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. 5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

    Science.gov (United States)

    Stephan, Christian; Hamacher, Michael; Blüggel, Martin; Körting, Gerhard; Chamrad, Daniel; Scheer, Christian; Marcus, Katrin; Reidegeld, Kai A; Lohaus, Christiane; Schäfer, Heike; Martens, Lennart; Jones, Philip; Müller, Michael; Auyeung, Kevin; Taylor, Chris; Binz, Pierre-Alain; Thiele, Herbert; Parkinson, David; Meyer, Helmut E; Apweiler, Rolf

    2005-09-01

    The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

  3. 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...

  4. 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

  5. Virginia Bioinformatics Institute to expand cyberinfrastructure education and outreach project

    OpenAIRE

    Whyte, Barry James

    2008-01-01

    The National Science Foundation has awarded the Virginia Bioinformatics Institute at Virginia Tech $918,000 to expand its education and outreach program in Cyberinfrastructure - Training, Education, Advancement and Mentoring, commonly known as the CI-TEAM.

  6. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

    Science.gov (United States)

    Ibrahim, Bashar; Arkhipova, Ksenia; Andeweg, Arno C; Posada-Céspedes, Susana; Enault, François; Gruber, Arthur; Koonin, Eugene V; Kupczok, Anne; Lemey, Philippe; McHardy, Alice C; McMahon, Dino P; Pickett, Brett E; Robertson, David L; Scheuermann, Richard H; Zhernakova, Alexandra; Zwart, Mark P; Schönhuth, Alexander; Dutilh, Bas E; Marz, Manja

    2018-05-14

    The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.

  7. 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…

  8. 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...

  9. The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

    OpenAIRE

    Bultet, Lisandra Aguilar; Aguilar Rodriguez, Jose; Ahrens, Christian H; Ahrne, Erik Lennart; Ai, Ni; Aimo, Lucila; Akalin, Altuna; Aleksiev, Tyanko; Alocci, Davide; Altenhoff, Adrian; Alves, Isabel; Ambrosini, Giovanna; Pedone, Pascale Anderle; Angelina, Paolo; Anisimova, Maria

    2016-01-01

    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB'...

  10. 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.

  11. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

    Science.gov (United States)

    Boutselakis, H; Dimitropoulos, D; Fillon, J; Golovin, A; Henrick, K; Hussain, A; Ionides, J; John, M; Keller, P A; Krissinel, E; McNeil, P; Naim, A; Newman, R; Oldfield, T; Pineda, J; Rachedi, A; Copeland, J; Sitnov, A; Sobhany, S; Suarez-Uruena, A; Swaminathan, J; Tagari, M; Tate, J; Tromm, S; Velankar, S; Vranken, W

    2003-01-01

    The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

  12. FINANCING CULTURE INSTITUTIONS IN EUROPEAN CONTEXT

    Directory of Open Access Journals (Sweden)

    Cezar Corneliu MANDA

    2017-05-01

    Full Text Available The paper, on the coordinates of the analysis of the problematic of financing culture institutions within the European Union member states, performs a comparative analysis focused on the financing mechanism available to the cultural sector, created both at the level of the public, and of the private sector. For the comparative analysis, the paper selected several EU member states, grouped on four geographical areas (North, South, East and Center. The analysis performed in the paper emphasized that most EU member states make significant efforts to finance the cultural sector, but the effects of the economic crisis have had a negative impact on this financing, causing, from this perspective, a gap between the states in the north and center of the EU, on the one hand, and the states in the south and east of the EU, on the other hand and outlining a cultural Europe with two peripheries.

  13. European Institutional and Organisational Tools for Maritime Human Resources Development

    OpenAIRE

    Dragomir Cristina

    2012-01-01

    Seafarers need to continuously develop their career, at all stages of their professional life. This paper presents some tools of institutional and organisational career development. At insitutional level there are presented vocational education and training tools provided by the European Union institutions while at organisational level are exemplified some tools used by private crewing companies for maritime human resources assessment and development.

  14. 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.

