Mayer, Gert; Heinze, Georg; Mischak, Harald

    2011-01-01

    research procedures) has become applicable. However, numerous issues have to be considered for deriving meaningful results from Omics, and bioinformatics has to respect these in data analysis and interpretation. Aspects include sample type and quality, concise definition of the (clinical) question...... in parallel in an Omics experiment. This setting makes the identification of relevant features with respect to a phenotype under analysis error prone from a statistical perspective. From this sample size calculation for screening studies and for verification of results from Omics, bioinformatics is essential....... Here we present key elements to be considered for embedding Omics bioinformatics in a quality controlled workflow for Omics screening, feature identification, and validation. Relevant items include sample and clinical data management, minimum sample quality requirements, sample size estimates...

  17. Bioinformatics projects supporting life-sciences learning in high schools.

    Directory of Open Access Journals (Sweden)

    Isabel Marques

    2014-01-01

    Full Text Available The interdisciplinary nature of bioinformatics makes it an ideal framework to develop activities enabling enquiry-based learning. We describe here the development and implementation of a pilot project to use bioinformatics-based research activities in high schools, called "Bioinformatics@school." It includes web-based research projects that students can pursue alone or under teacher supervision and a teacher training program. The project is organized so as to enable discussion of key results between students and teachers. After successful trials in two high schools, as measured by questionnaires, interviews, and assessment of knowledge acquisition, the project is expanding by the action of the teachers involved, who are helping us develop more content and are recruiting more teachers and schools.

  18. Bioinformatics projects supporting life-sciences learning in high schools.

    Science.gov (United States)

    Marques, Isabel; Almeida, Paulo; Alves, Renato; Dias, Maria João; Godinho, Ana; Pereira-Leal, José B

    2014-01-01

    The interdisciplinary nature of bioinformatics makes it an ideal framework to develop activities enabling enquiry-based learning. We describe here the development and implementation of a pilot project to use bioinformatics-based research activities in high schools, called "Bioinformatics@school." It includes web-based research projects that students can pursue alone or under teacher supervision and a teacher training program. The project is organized so as to enable discussion of key results between students and teachers. After successful trials in two high schools, as measured by questionnaires, interviews, and assessment of knowledge acquisition, the project is expanding by the action of the teachers involved, who are helping us develop more content and are recruiting more teachers and schools.

  19. Europeanness: A Path To Unity Within The European Union

    Directory of Open Access Journals (Sweden)

    Piasecki Ryszard

    2016-03-01

    Full Text Available The postwar experience has shown that the implanting of European consciousness, or Europeanness, calls for coordinated efforts among the European institutions, national states, and NGOs. Such consciousness, a key pillar of the European integration, is necessary for the EU to effectively function and motivate member states’ − also the EU’s − citizens. And yet European institutions and EU governments show little interest in promoting the formation of this European consciousness. Pro-European social movements are weak, while anti- European ones gain strength. This désintéressement of the EU countries probably results from the conviction that the goal has been reached and that there is no more need for a widespread pro-European education of their societies. However analysis of the problem, and in particular of the interaction between European and national identities, shows that this is not the case. We fear that this lack of proactive measures mobilizing EU citizens to keep on struggling for a common Europe will lead to the erosion of existing achievements of integration within the EU, and undermine European values. It may threaten the future of the EU, which is not an ordinary integration grouping but a great peaceful, civilizational, social and economic project. Our hypothesis − positively verified in this article − is that the promotion of Europeanness in the EU societies is urgently needed to maintain the unity (and even membership of the Union, and to avert trends unfavorable for all of Europe and therefore for the West as a whole.

  20. Bioinformatic training needs at a health sciences campus.

    Science.gov (United States)

    Oliver, Jeffrey C

    2017-01-01

    Health sciences research is increasingly focusing on big data applications, such as genomic technologies and precision medicine, to address key issues in human health. These approaches rely on biological data repositories and bioinformatic analyses, both of which are growing rapidly in size and scope. Libraries play a key role in supporting researchers in navigating these and other information resources. With the goal of supporting bioinformatics research in the health sciences, the University of Arizona Health Sciences Library established a Bioinformation program. To shape the support provided by the library, I developed and administered a needs assessment survey to the University of Arizona Health Sciences campus in Tucson, Arizona. The survey was designed to identify the training topics of interest to health sciences researchers and the preferred modes of training. Survey respondents expressed an interest in a broad array of potential training topics, including "traditional" information seeking as well as interest in analytical training. Of particular interest were training in transcriptomic tools and the use of databases linking genotypes and phenotypes. Staff were most interested in bioinformatics training topics, while faculty were the least interested. Hands-on workshops were significantly preferred over any other mode of training. The University of Arizona Health Sciences Library is meeting those needs through internal programming and external partnerships. The results of the survey demonstrate a keen interest in a variety of bioinformatic resources; the challenge to the library is how to address those training needs. The mode of support depends largely on library staff expertise in the numerous subject-specific databases and tools. Librarian-led bioinformatic training sessions provide opportunities for engagement with researchers at multiple points of the research life cycle. When training needs exceed library capacity, partnering with intramural and

  1. PineappleDB: An online pineapple bioinformatics resource

    Directory of Open Access Journals (Sweden)

    Fairbairn David J

    2005-10-01

    Full Text Available Abstract Background A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences. Description PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information. Conclusion The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.

  2. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

    Directory of Open Access Journals (Sweden)

    Martin Hofmann-Apitius

    2015-12-01

    Full Text Available Since the decoding of the Human Genome, techniques from bioinformatics, statistics, and machine learning have been instrumental in uncovering patterns in increasing amounts and types of different data produced by technical profiling technologies applied to clinical samples, animal models, and cellular systems. Yet, progress on unravelling biological mechanisms, causally driving diseases, has been limited, in part due to the inherent complexity of biological systems. Whereas we have witnessed progress in the areas of cancer, cardiovascular and metabolic diseases, the area of neurodegenerative diseases has proved to be very challenging. This is in part because the aetiology of neurodegenerative diseases such as Alzheimer´s disease or Parkinson´s disease is unknown, rendering it very difficult to discern early causal events. Here we describe a panel of bioinformatics and modeling approaches that have recently been developed to identify candidate mechanisms of neurodegenerative diseases based on publicly available data and knowledge. We identify two complementary strategies—data mining techniques using genetic data as a starting point to be further enriched using other data-types, or alternatively to encode prior knowledge about disease mechanisms in a model based framework supporting reasoning and enrichment analysis. Our review illustrates the challenges entailed in integrating heterogeneous, multiscale and multimodal information in the area of neurology in general and neurodegeneration in particular. We conclude, that progress would be accelerated by increasing efforts on performing systematic collection of multiple data-types over time from each individual suffering from neurodegenerative disease. The work presented here has been driven by project AETIONOMY; a project funded in the course of the Innovative Medicines Initiative (IMI; which is a public-private partnership of the European Federation of Pharmaceutical Industry Associations

  3. Naturally selecting solutions: the use of genetic algorithms in bioinformatics.

    Science.gov (United States)

    Manning, Timmy; Sleator, Roy D; Walsh, Paul

    2013-01-01

    For decades, computer scientists have looked to nature for biologically inspired solutions to computational problems; ranging from robotic control to scheduling optimization. Paradoxically, as we move deeper into the post-genomics era, the reverse is occurring, as biologists and bioinformaticians look to computational techniques, to solve a variety of biological problems. One of the most common biologically inspired techniques are genetic algorithms (GAs), which take the Darwinian concept of natural selection as the driving force behind systems for solving real world problems, including those in the bioinformatics domain. Herein, we provide an overview of genetic algorithms and survey some of the most recent applications of this approach to bioinformatics based problems.

  4. Bioinformatic scaling of allosteric interactions in biomedical isozymes

    Science.gov (United States)

    Phillips, J. C.

    2016-09-01

    Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit cancer cell metabolism. Many parallel features are apparent, which explain how even one amino acid mutation, remote from active sites, can alter medical results. The enzyme twins involved are cyclooxygenase (aspirin) and isocitrate dehydrogenase (IDH). The IDH results are accurate to 1% and are overdetermined by adjusting a single bioinformatic scaling parameter. It appears that the final stage in optimizing protein functionality may involve leveling of the hydrophobic limits of the arms of conformational hydrophilic hinges.

  5. Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

    DEFF Research Database (Denmark)

    Leclère, Valérie; Weber, Tilmann; Jacques, Philippe

    2016-01-01

    This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes and the decip......This chapter helps in the use of bioinformatics tools relevant to the discovery of new nonribosomal peptides (NRPs) produced by microorganisms. The strategy described can be applied to draft or fully assembled genome sequences. It relies on the identification of the synthetase genes...

  6. Approaches in integrative bioinformatics towards the virtual cell

    CERN Document Server

    Chen, Ming

    2014-01-01

    Approaches in Integrative Bioinformatics provides a basic introduction to biological information systems, as well as guidance for the computational analysis of systems biology. This book also covers a range of issues and methods that reveal the multitude of omics data integration types and the relevance that integrative bioinformatics has today. Topics include biological data integration and manipulation, modeling and simulation of metabolic networks, transcriptomics and phenomics, and virtual cell approaches, as well as a number of applications of network biology. It helps to illustrat

  7. High-performance computational solutions in protein bioinformatics

    CERN Document Server

    Mrozek, Dariusz

    2014-01-01

    Recent developments in computer science enable algorithms previously perceived as too time-consuming to now be efficiently used for applications in bioinformatics and life sciences. This work focuses on proteins and their structures, protein structure similarity searching at main representation levels and various techniques that can be used to accelerate similarity searches. Divided into four parts, the first part provides a formal model of 3D protein structures for functional genomics, comparative bioinformatics and molecular modeling. The second part focuses on the use of multithreading for

  8. Bioinformatics for Precision Medicine in Oncology: principles and application to the SHIVA clinical trial

    Directory of Open Access Journals (Sweden)

    Nicolas eServant

    2014-05-01

    Full Text Available Precision medicine (PM requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of i warranting the integration and the traceability of data, ii ensuring the correct processing and analyses of genomic data and iii applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application.

  9. European Analytical Column

    DEFF Research Database (Denmark)

    Karlberg, B.; Grasserbauer, M.; Andersen, Jens Enevold Thaulov

    2009-01-01

    The European Analytical Column has once more invited a guest columnist to give his views on various matters related to analytical chemistry in Europe. This year, we have invited Professor Manfred Grasserbauer of the Vienna University of Technology to present some of the current challenges...... for European analytical chemistry. During the period 2002–07, Professor Grasserbauer was Director of the Institute for Environment and Sustainability, Joint Research Centre of the European Commission (EC), Ispra, Italy. There is no doubt that many challenges exist at the present time for all of us representing...... a major branch of chemistry, namely analytical chemistry. The global financial crisis is affecting all branches of chemistry, but analytical chemistry, in particular, since our discipline by tradition has many close links to industry. We have already noticed decreased industrial commitment with respect...