  15. 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.

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

    Science.gov (United States)

    Lenz, Tobias; Burilkov, Alexandr

    2017-09-01

    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.

  17. Institutions in European and Asian energy markets: A methodological overview

    International Nuclear Information System (INIS)

    Aalto, Pami

    2014-01-01

    This article introduces a methodological framework to study institutions in European and Asian energy markets with a comparative case study on the EU and east Asia. A distinction is made between informal and three types of formal institutions; and their transaction cost reducing, order creating and ecological/climatic functions. The operation of energy markets is explained through the structure of institutions, their types and functions. It is found that order-creating institutions guarantee enough stability, (mutual) trust and solidarity among EU Member States to support the competitive markets institution and supranational formal institutions as the underpinnings of trade in the internal energy market, which nevertheless retains some corporatist features. In the east Asian markets the nature of order-creating institutions sovereignty, energy diplomacy and great power management prevents the emergence of supranational formal institutions and a shared idea of trade. The prevailing structure has a large number of sub-regional organisations with overlapping tasks and few powers. In both markets the functions of institutions signify more than their number; transaction cost reducing institutions are dependent on order-creating institutions, while both of these functions are better realised on the regional level than ecological/climatic functions; ultimately informal institutions are most influential. - Highlights: • Institutions include informal types and three formal types. • The functions of institutions relate to transaction costs, order and ecology. • Transaction cost reduction depends on order creating institutions. • Ecological functions are the most difficult to realise regionally. • Informal institutions are most influential in the EU and east Asian markets

  18. INSTITUTIONAL MANAGEMENT OF EUROPEAN STATISTICS AND OF THEIR QUALITY - CURRENT CONCERNS AT EUROPEAN LEVEL

    Directory of Open Access Journals (Sweden)

    Daniela ŞTEFĂNESCU

    2011-08-01

    Full Text Available The issues referring to official statistics quality and reliability became the main topics of debates as far as statistical governance in Europe is concerned. The Council welcomed the Commission Communication to the European Parliament and to the Council « Towards robust quality management for European Statistics » (COM 211, appreciating that the approach and the objective of the strategy would confer the European Statistical System (ESS the quality management framework for the coordination of consolidated economic policies. The Council pointed out that the European Statistical System management was improved during recent years, that progress was noticed in relation with high quality statistics production and dissemination within the European Union, but has also noticed that, in the context of recent financial crisis, certain weaknesses were identified, particularly related to quality management general framework.„Greece Case” proved that progresses were not enough for guaranteeing the complete independence of national statistical institutes and entailed the need for further consolidating ESS governance. Several undertakings are now in the preparatory stage, in accordance with the Commission Communication; these actions are welcomed, but the question arise: are these sufficient for definitively solving the problem?The paper aims to go ahead in the attempt of identifying a different way, innovative (courageous! on the long run, towards an advanced institutional structure of ESS, by setting up the European System of Statistical Institutes, similar to the European System of Central Banks, that would require a change in the Treaty.

  19. New institutional analysis of European electric power reforms

    International Nuclear Information System (INIS)

    Perez, Yannick

    2002-01-01

    This research thesis reports a comparative analysis of reforms of the electric power sector implemented in European countries. In the first part, the authors proposes a presentation of the theoretical framework adopted for this analysis which is notably based on the New Institutional Economy approach. He also proposes an approach to the electric power industry based on the Transaction Cost Theory, and presents an overview of the various European reforms in the field of electricity, and of still unresolved problems which emerged after the creation of different power markets. The next part addresses an assessment of the attractive and desirable characters of reforms which have been implemented in the United Kingdom, in Germany and in Spain, with an attempt to identify winners and losers, and to classify these reforms. In the third part, the author defines a framework for the analysis of the feasibility of reforms which combine institutional and industrial dimensions, notably by reference to Noll and Williamson works. In the last part, the author sheds a new light on the concept of credibility. He introduces the conventional arbitrage of the Transaction Cost Theory between commitment stability and flexibility to generate uncertainty. He notably shows that the main problem in centralised institutional environments, is to guarantee the stability of commitments in front of opportunism, whereas in decentralised institutional environments, the main problem is to produce flexibility to manage uncertainty [fr

  20. 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.