  10. SOME ISSUES OF TEACHING AND LEARNING OF CORPORATE GOVERNANCE IN LAW INSTITUTIONS AND UNIVERSITIES IN THE CONTEXT OF THE INTERNATIONAL MASTER’S DOUBLE DEGREE PROGRAM «EUROPEAN AND INTERNATIONAL LAW»

    Directory of Open Access Journals (Sweden)

    Sergey Yu. Marochkin

    2015-01-01

    Full Text Available The focus of this paper is a necessity for law-students not only to master professional legal knowledge, but also knowledge and skills in the management of corporations and enterprises. This issue is particularly relevant for the course of European law, as well as for the corresponding master’s degree programs «Jurisprudence». Key attention is paid to the necessity of including such academic disciplines for students as the topic «Corporate governance» and the theme «Corporate Law» into the magister program of two diplomas «European and International Law» for the universities of Eastern Europe. In this context, development of corporate governance in Central Europe and Russia is compared; the problems of such management in the Russian economy are designated. The aim of this study is analysis and systematization of theoretical and methodological aspects, as well as practical guidance in the development of teaching and studying of corporate governance in high law schools and colleges. To achieve this task the following objectives were: to analyze the basic acting model of legal education and modern educational technologies necessary for the implementation of the system of higher education; organize and summarize the theoretical and methodical bases of corporate governance, its principles; define the role corporate governance in the implementation of business activity, as well as to compare its role in Russia and Central Europe; explore the practical importance of training in the field of corporate law Methods. The research is based on the dialectic method regulating legislative norms, including the corporate right and activity of managing subjects. The retrospective analysis of pedagogical achievements and forecasting were used. Results. Working models of the juridical education and the modern educational technologies are considered in the present paper. Such models help promote systemization and generalisation of leading positions of a

  11. The European Identity

    Directory of Open Access Journals (Sweden)

    Alberto Martinelli

    2017-09-01

    Full Text Available European identity is not only a scientifically interesting question, but also a politically important issue: in fact, sixty years after the signing of the Treaty of Rome, the European Union finds itself for the first time facing risks that threaten its own existence. The European Union is a limited and incomplete project because Europe’s economic integration has not been accompanied by a genuine supranational political union and greater cultural integration. The deficit of democratic representation and cultural integration is due to the fact that the community process is based only on economic rationality and not on a feeling of common belonging. In the current situation in which the Union faces difficult challenges which threaten to undermine the future, it necessary to affirm the policy of interests with a policy of identity. In this essay, we will first concentrate on the concept of identity – that is on the nucleus of values and common institutions –; then we will discuss how the European identity has changed over time (also in relation to national identities and what are the mechanisms that may favour its taking root in the current situation. The European project of political unification needs to be re-emphasized, finding the way to a European collective identity, not contrasted with but alongside the different national identities, referring to loyalty and shared commitment to a whole collection of cultural values: fundamental human rights, civil liberties, democratic political institutions, rule of law, freedom of movement of people, goods and capital, social justice and non-violent resolution of conflicts.

  12. Parameters of measuring of european political consciousness

    Directory of Open Access Journals (Sweden)

    M. M. Pikula

    2015-09-01

    Full Text Available In the article the author analyzes the parameters of European political consciousness, i.e. European research field of political consciousness in qualitative and quantitative terms, which may be based on different indicators. The issue of emergence and development of European political consciousness becomes topical because firstly, its formation as the subjective dimension of European integration policy is not a spontaneous process and, secondly, European integration is carried out not only from the top but from the bottom, requiring deliberate interference of the public with the process; the public possesses the formed European political consciousness. Since the latter is a specific mental construct, the author offers to apply the triad «criteria ­ parameters – indicators». The characteristic that makes it possible to evaluate certain processes or phenomena in the system of Europeanness / Europeanism and specifies the quality system of views and opinions, which are realized in European behavior, is considered to be the criterion of European political consciousness. The European political consciousness parameters are seen to include the relevant historical memory, trends of public opinion and awareness regarding the European Union and position of its members in the European integration process, including the assessment of the existence and development of the EU; knowledge and views on the main EU institutions, assessing the importance of the main institutions of the EU and trust in them; a positive vision for the future of the European Union etc. The author considers the performance and objective characteristics and dimensions, including positive correlation of national and European levels of identity (European identity and European behavior to be the indicatiors of European political awareness. On the basis of these indicators the control of the condition and trends of European political consciousness development will be carried out.

  13. Mathematics and evolutionary biology make bioinformatics education comprehensible.

    Science.gov (United States)

    Jungck, John R; Weisstein, Anton E

    2013-09-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes-the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software-the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a 'two-culture' problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses.

  14. Bioinformatic approaches to interrogating vitamin D receptor signaling.

    Science.gov (United States)

    Campbell, Moray J

    2017-09-15

    Bioinformatics applies unbiased approaches to develop statistically-robust insight into health and disease. At the global, or "20,000 foot" view bioinformatic analyses of vitamin D receptor (NR1I1/VDR) signaling can measure where the VDR gene or protein exerts a genome-wide significant impact on biology; VDR is significantly implicated in bone biology and immune systems, but not in cancer. With a more VDR-centric, or "2000 foot" view, bioinformatic approaches can interrogate events downstream of VDR activity. Integrative approaches can combine VDR ChIP-Seq in cell systems where significant volumes of publically available data are available. For example, VDR ChIP-Seq studies can be combined with genome-wide association studies to reveal significant associations to immune phenotypes. Similarly, VDR ChIP-Seq can be combined with data from Cancer Genome Atlas (TCGA) to infer the impact of VDR target genes in cancer progression. Therefore, bioinformatic approaches can reveal what aspects of VDR downstream networks are significantly related to disease or phenotype. Copyright © 2017 The Author. Published by Elsevier B.V. All rights reserved.

  15. Omics-bioinformatics in the context of clinical data.

    Science.gov (United States)

    Mayer, Gert; Heinze, Georg; Mischak, Harald; Hellemons, Merel E; Heerspink, Hiddo J Lambers; Bakker, Stephan J L; de Zeeuw, Dick; Haiduk, Martin; Rossing, Peter; Oberbauer, Rainer

    2011-01-01

    The Omics revolution has provided the researcher with tools and methodologies for qualitative and quantitative assessment of a wide spectrum of molecular players spanning from the genome to the meta-bolome level. As a consequence, explorative analysis (in contrast to purely hypothesis driven research procedures) has become applicable. However, numerous issues have to be considered for deriving meaningful results from Omics, and bioinformatics has to respect these in data analysis and interpretation. Aspects include sample type and quality, concise definition of the (clinical) question, and selection of samples ideally coming from thoroughly defined sample and data repositories. Omics suffers from a principal shortcoming, namely unbalanced sample-to-feature matrix denoted as "curse of dimensionality", where a feature refers to a specific gene or protein among the many thousands assayed in parallel in an Omics experiment. This setting makes the identification of relevant features with respect to a phenotype under analysis error prone from a statistical perspective. From this sample size calculation for screening studies and for verification of results from Omics, bioinformatics is essential. Here we present key elements to be considered for embedding Omics bioinformatics in a quality controlled workflow for Omics screening, feature identification, and validation. Relevant items include sample and clinical data management, minimum sample quality requirements, sample size estimates, and statistical procedures for computing the significance of findings from Omics bioinformatics in validation studies.

  16. Rapid cloning and bioinformatic analysis of spinach Y chromosome ...

    Indian Academy of Sciences (India)

    The female spinach genome was taken as blocker and cDNA library specifically expressed in Y chromosome was constructed. Moreover, expressed sequence tag (EST) sequences in cDNA library were cloned, sequenced and bioinformatics was analysed. There were 63 valid EST sequences obtained in this study.

  17. CROSSWORK for Glycans: Glycan Identificatin Through Mass Spectrometry and Bioinformatics

    DEFF Research Database (Denmark)

    Rasmussen, Morten; Thaysen-Andersen, Morten; Højrup, Peter

      We have developed "GLYCANthrope " - CROSSWORKS for glycans:  a bioinformatics tool, which assists in identifying N-linked glycosylated peptides as well as their glycan moieties from MS2 data of enzymatically digested glycoproteins. The program runs either as a stand-alone application or as a plug...

  18. Hidden in the Middle: Culture, Value and Reward in Bioinformatics

    Science.gov (United States)

    Lewis, Jamie; Bartlett, Andrew; Atkinson, Paul

    2016-01-01

    Bioinformatics--the so-called shotgun marriage between biology and computer science--is an interdiscipline. Despite interdisciplinarity being seen as a virtue, for having the capacity to solve complex problems and foster innovation, it has the potential to place projects and people in anomalous categories. For example, valorised…

  19. Bioinformatic analysis of dihydrofolate reductase predicted in the ...

    African Journals Online (AJOL)

    olayemitoyin

    Bioinformatic analysis of dihydrofolate reductase predicted in the genome sequence of Lactobacillus pentosus KCA1. *Kingsley C. Anukam. 1 and Uche Oge. 2. 1TWAS Genomic Research Unit, Department of Medical Laboratory Science, 2Department of Physiology,. School of Basic Medical Sciences, University of Benin, ...

  20. Bioinformatic analyses of kappa casein gene in mammalian ...

    African Journals Online (AJOL)

    Kappa casein (CSN3) gene is a variant of the milk protein highly conserved in mammalian species. Genetic variations in CSN3 gene of six mammalian livestock species were investigated using bioinformatics approach. A total of twenty-seven CSN3 gene sequences with corresponding amino acids belonging to the six ...

  1. Robust enzyme design: bioinformatic tools for improved protein stability.

    Science.gov (United States)

    Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas

    2015-03-01

    The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Science Academies' Refresher Course on Bioinformatics in Modern ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 19; Issue 2. Science Academies' Refresher Course on Bioinformatics in Modern Biology. Information and Announcements Volume 19 Issue 2 February 2014 pp 192-192. Fulltext. Click here to view fulltext PDF. Permanent link:

  3. Bioinformatic analysis of dihydrofolate reductase predicted in the ...

    African Journals Online (AJOL)

    The genome has open reading frames coding for the complete genes required for folate biosynthesis. Our previous study shows that rats fed with L. pentosus KCA1 led to enhancement of haematological parameters. Bioinformatic tool such as ClustalW algorithm was used to analyze dihydrofolate reductase (folA/dfrA) ...

  4. current status and future perspectives of bioinformatics in tanzania

    African Journals Online (AJOL)

    nb

    high throughput technologies such as next generation sequencing. Although bioinformatics has been making major progress and contributing to the development in the rest of the world, it has still not yet fully integrated the tertiary education and research sector in Tanzania. ... being directed towards recently emerging.

  5. Learning Genetics through an Authentic Research Simulation in Bioinformatics

    Science.gov (United States)

    Gelbart, Hadas; Yarden, Anat

    2006-01-01

    Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process…

  6. Bioinformatics in the Netherlands : The value of a nationwide community

    NARCIS (Netherlands)

    van Gelder, Celia W.G.; Hooft, Rob; van Rijswijk, Merlijn; van den Berg, Linda; Kok, Ruben; Reinders, M.J.T.; Mons, Barend; Heringa, Jaap

    2017-01-01

    This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures

  7. Science Academies' Refresher Course on Bioinformatics in Modern ...

    Indian Academy of Sciences (India)

    IAS Admin

    A Refresher Course on 'Bioinformatics in Modern Biology' for graduate and postgraduate college/university teachers will be held at School of Life Sciences, Manipal University, Manipal for two weeks from 5 to 17 May 2014. The objective of this Course is to improvise on teaching methodologies incorporating online teaching ...

  8. The structural bioinformatics library: modeling in biomolecular science and beyond.

    Science.gov (United States)

    Cazals, Frédéric; Dreyfus, Tom

    2017-04-01

    Software in structural bioinformatics has mainly been application driven. To favor practitioners seeking off-the-shelf applications, but also developers seeking advanced building blocks to develop novel applications, we undertook the design of the Structural Bioinformatics Library ( SBL , http://sbl.inria.fr ), a generic C ++/python cross-platform software library targeting complex problems in structural bioinformatics. Its tenet is based on a modular design offering a rich and versatile framework allowing the development of novel applications requiring well specified complex operations, without compromising robustness and performances. The SBL involves four software components (1-4 thereafter). For end-users, the SBL provides ready to use, state-of-the-art (1) applications to handle molecular models defined by unions of balls, to deal with molecular flexibility, to model macro-molecular assemblies. These applications can also be combined to tackle integrated analysis problems. For developers, the SBL provides a broad C ++ toolbox with modular design, involving core (2) algorithms , (3) biophysical models and (4) modules , the latter being especially suited to develop novel applications. The SBL comes with a thorough documentation consisting of user and reference manuals, and a bugzilla platform to handle community feedback. The SBL is available from http://sbl.inria.fr. Frederic.Cazals@inria.fr. Supplementary data are available at Bioinformatics online.

  9. Mathematics and evolutionary biology make bioinformatics education comprehensible

    Science.gov (United States)

    Weisstein, Anton E.

    2013-01-01

    The patterns of variation within a molecular sequence data set result from the interplay between population genetic, molecular evolutionary and macroevolutionary processes—the standard purview of evolutionary biologists. Elucidating these patterns, particularly for large data sets, requires an understanding of the structure, assumptions and limitations of the algorithms used by bioinformatics software—the domain of mathematicians and computer scientists. As a result, bioinformatics often suffers a ‘two-culture’ problem because of the lack of broad overlapping expertise between these two groups. Collaboration among specialists in different fields has greatly mitigated this problem among active bioinformaticians. However, science education researchers report that much of bioinformatics education does little to bridge the cultural divide, the curriculum too focused on solving narrow problems (e.g. interpreting pre-built phylogenetic trees) rather than on exploring broader ones (e.g. exploring alternative phylogenetic strategies for different kinds of data sets). Herein, we present an introduction to the mathematics of tree enumeration, tree construction, split decomposition and sequence alignment. We also introduce off-line downloadable software tools developed by the BioQUEST Curriculum Consortium to help students learn how to interpret and critically evaluate the results of standard bioinformatics analyses. PMID:23821621

  10. Opportunities and challenges provided by cloud repositories for bioinformatics-enabled drug discovery.

    Science.gov (United States)

    Dalpé, Gratien; Joly, Yann

    2014-09-01

    Healthcare-related bioinformatics databases are increasingly offering the possibility to maintain, organize, and distribute DNA sequencing data. Different national and international institutions are currently hosting such databases that offer researchers website platforms where they can obtain sequencing data on which they can perform different types of analysis. Until recently, this process remained mostly one-dimensional, with most analysis concentrated on a limited amount of data. However, newer genome sequencing technology is producing a huge amount of data that current computer facilities are unable to handle. An alternative approach has been to start adopting cloud computing services for combining the information embedded in genomic and model system biology data, patient healthcare records, and clinical trials' data. In this new technological paradigm, researchers use virtual space and computing power from existing commercial or not-for-profit cloud service providers to access, store, and analyze data via different application programming interfaces. Cloud services are an alternative to the need of larger data storage; however, they raise different ethical, legal, and social issues. The purpose of this Commentary is to summarize how cloud computing can contribute to bioinformatics-based drug discovery and to highlight some of the outstanding legal, ethical, and social issues that are inherent in the use of cloud services. © 2014 Wiley Periodicals, Inc.

  11. European Whiteness?

    DEFF Research Database (Denmark)

    Blaagaard, Bolette

    2008-01-01

    Born out of the United States’ (U.S.) history of slavery and segregation and intertwined with gender studies and feminism, the field of critical whiteness studies does not fit easily into a European setting and the particular historical context that entails. In order for a field of European...... critical whiteness studies to emerge, its relation to the U.S. theoretical framework, as well as the particularities of the European context need to be taken into account.. The article makes a call for a multi-layered approach to take over from the identity politics so often employed in the fields of U...

  12. BioWarehouse: a bioinformatics database warehouse toolkit

    Directory of Open Access Journals (Sweden)

    Stringer-Calvert David WJ

    2006-03-01

    Full Text Available Abstract Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the

  13. BioWarehouse: a bioinformatics database warehouse toolkit

    Science.gov (United States)

    Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David WJ; Tenenbaum, Jessica D; Karp, Peter D

    2006-01-01

    Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the database integration problem for

  14. Missing "Links" in Bioinformatics Education: Expanding Students' Conceptions of Bioinformatics Using a Biodiversity Database of Living and Fossil Reef Corals

    Science.gov (United States)

    Nehm, Ross H.; Budd, Ann F.

    2006-01-01

    NMITA is a reef coral biodiversity database that we use to introduce students to the expansive realm of bioinformatics beyond genetics. We introduce a series of lessons that have students use this database, thereby accessing real data that can be used to test hypotheses about biodiversity and evolution while targeting the "National Science …

  15. European Security

    DEFF Research Database (Denmark)

    Møller, Bjørn

    Theoretical chapters on "Security", "Organisations" and "Regions," Historical Chapters on "Europe and Its Distinguishing Features" and on "The United Nations," "NATO," "The CSCE/OSCE and the Council of Europe" and "The European Union"......Theoretical chapters on "Security", "Organisations" and "Regions," Historical Chapters on "Europe and Its Distinguishing Features" and on "The United Nations," "NATO," "The CSCE/OSCE and the Council of Europe" and "The European Union"...

  16. GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics

    Science.gov (United States)

    Samson, Delphine; Legeai, Fabrice; Karsenty, Emmanuelle; Reboux, Sébastien; Veyrieras, Jean-Baptiste; Just, Jeremy; Barillot, Emmanuel

    2003-01-01

    Génoplante is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis software), that are being integrated and made public at the public bioinformatics resource centre of Génoplante: GénoPlante-Info (GPI). This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/. PMID:12519976

  17. Vertical and Horizontal Integration of Bioinformatics Education: A Modular, Interdisciplinary Approach

    Science.gov (United States)

    Furge, Laura Lowe; Stevens-Truss, Regina; Moore, D. Blaine; Langeland, James A.

    2009-01-01

    Bioinformatics education for undergraduates has been approached primarily in two ways: introduction of new courses with largely bioinformatics focus or introduction of bioinformatics experiences into existing courses. For small colleges such as Kalamazoo, creation of new courses within an already resource-stretched setting has not been an option.…

  18. Introductory Bioinformatics Exercises Utilizing Hemoglobin and Chymotrypsin to Reinforce the Protein Sequence-Structure-Function Relationship

    Science.gov (United States)

    Inlow, Jennifer K.; Miller, Paige; Pittman, Bethany

    2007-01-01

    We describe two bioinformatics exercises intended for use in a computer laboratory setting in an upper-level undergraduate biochemistry course. To introduce students to bioinformatics, the exercises incorporate several commonly used bioinformatics tools, including BLAST, that are freely available online. The exercises build upon the students'…

  19. What Makes Institutional Long-Term Care the Most Appropriate Setting for People With Dementia? Exploring the Influence of Client Characteristics, Decision-Maker Attributes, and Country in 8 European Nations.

    Science.gov (United States)

    Tucker, Sue; Brand, Christian; Sutcliffe, Caroline; Challis, David; Saks, Kai; Verbeek, Hilde; Cabrera, Esther; Karlsson, Staffan; Leino-Kilpi, Helena; Stephan, Astrid; Soto, Maria E

    2016-05-01

    To explore the extent to which client characteristics, decision-maker attributes, and country influence judgments of institutional long-term care (ILTC) appropriateness for people with dementia. A total of 161 experts in dementia care from 8 European countries reviewed a series of 14 vignettes representing people with dementia on the cusp of ILTC admission and indicated the most appropriate setting in which to support each case in a simple discrete choice exercise: own home, very sheltered housing, residential home, or nursing home. At least 16 experts participated in each country (Estonia, Finland, France, Germany, the Netherlands, Spain, Sweden, and the United Kingdom). Descriptive statistics were used to characterize the experts and their placement preferences. Logistic regression modeling was used to explore the extent to which the sociodemographic and clinical characteristics of people with dementia, and the profession, workplace, and country of decision-makers were associated with ILTC recommendation. Client characteristics, decision-maker attributes, and country all seemed to play a part in influencing professionals' perceptions of the appropriateness of ILTC for people with dementia. Expert decision-makers were more likely to recommend ILTC for individuals who required help with mobility or had multiple care needs, and appeared to give more weight to carers' than clients' wishes. Community-based social workers were less likely than other professional groups to favor ILTC placement. Experts in Finland, Germany, and the United Kingdom were less likely to recommend ILTC than experts in France, the Netherlands, and Estonia; experts in Sweden and Spain took an intermediate position. This study provides new understanding of the factors that shape professionals' perceptions of ILTC appropriateness and highlights the need to construct multifaceted models of institutionalization when planning services for people with dementia. It also has several important clinical

  20. Unlocking the potential of electronic health records for translational research. Findings from the section on bioinformatics and translational informatics.

    Science.gov (United States)

    Yip, Y L

    2012-01-01

    To review current excellent research and trend in the field of bioinformatics and translational informatics with direct application in the medical domain. Synopsis of the articles selected for the IMIA Yearbook 2012. Six excellent articles were selected in this Yearbook's section on Bioinformatics and Translational Informatics. They exemplify current key advances in the use of patient information for translational research and health surveillance. First, two proof-of-concept studies demonstrated the cross-institutional and -geographic use of Electronic Health Records (EHR) for clinical trial subjects identification and drug safety signals detection. These reports pave ways to global large-scale population monitoring. Second, there is further evidence on the importance of coupling phenotypic information in EHR with genotypic information (either in biobank or in gene association studies) for new biomedical knowledge discovery. Third, patient data gathered via social media and self-reporting was found to be comparable to existent data and less labor intensive. This alternative means could potentially overcome data collection challenge in cohort and prospective studies. Finally, it can be noted that metagenomic studies are gaining momentum in bioinformatics and system-level analysis of human microbiome sheds important light on certain human diseases. The current literature showed that the traditional bench to bedside translational research is increasing being complemented by the reverse approach, in which bedside information can be used to provide novel biomedical insights.

  1. Quantum Bio-Informatics II From Quantum Information to Bio-Informatics

    Science.gov (United States)

    Accardi, L.; Freudenberg, Wolfgang; Ohya, Masanori

    2009-02-01

    / H. Kamimura -- Massive collection of full-length complementary DNA clones and microarray analyses: keys to rice transcriptome analysis / S. Kikuchi -- Changes of influenza A(H5) viruses by means of entropic chaos degree / K. Sato and M. Ohya -- Basics of genome sequence analysis in bioinformatics - its fundamental ideas and problems / T. Suzuki and S. Miyazaki -- A basic introduction to gene expression studies using microarray expression data analysis / D. Wanke and J. Kilian -- Integrating biological perspectives: a quantum leap for microarray expression analysis / D. Wanke ... [et al.].

  2. The European Parliament and the European future of Albania

    Directory of Open Access Journals (Sweden)

    Skerdilajd Bajramaj

    2015-07-01

    Full Text Available On 06.24.2014 Albania was granted the status of candidate country. The foreign ministers of the 28 European Union member states decided unanimously to grant the candidate status for Albania. After receiving the status of “candidate country” for EU membership, the institutional relations with European international bodies are becoming stronger. One of these institutions, which during this time has increased its authority with Albania, is the European Parliament. In this paper will be analyzed the composition, competences and functioning of this particular institution, which is not only important for the future of the European Union and its Member States, but also for those who aim to join in. The study will be based on decisions made by this legislative body, as the only direct representative of the citizens of the European Union, and the impact they have on the performance and functioning of the Member States and the EU itself. In order to verify the validity of these claims, the analysis aims to assess the scope of the legislative function of the European Parliament post-Lisbon, examining its participation in the EU lawmaking both from the point of view of quantity and quality in over the past legislatures. Particular attention has been given to the examination of the changes that have taken place with the entry into force of the Lisbon Treaty, and the areas most affected. We will finally look at the work and contribution of the European Parliament, through the instruments at his disposal, on behalf of Albania’s progress towards full accession in the European Union.

  3. European visit

    CERN Multimedia

    2006-01-01

    The European Commissioner for Science and Research, Janez Potočnik, (on the right) visited the CMS assembly hall accompanied by Jim Virdee, Deputy Spokesman of CMS (on the left), and Robert Aymar, Director-General of CERN. The European Commissioner for Science and Research, Janez Potočnik, visited CERN on Tuesday 31 January. He was welcomed by the Director-General, Robert Aymar, who described the missions and current activities of CERN to him, in particular the realisation of the LHC with its three components: accelerator, detectors, storage and processing of data. The European Commissioner then visited the CMS assembly hall, then the hall for testing the LHC magnets and the ATLAS cavern. During this first visit since his appointment at the end of 2004, Janez Potočnik appeared very interested by the operation of CERN, an example of successful scientific co-operation on a European scale. The many projects (30 on average) that CERN and the European Commission carry out jointly for the benefit of res...

  4. Data Mining for Grammatical Inference with Bioinformatics Criteria

    Science.gov (United States)

    López, Vivian F.; Aguilar, Ramiro; Alonso, Luis; Moreno, María N.; Corchado, Juan M.

    In this paper we describe both theoretical and practical results of a novel data mining process that combines hybrid techniques of association analysis and classical sequentiation algorithms of genomics to generate grammatical structures of a specific language. We used an application of a compilers generator system that allows the development of a practical application within the area of grammarware, where the concepts of the language analysis are applied to other disciplines, such as Bioinformatic. The tool allows the complexity of the obtained grammar to be measured automatically from textual data. A technique of incremental discovery of sequential patterns is presented to obtain simplified production rules, and compacted with bioinformatics criteria to make up a grammar.

  5. 2nd Colombian Congress on Computational Biology and Bioinformatics

    CERN Document Server

    Cristancho, Marco; Isaza, Gustavo; Pinzón, Andrés; Rodríguez, Juan

    2014-01-01

    This volume compiles accepted contributions for the 2nd Edition of the Colombian Computational Biology and Bioinformatics Congress CCBCOL, after a rigorous review process in which 54 papers were accepted for publication from 119 submitted contributions. Bioinformatics and Computational Biology are areas of knowledge that have emerged due to advances that have taken place in the Biological Sciences and its integration with Information Sciences. The expansion of projects involving the study of genomes has led the way in the production of vast amounts of sequence data which needs to be organized, analyzed and stored to understand phenomena associated with living organisms related to their evolution, behavior in different ecosystems, and the development of applications that can be derived from this analysis.  .

  6. Architecture exploration of FPGA based accelerators for bioinformatics applications

    CERN Document Server

    Varma, B Sharat Chandra; Balakrishnan, M

    2016-01-01

    This book presents an evaluation methodology to design future FPGA fabrics incorporating hard embedded blocks (HEBs) to accelerate applications. This methodology will be useful for selection of blocks to be embedded into the fabric and for evaluating the performance gain that can be achieved by such an embedding. The authors illustrate the use of their methodology by studying the impact of HEBs on two important bioinformatics applications: protein docking and genome assembly. The book also explains how the respective HEBs are designed and how hardware implementation of the application is done using these HEBs. It shows that significant speedups can be achieved over pure software implementations by using such FPGA-based accelerators. The methodology presented in this book may also be used for designing HEBs for accelerating software implementations in other domains besides bioinformatics. This book will prove useful to students, researchers, and practicing engineers alike.

  7. Statistical modelling in biostatistics and bioinformatics selected papers

    CERN Document Server

    Peng, Defen

    2014-01-01

    This book presents selected papers on statistical model development related mainly to the fields of Biostatistics and Bioinformatics. The coverage of the material falls squarely into the following categories: (a) Survival analysis and multivariate survival analysis, (b) Time series and longitudinal data analysis, (c) Statistical model development and (d) Applied statistical modelling. Innovations in statistical modelling are presented throughout each of the four areas, with some intriguing new ideas on hierarchical generalized non-linear models and on frailty models with structural dispersion, just to mention two examples. The contributors include distinguished international statisticians such as Philip Hougaard, John Hinde, Il Do Ha, Roger Payne and Alessandra Durio, among others, as well as promising newcomers. Some of the contributions have come from researchers working in the BIO-SI research programme on Biostatistics and Bioinformatics, centred on the Universities of Limerick and Galway in Ireland and fu...

  8. A Survey on Evolutionary Algorithm Based Hybrid Intelligence in Bioinformatics

    Directory of Open Access Journals (Sweden)

    Shan Li

    2014-01-01

    Full Text Available With the rapid advance in genomics, proteomics, metabolomics, and other types of omics technologies during the past decades, a tremendous amount of data related to molecular biology has been produced. It is becoming a big challenge for the bioinformatists to analyze and interpret these data with conventional intelligent techniques, for example, support vector machines. Recently, the hybrid intelligent methods, which integrate several standard intelligent approaches, are becoming more and more popular due to their robustness and efficiency. Specifically, the hybrid intelligent approaches based on evolutionary algorithms (EAs are widely used in various fields due to the efficiency and robustness of EAs. In this review, we give an introduction about the applications of hybrid intelligent methods, in particular those based on evolutionary algorithm, in bioinformatics. In particular, we focus on their applications to three common problems that arise in bioinformatics, that is, feature selection, parameter estimation, and reconstruction of biological networks.

  9. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  10. Open discovery: An integrated live Linux platform of Bioinformatics tools.

    Science.gov (United States)

    Vetrivel, Umashankar; Pilla, Kalabharath

    2008-01-01

    Historically, live linux distributions for Bioinformatics have paved way for portability of Bioinformatics workbench in a platform independent manner. Moreover, most of the existing live Linux distributions limit their usage to sequence analysis and basic molecular visualization programs and are devoid of data persistence. Hence, open discovery - a live linux distribution has been developed with the capability to perform complex tasks like molecular modeling, docking and molecular dynamics in a swift manner. Furthermore, it is also equipped with complete sequence analysis environment and is capable of running windows executable programs in Linux environment. Open discovery portrays the advanced customizable configuration of fedora, with data persistency accessible via USB drive or DVD. The Open Discovery is distributed free under Academic Free License (AFL) and can be downloaded from http://www.OpenDiscovery.org.in.

  11. Bioengineering and Bioinformatics Summer Institutes: Meeting Modern Challenges in Undergraduate Summer Research

    Science.gov (United States)

    Butler, Peter J.; Dong, Cheng; Snyder, Alan J.; Jones, A. Daniel; Sheets, Erin D.

    2008-01-01

    Summer undergraduate research programs in science and engineering facilitate research progress for faculty and provide a close-ended research experience for students, which can prepare them for careers in industry, medicine, and academia. However, ensuring these outcomes is a challenge when the students arrive ill-prepared for substantive research…

  12. MAPI: towards the integrated exploitation of bioinformatics Web Services

    OpenAIRE

    Karlsson Johan; Ramirez Sergio; Trelles Oswaldo

    2011-01-01

    Abstract Background Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. Results To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessar...

  13. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra

    2013-06-25

    The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

  14. BioWeka--extending the Weka framework for bioinformatics.

    Science.gov (United States)

    Gewehr, Jan E; Szugat, Martin; Zimmer, Ralf

    2007-03-01

    Given the growing amount of biological data, data mining methods have become an integral part of bioinformatics research. Unfortunately, standard data mining tools are often not sufficiently equipped for handling raw data such as e.g. amino acid sequences. One popular and freely available framework that contains many well-known data mining algorithms is the Waikato Environment for Knowledge Analysis (Weka). In the BioWeka project, we introduce various input formats for bioinformatics data and bioinformatics methods like alignments to Weka. This allows users to easily combine them with Weka's classification, clustering, validation and visualization facilities on a single platform and therefore reduces the overhead of converting data between different data formats as well as the need to write custom evaluation procedures that can deal with many different programs. We encourage users to participate in this project by adding their own components and data formats to BioWeka. The software, documentation and tutorial are available at http://www.bioweka.org.

  15. HotSwap for bioinformatics: A STRAP tutorial

    Directory of Open Access Journals (Sweden)

    Robinson Peter N

    2006-02-01

    Full Text Available Abstract Background Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the Java HotSwap technique. Results Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs. Saving changes to the Java file causes STRAP to recompile the plugin and automatically update its user interface without requiring recompilation of STRAP or reloading of protein data. This article presents a tutorial on how to develop HotSwap plugins. STRAP is available at http://strapjava.de and http://www.charite.de/bioinf/strap. Conclusion HotSwap is a useful and time-saving technique for bioinformatics developers. HotSwap can be used to efficiently develop bioinformatics applications that require loading large amounts of data into memory.

  16. [A review on the bioinformatics pipelines for metagenomic research].

    Science.gov (United States)

    Ye, Dan-Dan; Fan, Meng-Meng; Guan, Qiong; Chen, Hong-Ju; Ma, Zhan-Shan

    2012-12-01

    Metagenome, a term first dubbed by Handelsman in 1998 as "the genomes of the total microbiota found in nature", refers to sequence data directly sampled from the environment (which may be any habitat in which microbes live, such as the guts of humans and animals, milk, soil, lakes, glaciers, and oceans). Metagenomic technologies originated from environmental microbiology studies and their wide application has been greatly facilitated by next-generation high throughput sequencing technologies. Like genomics studies, the bottle neck of metagenomic research is how to effectively and efficiently analyze the gigantic amount of metagenomic sequence data using the bioinformatics pipelines to obtain meaningful biological insights. In this article, we briefly review the state-of-the-art bioinformatics software tools in metagenomic research. Due to the differences between the metagenomic data obtained from whole genome sequencing (i.e., shotgun metagenomics) and amplicon sequencing (i.e., 16S-rRNA and gene-targeted metagenomics) methods, there are significant differences between the corresponding bioinformatics tools for these data; accordingly, we review the computational pipelines separately for these two types of data.

  17. Bioinformatics: Current practice and future challenges for life science education.

    Science.gov (United States)

    Hack, Catherine; Kendall, Gary

    2005-03-01

    It is widely predicted that the application of high-throughput technologies to the quantification and identification of biological molecules will cause a paradigm shift in the life sciences. However, if the biosciences are to evolve from a predominantly descriptive discipline to an information science, practitioners will require enhanced skills in mathematics, computing, and statistical analysis. Universities have responded to the widely perceived skills gap primarily by developing masters programs in bioinformatics, resulting in a rapid expansion in the provision of postgraduate bioinformatics education. There is, however, a clear need to improve the quantitative and analytical skills of life science undergraduates. This article reviews the response of academia in the United Kingdom and proposes the learning outcomes that graduates should achieve to cope with the new biology. While the analysis discussed here uses the development of bioinformatics education in the United Kingdom as an illustrative example, it is hoped that the issues raised will resonate with all those involved in curriculum development in the life sciences. Copyright © 2005 International Union of Biochemistry and Molecular Biology, Inc.

  18. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  19. Emergent unsupervised clustering paradigms with potential application to bioinformatics.

    Science.gov (United States)

    Miller, David J; Wang, Yue; Kesidis, George

    2008-01-01

    In recent years, there has been a great upsurge in the application of data clustering, statistical classification, and related machine learning techniques to the field of molecular biology, in particular analysis of DNA microarray expression data. Clustering methods can be used to group co-expressed genes, shedding light on gene function and co-regulation. Alternatively, they can group samples or conditions to identify phenotypical groups, disease subgroups, or to help identify disease pathways. A rich variety of unsupervised techniques have been applied, including partitional, hierarchical, graph-based, model-based, and biclustering methods. While a number of machine learning problems and tools have found mainstream applications in bioinformatics, in this article we identify some challenging problems which, though clearly relevant to bioinformatics, have not been extensively investigated in this domain. These include i) unsupervised clustering with unsupervised feature selection, ii) semisupervised learning, iii) unsupervised learning (and supervised learning) in the presence of confounding variables, and iv) stability of clustering solutions. We review recent methods which address these problems and take the position that these methods are well-suited to addressing some common scenarios that occur in bioinformatics.

  20. p3d--Python module for structural bioinformatics.

    Science.gov (United States)

    Fufezan, Christian; Specht, Michael

    2009-08-21

    High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches. The development of such tools requires a robust interface to access the structural data in an easy way. For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. p3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  1. A comparison of common programming languages used in bioinformatics.

    Science.gov (United States)

    Fourment, Mathieu; Gillings, Michael R

    2008-02-05

    The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

  2. Statistical Contributions to Bioinformatics: Design, Modeling, Structure Learning, and Integration.

    Science.gov (United States)

    Morris, Jeffrey S; Baladandayuthapani, Veerabhadran

    2017-01-01

    The advent of high-throughput multi-platform genomics technologies providing whole-genome molecular summaries of biological samples has revolutionalized biomedical research. These technologiees yield highly structured big data, whose analysis poses significant quantitative challenges. The field of Bioinformatics has emerged to deal with these challenges, and is comprised of many quantitative and biological scientists working together to effectively process these data and extract the treasure trove of information they contain. Statisticians, with their deep understanding of variability and uncertainty quantification, play a key role in these efforts. In this article, we attempt to summarize some of the key contributions of statisticians to bioinformatics, focusing on four areas: (1) experimental design and reproducibility, (2) preprocessing and feature extraction, (3) unified modeling, and (4) structure learning and integration. In each of these areas, we highlight some key contributions and try to elucidate the key statistical principles underlying these methods and approaches. Our goals are to demonstrate major ways in which statisticians have contributed to bioinformatics, encourage statisticians to get involved early in methods development as new technologies emerge, and to stimulate future methodological work based on the statistical principles elucidated in this article and utilizing all availble information to uncover new biological insights.

  3. European Metals Conference

    CERN Document Server

    Vereecken, Jean

    1991-01-01

    This volume contains the papers that will be presented at 'EMC '91 '-the European Metals Conference-to be held in Brussels, Belgium, from 15 to 20 September 1991, and organized by Benelux Metallurgie, GDMB (Gesellschaft Deutscher Metallhutten­ und Bergleute) and IMM (the Institution of Mining and Metallurgy). 'EMC '91' is the first of an intended major series organized at the European level with the aim of bringing together all those who are involved with the extraction and processing of non-ferrous metals-European metallurgists and their international colleagues-to provide them with the opportunity to exchange views on the state and evolution of their industry. The programme covers all the different aspects of the metallurgy of non-ferrous metals from mining to fabricated products. Particular attention is being paid to the European non -ferrous industry with respect to changes in demand, the technology used, pressures on the environment and the competitive position of manufacturers. The contributions of the...

  4. Evolutionary institutionalism.

    Science.gov (United States)

    Fürstenberg, Dr Kai

    Institutions are hard to define and hard to study. Long prominent in political science have been two theories: Rational Choice Institutionalism (RCI) and Historical Institutionalism (HI). Arising from the life sciences is now a third: Evolutionary Institutionalism (EI). Comparative strengths and weaknesses of these three theories warrant review, and the value-to-be-added by expanding the third beyond Darwinian evolutionary theory deserves consideration. Should evolutionary institutionalism expand to accommodate new understanding in ecology, such as might apply to the emergence of stability, and in genetics, such as might apply to political behavior? Core arguments are reviewed for each theory with more detailed exposition of the third, EI. Particular attention is paid to EI's gene-institution analogy; to variation, selection, and retention of institutional traits; to endogeneity and exogeneity; to agency and structure; and to ecosystem effects, institutional stability, and empirical limitations in behavioral genetics. RCI, HI, and EI are distinct but complementary. Institutional change, while amenable to rational-choice analysis and, retrospectively, to criticaljuncture and path-dependency analysis, is also, and importantly, ecological. Stability, like change, is an emergent property of institutions, which tend to stabilize after change in a manner analogous to allopatric speciation. EI is more than metaphorically biological in that institutional behaviors are driven by human behaviors whose evolution long preceded the appearance of institutions themselves.

  5. Institutional advantage

    NARCIS (Netherlands)

    Martin, Xavier

    Is there such a thing as institutional advantage—and what does it mean for the study of corporate competitive advantage? In this article, I develop the concept of institutional competitive advantage, as distinct from plain competitive advantage and from comparative institutional advantage. I first

  6. European Corporate Law

    DEFF Research Database (Denmark)

    Werlauff, Erik; Dorresteijn, Adriaan; Teichmann, Christoph

    This fully updated new edition provides the best-known practical overview of the law regarding companies, business activities, and capital markets in Europe, at both the European Union (EU) and Member State levels. It incorporates analysis of recent developments including the impact of global......; - a company’s freedom to incorporate in a jurisdiction not its own; - competition among the legal forms of different Member States; and - safeguarding of employee involvement in cross-border transactions. With respect to national law, the laws of Belgium, France, Germany, the Netherlands, Poland, Spain...... initiatives in such aspects of the corporate environment as regulation of financial institutions and non-financial reporting obligations with a view to sustainability and other social responsibility concerns. The authors, all leading experts in European corporate law, describe current and emerging trends...

  7. The European Public on Social Media

    DEFF Research Database (Denmark)

    Tarta, Ancuta-Gabriela

    This study explorers the European public on social media by discussing the case of communicative interactions taking place on the official Facebook page of the European Parliament. Based on the theoretical framework conceptualizing the public and the public sphere on social network sites, the study...... examines the European social media public from two perspectives. The first is a top-down, institutional perspective of European Parliament, based on a case-study approach to the way this European institution constructs and addresses the public through its social media communication. The second is a bottom......-up perspective of the public of social media users, informed by a content analysis of Facebook comments and a discourse analysis of live chat interactions with Members of the European Parliament. Results confirm a discursive potential of the Facebook public of users. In the case of the Facebook comment threads...

  8. European Cinema

    NARCIS (Netherlands)

    Elsaesser, Thomas

    2005-01-01

    In the face of renewed competition from Hollywood since the early 1980s and the challenges posed to Europe's national cinemas by the fall of the Wall in 1989, independent filmmaking in Europe has begun to re-invent itself. European Cinema: Face to Face with Hollywood re-assesses the different

  9. Institutional entrepreneurship:

    DEFF Research Database (Denmark)

    Gretzinger, Susanne

    2018-01-01

    of agents or organisations in the policy arena. The present chapter understands institutional entrepreneurship as the process of changing institutionalised practices. Based on a literature review, it describes the triggers, activities and potential effects of institutional entrepreneurs. The chapter......Institutional entrepreneurship pays specific attention to the process and outcomes of agents who are willing and capable of changing institutions. It has some common ground with the political entrepreneur, a concept that proposes change in norms and institutions because of commitment and activities...... concludes by tentatively arguing that political entrepreneurs can be institutional entrepreneurs, but institutional entrepreneurship can be considered as the broader concept that incorporates strategies and visions as well as interpretative-discursive power into the conceptual framework....

  10. European Union Financial Crisis: a Marxist Analysis

    OpenAIRE

    Farneubun, Petrus K.

    2016-01-01

    European financial crisis poses a serious challenge to the fundamental structure of the European Union, political and financial institutions, as well as the values that bind European together. Different factors have been suggested as the causes of the crisis notably the failure of national government and economic policies. Responding to the crisis, numerous attemps have been proposed to accelerate the recovery, but the crisis still hit Eurozone and brought serious consequences politically and...

  11. The spatialization of the european project

    DEFF Research Database (Denmark)

    Richardson, Tim; Jensen, Ole B.

    This paper argues the need for more critical analysis of the ?spatialisation of the European Project? than has been the case in much previous academic work on the European Union`s spatial policy so far. The focus is on the EU, and the way that this huge institutional and territorial setting...... is organised, driven and imagined according to a particular hegemonic spatiality which gives shape to the political, economic, social and territorial dimensions of the European project....

  12. European Industrial Doctorates: Marie Curie Actions

    Science.gov (United States)

    European Commission, 2012

    2012-01-01

    European industrial doctorates are joint doctoral training projects funded by the European Union (EU) and open to all research fields. The project brings together an academic participant (university, research institution, etc.) and a company. They have to be established in two different EU Member States or associated countries. Associated partners…

  13. European side markers effect on traffic safety

    NARCIS (Netherlands)

    Roelfsema, A.; Theeuwes, J.; Alferdinck, J.W.A.M

    1999-01-01

    In 1993 new European legislation regarding side-markers for passenger cars became effective. Volvo requested the TNO-Human Factors Research Institute (HFRI) to investigate the possible safety benefit of this European side-markers configuration. A test panel at TNO- HFRI was used to determine the

  14. A European Vision for Adult Education

    Science.gov (United States)

    Waddington, Sue; Tuckett, Alan; Boucher, Fiona

    2012-01-01

    The National Institute of Adult Continuing Education (NIACE) is the UK national coordinator for the European Agenda for Adult Learning, with the challenge of creating a coherent message across the four countries to inform European cooperation on adult learning. To start the debate, the journal staff asked Sue Waddington, Alan Tuckett, and Fiona…

  15. Five political ideas of European contract law

    NARCIS (Netherlands)

    Hesselink, M.W.

    2011-01-01

    This paper explores the possible implications of leading contemporary theories of political philosophy for some of the main questions that the political institutions of the European Union will have to decide on concerning the future of European contract law. Thus, it explores what a utilitarian,

  16. The Politics of European Human Rights Culture

    Czech Academy of Sciences Publication Activity Database

    Agha, Petr

    2017-01-01

    Roč. 7, č. 3 (2017), s. 200-215 ISSN 1805-8396 R&D Projects: GA ČR GA13-30299S Institutional support: RVO:68378122 Keywords : Court of Justice of the European Union * European Court of Human Rights * religious symbols Subject RIV: AG - Legal Sciences

  17. European and Integration Studies

    Directory of Open Access Journals (Sweden)

    N. Yu. Kaveshnikov

    2014-01-01

    Full Text Available Soviet scientific school of pan-European integration studies began to emerge in the 1960s at the Institute of World Economy and International Relations (Russian Academy of Science. Among the leading scientists who have developed methodological approaches of Soviet integration studies were M.M. Maximova, Y.A. Borko, Y. Shishkov, L.I. Capercaillie. Later, a new center for integration studies became the Institute of Europe, created in 1987. It was led by such renowned scientists as Academicians V.V. Zhurkin and N.P. Shmelev. In the 1980s the subject of the integration process in Europe attracted attention of experts from MGIMO. An important role in the development of school of integration research in the USSR was played by a MGIMO professor, head of the chair of history of international relations and foreign policy of the USSR V.B. Knyazhinskiy. His work contributed to the deliverance of the national scientific community from skepticism about the prospects for European integration. Ideas of V.B. Knyazhinsky are developed today in MGIMO by his followers A.V. Mal'gin and T.V. Ur'eva. In the mid-1990s, having retired from diplomatic service, professor Yu. Matveevskiy started to work at MGIMO. With a considerable practical experience in the field, he produced a series of monographs on the history of European integration. In his works, he analyses the development of integration processes in Western Europe from their inception to the present day, showing the gradual maturation of the necessary spiritual and material prerequisites for the start of integration and traces the various stages of the "integration". In the late 1990s, the growing demand from the domestic business and government for professionals who are capable of interacting with the European Union, has produced the necessary supply in the form of educational programs based on accumulated scientific knowledge. Setting up a discipline "European Integration" was a major step in the development

  18. Bioinformatics in microbial biotechnology – a mini review

    Directory of Open Access Journals (Sweden)

    Bansal Arvind K

    2005-06-01

    Full Text Available Abstract The revolutionary growth in the computation speed and memory storage capability has fueled a new era in the analysis of biological data. Hundreds of microbial genomes and many eukaryotic genomes including a cleaner draft of human genome have been sequenced raising the expectation of better control of microorganisms. The goals are as lofty as the development of rational drugs and antimicrobial agents, development of new enhanced bacterial strains for bioremediation and pollution control, development of better and easy to administer vaccines, the development of protein biomarkers for various bacterial diseases, and better understanding of host-bacteria interaction to prevent bacterial infections. In the last decade the development of many new bioinformatics techniques and integrated databases has facilitated the realization of these goals. Current research in bioinformatics can be classified into: (i genomics – sequencing and comparative study of genomes to identify gene and genome functionality, (ii proteomics – identification and characterization of protein related properties and reconstruction of metabolic and regulatory pathways, (iii cell visualization and simulation to study and model cell behavior, and (iv application to the development of drugs and anti-microbial agents. In this article, we will focus on the techniques and their limitations in genomics and proteomics. Bioinformatics research can be classified under three major approaches: (1 analysis based upon the available experimental wet-lab data, (2 the use of mathematical modeling to derive new information, and (3 an integrated approach that integrates search techniques with mathematical modeling. The major impact of bioinformatics research has been to automate the genome sequencing, automated development of integrated genomics and proteomics databases, automated genome comparisons to identify the genome function, automated derivation of metabolic pathways, gene

  19. Continent of pessimism or continent of realism? A multilevel study into the impact of macro-economic outcomes and political institutions on societal pessimism, European Union 2006–2012

    NARCIS (Netherlands)

    Steenvoorden, E.H. (Eefje H); van der Meer, T.W.G. (Tom W G)

    2017-01-01

    textabstractThe often-posed claim that Europe is a pessimistic continent is not unjustified. In 2012, 53 percent of European Union (EU) citizens were pessimistic about their country. Surprisingly, however, societal pessimism has received very little scientific attention. In this article, we examine

  20. A bioinformatic analysis of the Alp8 family

    OpenAIRE

    Wooton, Jesse Meredith

    2009-01-01

    The majority of bacterial actins reside on mobile genetic elements. As of yet, the only known function of any of these genes is plasmid partitioning, and it has been assumed that all plasmid borne actins participate in this process. In this project, I conduct a bioinformatic analysis of one such actin family--the Alp8 family--and suggest an entirely new function. Based on an analysis of their genetic context and their conserved conjugative apparatuses with which they appear to have evolved in...

  1. Multilevel Cellular Automata as a Tool for Studying Bioinformatic Processes

    Science.gov (United States)

    Hogeweg, Paulien

    The signature feature of Cellular Automata is the realization that "simple rules can give rise to complex behavior". In particular how fixed "rock-bottom" simple rules can give rise to multiple levels of organization. Here we describe Multilevel Cellular Automata, in which the microscopic entities (states) and their transition rules themselves are adjusted by the mesoscale patterns that they themselves generate. Thus we study the feedback of higher levels of organization on the lower levels. Such an approach is preeminently important for studying bioinformatic systems. We will here focus on an evolutionary approach to formalize such Multilevel Cellular Automata, and review examples of studies that use them.

  2. The Austronesian Basic Vocabulary Database: From Bioinformatics to Lexomics

    Science.gov (United States)

    Greenhill, Simon J.; Blust, Robert; Gray, Russell D.

    2008-01-01

    Phylogenetic methods have revolutionised evolutionary biology and have recently been applied to studies of linguistic and cultural evolution. However, the basic comparative data on the languages of the world required for these analyses is often widely dispersed in hard to obtain sources. Here we outline how our Austronesian Basic Vocabulary Database (ABVD) helps remedy this situation by collating wordlists from over 500 languages into one web-accessible database. We describe the technology underlying the ABVD and discuss the benefits that an evolutionary bioinformatic approach can provide. These include facilitating computational comparative linguistic research, answering questions about human prehistory, enabling syntheses with genetic data, and safe-guarding fragile linguistic information. PMID:19204825

  3. Bpipe: a tool for running and managing bioinformatics pipelines.

    Science.gov (United States)

    Sadedin, Simon P; Pope, Bernard; Oshlack, Alicia

    2012-06-01

    Bpipe is a simple, dedicated programming language for defining and executing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, Bpipe is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments. Bpipe is freely available from http://bpipe.org under a BSD License.

  4. European Higher Health Care Education Curriculum

    DEFF Research Database (Denmark)

    Koskinen, Liisa; Kelly, Hélène; Bergknut, Eva

    2012-01-01

    Education in Health and Rehabilitation, whose goal is to nurture educational development and networking among member institutions. The framework is the result of a collaborative endeavor by nine nurse educators from five different European countries. The production of the framework will be described......This article concerns the European Curriculum in Cultural Care Project (2005-2009), which aimed at developing a curriculum framework for the enhancement of cultural competence in European health care education. The project was initiated and supported by the Consortium of Institutes in Higher...

  5. Ludvig, Zsuzsa (ed.) Eurasian challenges : partnerships with Russia and other issues of the post-Soviet area. East European Studies, No. 4, Budabest Institute of World Economics and Regional Studies, Hungarian Academy of Sciences, 2013, 163pp. / Csab

    Index Scriptorium Estoniae

    Weiner, Csaba

    2013-01-01

    Arvustus: Ludvig, Zsuzsa (ed.) Eurasian challenges : partnerships with Russia and other issues of the post-Soviet area. Budabest Institute of World Economics and Regional Studies, Hungarian Academy of Sciences, 2013

  6. The institutional functioning of the EU

    NARCIS (Netherlands)

    van der Mei, A.P.; Vos, E.I.L.

    2011-01-01

    This book contains selected papers that were first presented at a Student Conference on 9 December 2010. This conference was convened in the context of the course "EU Law Foundations - The Institutional Functioning of the European Union", which is part of the Bachelor Programme European Law School

  7. Bioinformatics, interaction network analysis, and neural networks to characterize gene expression of radicular cyst and periapical granuloma.

    Science.gov (United States)

    Poswar, Fabiano de Oliveira; Farias, Lucyana Conceição; Fraga, Carlos Alberto de Carvalho; Bambirra, Wilson; Brito-Júnior, Manoel; Sousa-Neto, Manoel Damião; Santos, Sérgio Henrique Souza; de Paula, Alfredo Maurício Batista; D'Angelo, Marcos Flávio Silveira Vasconcelos; Guimarães, André Luiz Sena

    2015-06-01

    Bioinformatics has emerged as an important tool to analyze the large amount of data generated by research in different diseases. In this study, gene expression for radicular cysts (RCs) and periapical granulomas (PGs) was characterized based on a leader gene approach. A validated bioinformatics algorithm was applied to identify leader genes for RCs and PGs. Genes related to RCs and PGs were first identified in PubMed, GenBank, GeneAtlas, and GeneCards databases. The Web-available STRING software (The European Molecular Biology Laboratory [EMBL], Heidelberg, Baden-Württemberg, Germany) was used in order to build the interaction map among the identified genes by a significance score named weighted number of links. Based on the weighted number of links, genes were clustered using k-means. The genes in the highest cluster were considered leader genes. Multilayer perceptron neural network analysis was used as a complementary supplement for gene classification. For RCs, the suggested leader genes were TP53 and EP300, whereas PGs were associated with IL2RG, CCL2, CCL4, CCL5, CCR1, CCR3, and CCR5 genes. Our data revealed different gene expression for RCs and PGs, suggesting that not only the inflammatory nature but also other biological processes might differentiate RCs and PGs. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  8. Bioinformatics Methods and Tools to Advance Clinical Care. Findings from the Yearbook 2015 Section on Bioinformatics and Translational Informatics.

    Science.gov (United States)

    Soualmia, L F; Lecroq, T

    2015-08-13

    To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. The selection and evaluation process of this Yearbook's section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and

  9. INTERNATIONAL AND EUROPEAN LAW PRINCIPLES

    Directory of Open Access Journals (Sweden)

    Dumitriţa FLOREA

    2016-06-01

    Full Text Available We live nowadays a posteriori establishment through institutional treaties and a well-built jurisprudence that set up some of the general treaties. The structure of the European Union as well as the particular nature of the community legal order led to the establishment of some general principles, such as the principle of the institutional balance, the principle of solidarity between member states, the principle of primacy, the principle of the immediate and direct effect of the European law. It is certain that the legal order of the community law has its basis in the legal order of the International public law from which it has continuously delineated. The European communities, as subjects of the International public law are obliged to comply with the general International law, its fundamental principles and its bases, leading to some obligations capable to produce effects in the community legal order. The Court Of Justice of the European Union established as principles applicable in the European law the principles of the International public law, especially when it was called to assert regarding the International relationships of the Community as well as those of the 28 member states, confirming in the matter of the applicability of the treaties, the pacta sunt servanda rule, the principle of the good faith, the legitimate faith or the rebus sic standibus exception, all of them belonging to the custom International law.

  10. The European Union's Eastward Enlargement

    Directory of Open Access Journals (Sweden)

    Hanns-D. Jacobsen

    1997-08-01

    Full Text Available In July 1997 the Commission of the European Union presented its Agenda 2000. This document not only suggested to start accession talks with some East and Central European countries (CEEC in early 1998 but it also provided proposals for a restructuring of EU expenditures. On this background this contribution discusses the state of readiness of the Central and East European countries to become EU members over the next few years and the Union's capacity to absorb up to ten CEEC over the next decade or so. This study concludes that the European Union has become an anchor of stability to the CEEC that guarantees both democracy and economic security--much more than could be expected only a couple of years ago. The Union's readiness to accept the membership of CEEC has, in a decisive way, contributed to their societal, political and economic stabilization. There is almost a contest among the CEEC on which one is going to meet the accession criteria first and best. The enlargement process, however, is connected to problems the resolution of which realistically postpone its successful conclusion at least into the year 2005. The main reasons are (1 the welfare gap between the EU area and the CEEC, (2 the need for more institutional and economic changes in the CEEC to make them ready for acces-sion, and, most importantly, (3 the necessity for the European Union to prepare herself for accession by a comprehensive financial reform and fundamental institutional changes.

  11. Teaching Bioinformatics and Neuroinformatics by Using Free Web-based Tools

    OpenAIRE

    Grisham, William; Schottler, Natalie A.; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson

    2010-01-01

    This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with anatomy (Mouse Brain Library), quantitative trait locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of Cal...

  12. Bioinformatic prediction and functional characterization of human KIAA0100 gene

    Directory of Open Access Journals (Sweden)

    He Cui

    2017-02-01

    Full Text Available Our previous study demonstrated that human KIAA0100 gene was a novel acute monocytic leukemia-associated antigen (MLAA gene. But the functional characterization of human KIAA0100 gene has remained unknown to date. Here, firstly, bioinformatic prediction of human KIAA0100 gene was carried out using online softwares; Secondly, Human KIAA0100 gene expression was downregulated by the clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated (Cas 9 system in U937 cells. Cell proliferation and apoptosis were next evaluated in KIAA0100-knockdown U937 cells. The bioinformatic prediction showed that human KIAA0100 gene was located on 17q11.2, and human KIAA0100 protein was located in the secretory pathway. Besides, human KIAA0100 protein contained a signalpeptide, a transmembrane region, three types of secondary structures (alpha helix, extended strand, and random coil , and four domains from mitochondrial protein 27 (FMP27. The observation on functional characterization of human KIAA0100 gene revealed that its downregulation inhibited cell proliferation, and promoted cell apoptosis in U937 cells. To summarize, these results suggest human KIAA0100 gene possibly comes within mitochondrial genome; moreover, it is a novel anti-apoptotic factor related to carcinogenesis or progression in acute monocytic leukemia, and may be a potential target for immunotherapy against acute monocytic leukemia.

  13. Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

    Science.gov (United States)

    Pauling, Josch; Klipp, Edda

    2016-12-22

    Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries. The computational biology and bioinformatics community has so far established methodology in genomics, transcriptomics and proteomics but there are many (combinatorial) challenges when it comes to structural diversity of lipids and their identification, quantification and interpretation. This review gives an overview and outlook on lipidomics research and illustrates ongoing computational and bioinformatics efforts. These efforts are important and necessary steps to advance the lipidomics field alongside analytic, biochemistry, biomedical and biology communities and to close the gap in available computational methodology between lipidomics and other omics sub-branches.

  14. jORCA: easily integrating bioinformatics Web Services.

    Science.gov (United States)

    Martín-Requena, Victoria; Ríos, Javier; García, Maximiliano; Ramírez, Sergio; Trelles, Oswaldo

    2010-02-15

    Web services technology is becoming the option of choice to deploy bioinformatics tools that are universally available. One of the major strengths of this approach is that it supports machine-to-machine interoperability over a network. However, a weakness of this approach is that various Web Services differ in their definition and invocation protocols, as well as their communication and data formats-and this presents a barrier to service interoperability. jORCA is a desktop client aimed at facilitating seamless integration of Web Services. It does so by making a uniform representation of the different web resources, supporting scalable service discovery, and automatic composition of workflows. Usability is at the top of the jORCA agenda; thus it is a highly customizable and extensible application that accommodates a broad range of user skills featuring double-click invocation of services in conjunction with advanced execution-control, on the fly data standardization, extensibility of viewer plug-ins, drag-and-drop editing capabilities, plus a file-based browsing style and organization of favourite tools. The integration of bioinformatics Web Services is made easier to support a wider range of users. .

  15. MAPI: towards the integrated exploitation of bioinformatics Web Services.

    Science.gov (United States)

    Ramirez, Sergio; Karlsson, Johan; Trelles, Oswaldo

    2011-10-27

    Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

  16. A review of bioinformatic methods for forensic DNA analyses.

    Science.gov (United States)

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Overview of Bioinformatics and its Application to Oral Genomics

    Directory of Open Access Journals (Sweden)

    Arvind Shetti

    2007-01-01

    Full Text Available The "informatics revolution" in both bioinformatics and dental informatics will eventually change the way we practice dentistry. This convergence will play a pivotal role in creating a bridge of opportunity by integrating scientific and clinical specialties to promote the advances in treatment, risk assessment, diagnosis, therapeutics, and oral health-care outcome. Bioinformatics has been an emerging field in the biomedical research community and has been gaining momentum in dental medicine. This area has created a steady stream of large and complex genomic data, which has transformed the way a clinical or basic science researcher approaches genomic research. This application to dental medicine, termed "oral genomics", can aid in the molecular understanding of the genes and proteins, their interactions, pathways, and networks that are responsible for the development and progression of oral diseases and disorders. As the result of the Human Genome Project, new advances have prompted Nigh-throughput technologies, such as DNA microarrays, which have become accepted tools in the biomedical research community. This manuscript reviews the two most commonly used microarray technologies, basic microarray data analysis, and the results from several ongoing oral cancer genomic studies.

  18. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Fabrizio Fierro

    2017-09-01

    Full Text Available Human G-protein coupled receptors (hGPCRs constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.

  19. MAPI: towards the integrated exploitation of bioinformatics Web Services

    Directory of Open Access Journals (Sweden)

    Karlsson Johan

    2011-10-01

    Full Text Available Abstract Background Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. Results To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. Conclusions The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others.

  20. European Identity between Ethnic and Civic Identities

    Directory of Open Access Journals (Sweden)

    Paul Kun

    2015-11-01

    Full Text Available The European identity is not a reality, but a necessity for a stabile future of the European political construction. The democratic deficit problem results from the fact that the European project was conceived as a top-down type of action. Its legitimization is however a bottom-up process. For this reason, the institutional project needs to be supported by an ideological project for a European identity. There are two ways, two different patterns for the second charge: the ethnic-cultural identity or the civic identity. Each has his advantages, but also disadvantages. This paper analyzes the results of one sociological research among young Romanian students.

  1. Experimentation and Bricolage on Institutions

    DEFF Research Database (Denmark)

    Cartel, Melodie; Boxenbaum, Eva; Aggeri, Franck

    This paper examines how innovative institutional arrangements are generated during processes of institutional bricolage. The aim of the paper is to highlight how an arrangement is selected among the others when many alternatives exist or are imaginable. To address this question, we present...... a qualitative study of institutional bricolage in the context of the making of the European carbon market. We suggest that, during episodes of experimental bricolage, alternative arrangements may be tested and evaluated inside experimental spaces named platforms. We identify three selection mechanisms...

  2. Institute annual report 2004

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    The mission of the ITU (Institute for Transuranium Elements) is to protect the European citizen against risk associated with the handling and storage of highly radioactive elements. The JRC (Joint Research Center) provide customer-driven scientific and technical support for the conception, development, implementation and monitoring of EU policies. In this framework this annual report presents the TU actions in: basic actinide research, spent fuel characterization, safety of nuclear fuels, partitioning and transmutation, alpha-immunotherapy/radiobiology, measurement of radioactivity in the environment, safeguards research and development. (A.L.B.)

  3. Institutions and Modernity

    Directory of Open Access Journals (Sweden)

    Witold Morawski

    2013-09-01

    Full Text Available Purpose: Modernity consists of many confl icting aspects: It brings many empty promises, yet has resulted in new institutions that create bridges between the values and interests of millions of people who seek freedom, prosperity, quality of life, strengthened democracy and social justice. In this paper I attempt to a gain and loss account against modernity, because institutional rules are not only conducive to cooperative interactions, but to hostile interactions as well. People are not always guided by moral commitment, but rather more often driven by cold calculation or coercion.Methodology: Modernity has at least three defi nitions. The fi rst defi nition is based on ideas that took over the imagination of the era. The second defi nition is based on an analysis of the behavior of people who respond to reason as well as emotion and believe that they act more rationally than their ancestors or the traditional “others”. The third defi nition is the one closest to my heart, consisting of the use of institutional categories. Institutions offer practical ways of connecting ideas and people. The challenge for them is the result of deepening local and national interdependencies, but increasingly often also regional (e.g. European and global. Interdependencies are the result of the scientifi c and technological revolution, global markets, global governance mechanisms, the emergence of new social forces and cultural confl icts (against the background of reconciling identity and differences.Conclusions: The most important task is to identify the mechanisms of complex systems so that people know how to act under conditions of uncertainty, risk and crisis. Hence, the expectations toward institutions often exceed their abilities. Even though new institutions are being created and old ones are being fixed, we are witnessing and participating in, institutional paralysis and the decay (e.g. corruption. In this situation, it is imperative not only to

  4. Institutional actorhood

    DEFF Research Database (Denmark)

    Madsen, Christian Uhrenholdt

    In this paper I describe the changing role of intra-organizational experts in the face of institutional complexity of their field. I do this through a qualitative investigation of the institutional and organizational roles of actors in Danish organizations who are responsible for the efforts...... to comply with the Danish work environment regulation. And by doing so I also describe how institutional complexity and organizational responses to this complexity are particular important for the changing modes of governance that characterizes contemporary welfare states....

  5. INSTITUTIONAL CHANGES IN EMERGING EUROPE

    Directory of Open Access Journals (Sweden)

    Oana Georgiana AMARANDEI

    2015-08-01

    Full Text Available The recent global economic crisis has created new conditions and situations for the economic environment and therefore, in this context the rethinking of the institutional system is mandatory. The present paper seeks to propose an empirical model and aims at capturing the interdependencies between the institutional changes and the economic progress in the European emerging countries, in order to emphasize that institutions are the key elements in the process of economic growth. After briefly reviewing the most relevant literatures that have documented the variety of the institutional changes, the paper focuses on the amplitude of the phenomena of institutional changes from the  European emerging countries. The research tries to establish a “stimulus – effect” relationship between the changing of the institutional environment and the rate of economic growth and human development. The conclusions for the methodological aspects illustrate that the level of social and economic development is a natural result of the quality of the institutional environment.

  6. Do labour market institutions matter?

    DEFF Research Database (Denmark)

    Geishecker, Ingo; Görg, Holger; Munch, Jakob Roland

    2010-01-01

    This paper studies the impact of outsourcing on individual wages in three European countries with markedly different labour market institutions: Germany, the UK and Denmark. To do so we use individual-level data sets for the three countries and construct comparable measures of outsourcing...... at the industry level, distinguishing outsourcing by broad region. We discuss some possible intuitive reasons for why there may be differences in the impact of outsourcing across the three countries, based on labour market institutions. This paper studies the impact of outsourcing on individual wages in three...... European countries with markedly different labour market institutions: Germany, the UK and Denmark. To do so we use individual-level data sets for the three countries and construct comparable measures of outsourcing at the industry level, distinguishing outsourcing by broad region. We discuss some possible...

  7. Institutional Controls

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of institutional control data from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different...

  8. Institutional upbringing

    DEFF Research Database (Denmark)

    Gulløv, Eva

    2008-01-01

    current testing of Danish language fluency levels among pre-school minority children. Testing language skills marks and defines distinctions that reinforce images of deviance that, in turn, legitimize initiatives to enrol children, specifically minority children, in child care institutions....

  9. Institutional ethnography

    DEFF Research Database (Denmark)

    Lund, Rebecca; Tienari, Janne

    2016-01-01

    of managerial respondents. This leads to another bias in the study of M&As: an managerial one. These critiques are an important step in pinpointing some of the problematic aspects in the field, which we suggest can be part remedied by institutional ethnography developed by Dorothy Smith and her colleagues....... In institutional ethnography the notion of objectification is applied to describe research processes like those that have been found to dominate in scholarly work on M&As. In this chapter, we offer an outline of Smiths critique of objectification, elucidate how institutional ethnography seeks to address it......, and point to some of the problems in M&A studies identified through this lens. Finally, we argue why institutional ethnography, in comparison with other methods of inquiry, is particularly fruitful in the study of mergers and acquisitions....

  10. The Europeanization of Welfare - The Domestic Impact of Intra-European Social Security

    DEFF Research Database (Denmark)

    Martinsen, Dorte Sindbjerg

    2005-01-01

    processes of change that thus condition impact. This article examines the impact of European social security integration on national welfare institutions in Denmark and Germany, and it traces the Europeanization process, which may explain the diverging impact of a common input in these two Member States...

  11. Drug use among adolescents within vocational schools: health promotion, social relations and institutional organization. Abstract. 13th Biennial Conference of the European Association for Research on Adolescence, Island of Spetses, Greece. 29 August – 1 September 2012 (p. 60)

    DEFF Research Database (Denmark)

    Ingholt, Liselotte; Sørensen, Betina Bang; Axel, Erik

    Druguse among Adolescents within Vocational Schools: Health Promotion, Social Relations and Institutional Organization. L. Ingholt1, B.B. Sørensen1, E. Axel2, V.A. Frank3 1 National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark. 2 The Department of Psychology....... Results: Learning in vocational education is part of how young people develop and coordinate their trajectory of everyday social life. Additionally drug use may become important in the process of forming peer relations. For some students, the focus is drifting from vocational to social interactions...

  12. The European Union Response to Regional Conflicts

    Science.gov (United States)

    2013-03-01

    into force of the Lisbon Treaty. (Cuadernos de Estrategia , 145-B. Spanish Institute for Strategic Studies, 2010), 18. 4 Felix Arteaga, The European...Security and Defense Policy after the entry into force of the Lisbon Treaty. (Cuadernos de Estrategia , 145-B. Spanish Institute for Strategic...Lisbon Treaty. (Cuadernos de Estrategia , 145-B. Spanish Institute for Strategic Studies. 2010), 37. 15 ENP regulates the EU’s relations with countries

  13. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN.

    Science.gov (United States)

    He, Yongqun; Xiang, Zuoshuang

    2010-09-27

    Brucella spp. are Gram-negative, facultative intracellular bacteria that cause brucellosis, one of the commonest zoonotic diseases found worldwide in humans and a variety of animal species. While several animal vaccines are available, there is no effective and safe vaccine for prevention of brucellosis in humans. VIOLIN (http://www.violinet.org) is a web-based vaccine database and analysis system that curates, stores, and analyzes published data of commercialized vaccines, and vaccines in clinical trials or in research. VIOLIN contains information for 454 vaccines or vaccine candidates for 73 pathogens. VIOLIN also contains many bioinformatics tools for vaccine data analysis, data integration, and vaccine target prediction. To demonstrate the applicability of VIOLIN for vaccine research, VIOLIN was used for bioinformatics analysis of existing Brucella vaccines and prediction of new Brucella vaccine targets. VIOLIN contains many literature mining programs (e.g., Vaxmesh) that provide in-depth analysis of Brucella vaccine literature. As a result of manual literature curation, VIOLIN contains information for 38 Brucella vaccines or vaccine candidates, 14 protective Brucella antigens, and 68 host response studies to Brucella vaccines from 97 peer-reviewed articles. These Brucella vaccines are classified in the Vaccine Ontology (VO) system and used for different ontological applications. The web-based VIOLIN vaccine target prediction program Vaxign was used to predict new Brucella vaccine targets. Vaxign identified 14 outer membrane proteins that are conserved in six virulent strains from B. abortus, B. melitensis, and B. suis that are pathogenic in humans. Of the 14 membrane proteins, two proteins (Omp2b and Omp31-1) are not present in B. ovis, a Brucella species that is not pathogenic in humans. Brucella vaccine data stored in VIOLIN were compared and analyzed using the VIOLIN query system. Bioinformatics curation and ontological representation of Brucella vaccines

  14. Atlas – a data warehouse for integrative bioinformatics

    Directory of Open Access Journals (Sweden)

    Yuen Macaire MS

    2005-02-01

    Full Text Available Abstract Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL calls that are implemented in a set of Application Programming Interfaces (APIs. The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD, Biomolecular Interaction Network Database (BIND, Database of Interacting Proteins (DIP, Molecular Interactions Database (MINT, IntAct, NCBI Taxonomy, Gene Ontology (GO, Online Mendelian Inheritance in Man (OMIM, LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First

  15. Bioinformatics Methods and Tools to Advance Clinical Care

    Science.gov (United States)

    Lecroq, T.

    2015-01-01

    Summary Objectives To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. Method We provide a synopsis of the articles selected for the IMIA Yearbook 2015, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor has evaluated separately the set of 1,594 articles and the evaluation results were merged for retaining 15 articles for peer-review. Results The selection and evaluation process of this Yearbook’s section on Bioinformatics and Translational Informatics yielded four excellent articles regarding data management and genome medicine that are mainly tool-based papers. In the first article, the authors present PPISURV a tool for uncovering the role of specific genes in cancer survival outcome. The second article describes the classifier PredictSNP which combines six performing tools for predicting disease-related mutations. In the third article, by presenting a high-coverage map of the human proteome using high resolution mass spectrometry, the authors highlight the need for using mass spectrometry to complement genome annotation. The fourth article is also related to patient survival and decision support. The authors present datamining methods of large-scale datasets of past transplants. The objective is to identify chances of survival. Conclusions The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on dedicated tools and methods to advance clinical care. Indeed, there is a need for powerful tools for managing and interpreting complex, large-scale genomic and biological datasets, but also a need for user-friendly tools developed for the clinicians in their

  16. Adherence to the World Cancer Research Fund/American Institute for Cancer Research guidelines and risk of death in Europe: results from the European Prospective Investigation into Nutrition and Cancer cohort study1,4

    NARCIS (Netherlands)

    Vergnaud, A.C.; Romaguera, D.; Peeters, P.H.M.; Gils, C.H. van; Chan, D.S.; Romieu, I.; Freisling, H.; Ferrari, P.; Clavel-Chapelon, F.; Fagherazzi, G.; Dartois, L.; Li, K.; Tikk, K.; Bergmann, M.M.; Boeing, H.; Tjonneland, A.; Olsen, A.; Overvad, K.; Dahm, C.C.; Redondo, M.L.; Agudo, A.; Sanchez, M.J.; Amiano, P.; Chirlaque, M.D.; Ardanaz, E.; Khaw, K.T.; Wareham, N.J.; Crowe, F.; Trichopoulou, A.; Orfanos, P.; Trichopoulos, D.; Masala, G.; Sieri, S.; Tumino, R.; Vineis, P.; Panico, S.; Bueno-De-Mesquita, H.B.; Ros, M.M.; May, A.; Wirfalt, E.; Sonestedt, E.; Johansson, I.; Hallmans, G.; Lund, E.; Weiderpass, E.; Parr, C.L.; Riboli, E.; Norat, T.

    2013-01-01

    BACKGROUND: In 2007, the World Cancer Research Fund (WCRF) and the American Institute for Cancer Research (AICR) issued recommendations on diet, physical activity, and weight management for cancer prevention on the basis of the most comprehensive collection of available evidence. OBJECTIVE: We

  17. Bioinformatics in the secondary science classroom: A study of state content standards and students' perceptions of, and performance in, bioinformatics lessons

    Science.gov (United States)

    Wefer, Stephen H.

    The proliferation of bioinformatics in modern Biology marks a new revolution in science, which promises to influence science education at all levels. This thesis examined state standards for content that articulated bioinformatics, and explored secondary students' affective and cognitive perceptions of, and performance in, a bioinformatics mini-unit. The results are presented as three studies. The first study analyzed secondary science standards of 49 U.S States (Iowa has no science framework) and the District of Columbia for content related to bioinformatics at the introductory high school biology level. The bionformatics content of each state's Biology standards were categorized into nine areas and the prevalence of each area documented. The nine areas were: The Human Genome Project, Forensics, Evolution, Classification, Nucleotide Variations, Medicine, Computer Use, Agriculture/Food Technology, and Science Technology and Society/Socioscientific Issues (STS/SSI). Findings indicated a generally low representation of bioinformatics related content, which varied substantially across the different areas. Recommendations are made for reworking existing standards to incorporate bioinformatics and to facilitate the goal of promoting science literacy in this emerging new field among secondary school students. The second study examined thirty-two students' affective responses to, and content mastery of, a two-week bioinformatics mini-unit. The findings indicate that the students generally were positive relative to their interest level, the usefulness of the lessons, the difficulty level of the lessons, likeliness to engage in additional bioinformatics, and were overall successful on the assessments. A discussion of the results and significance is followed by suggestions for future research and implementation for transferability. The third study presents a case study of individual differences among ten secondary school students, whose cognitive and affective percepts were

  18. Towards a Sociology of Intermediary Institutions

    DEFF Research Database (Denmark)

    Kjær, Poul F.

    2014-01-01

    The central ambition of this chapter is to develop dimensions of a theoretical and conceptual framework for the study of intermediary institutions, such as corporatist, neo-corporatist and governance institutions, in the European context. As such, it is designed to create a framework that is capa...

  19. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal

    2012-07-28

    Sequence alignment algorithms such as the Smith-Waterman algorithm are among the most important applications in the development of bioinformatics. Sequence alignment algorithms must process large amounts of data which may take a long time. Here, we introduce our Adaptive Hybrid Multiprocessor technique to accelerate the implementation of the Smith-Waterman algorithm. Our technique utilizes both the graphics processing unit (GPU) and the central processing unit (CPU). It adapts to the implementation according to the number of CPUs given as input by efficiently distributing the workload between the processing units. Using existing resources (GPU and CPU) in an efficient way is a novel approach. The peak performance achieved for the platforms GPU + CPU, GPU + 2CPUs, and GPU + 3CPUs is 10.4 GCUPS, 13.7 GCUPS, and 18.6 GCUPS, respectively (with the query length of 511 amino acid). © 2010 IEEE.

  20. iPTMnet: Integrative Bioinformatics for Studying PTM Networks.

    Science.gov (United States)

    Ross, Karen E; Huang, Hongzhan; Ren, Jia; Arighi, Cecilia N; Li, Gang; Tudor, Catalina O; Lv, Mengxi; Lee, Jung-Youn; Chen, Sheng-Chih; Vijay-Shanker, K; Wu, Cathy H

    2017-01-01

    Protein post-translational modification (PTM) is an essential cellular regulatory mechanism, and disruptions in PTM have been implicated in disease. PTMs are an active area of study in many fields, leading to a wealth of PTM information in the scientific literature. There is a need for user-friendly bioinformatics resources that capture PTM information from the literature and support analyses of PTMs and their functional consequences. This chapter describes the use of iPTMnet ( http://proteininformationresource.org/iPTMnet/ ), a resource that integrates PTM information from text mining, curated databases, and ontologies and provides visualization tools for exploring PTM networks, PTM crosstalk, and PTM conservation across species. We present several PTM-related queries and demonstrate how they can be addressed using iPTMnet.