  1. [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?

  2. The European Nuclear Safety Training and Tutoring Institute

    International Nuclear Information System (INIS)

    2012-01-01

    The European Nuclear Safety Training and Tutoring Institute, ENSTTI, is an initiative of European Technical Safety Organizations (TSO) in order to provide vocational training and tutoring in the methods and practices required to perform assessment in nuclear safety, nuclear security and radiation protection. ENSTTI calls on TSOs' expertise to maximize the transmission of safety and security knowledge, practical experience and culture. Training, tutoring and courses for specialists are achieved through practical lectures, working group and technical visits and lead to a certificate after knowledge testing. ENSTTI contributes to the harmonization of nuclear safety and security practices and to the networking of today and future nuclear safety experts in Europe and beyond. (A.C.)

  3. SOME CRITICAL ASPECTS CONCERNING THE INSTITUTIONAL SYSTEM OF EUROPEAN UNION

    Directory of Open Access Journals (Sweden)

    Timofte Claudia Simona

    2013-07-01

    Full Text Available In this paper we want to clarify and understand the decisional process in European which is related to the determination of the identity of the Union, answering to several questions concerning the implementation of the European Union into an organization, the different relations with other organizations and with the international law. In the family of the international organizations, the European Union has its own place because it realizes an economic integration project and a political one, a supranational but refusing the traditional categories of constitution and the international law. Qualifying as an international organization sui generis, EU developed a new legal order, deciding to create a supranational organization, formed by Member States and their citizens. The integration process is a permanent challenge opened to a new and developing process for solving all the internal and external problems of the EU. The States have an international "sensitivity" when the application of EU rules exceeds their obligations laid down in the Treaties to third countries and international organizations to which they have not exempted obligations. It was argued that the concept of "demos" or acting people is intrinsically linked to that of the nation-State. The issue of democratic deficit of the European Union is bound to four basic problems: the construction as a whole and therefore of the institutional system, under the principle of conferral, the Union shall act only within the limits that Member States have been conferred in the Treaties to attain the objectives that they set, The Treaty of Lisbon reinforces the legitimacy of the operation of the Union based on free and democratic will expressed by Member States. European construction is achieved through a democratic transfer of competences of the democratic States to a Commission subject to a weak democratic control, while the European Central Bank preserves absolute dominion over its monetary policy

  4. EUROPEAN INSTITUTIONS ON SOCIAL MEDIA ‒ SHAPING THE NOTION OF EUROPEAN CITIZENSHIP

    OpenAIRE

    Gaušis, E

    2017-01-01

    This study supports topical discussion about the possibilities to use social media as a tool for citizen involvement in democratic processes. Contemporary academic views and statistics on the use of social media for communication between institutions and citizens are gathered in the study. The research focus is on social media publications, analysing the content of four European Parliament`s social media accounts in Latvian during the period from 1 July 2015 to 31 December 2015. The aim of th...

  5. 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.

  6. Strategic Actions and Strategy Changes in European Universities: Clues from Institutional Evaluation Reports of the European University Association

    Science.gov (United States)

    Uslu, Baris

    2018-01-01

    This research examined strategic actions in European universities through the institutional evaluation reports of the EUA. EUA reports for 21 universities from seven European countries were included in the data set. Qualitative inquiry was carried out and six sub-sections in the reports were used as established themes. The findings were then…

  7. Professional Mobility and the Mutual Recognition of Qualifications in the European Union: Two Institutional Approaches.

    Science.gov (United States)

    Blitz, Brad K.

    1999-01-01

    Examines the role of transnational institutions (particularly the European Commission and committees of the European Parliament) in facilitating the mutual recognition of professional qualifications among members of the European Economic Community (EEC). Discusses relevant EEC directives, varying compliance among nations, and six cases of citizen…

  8. 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.

  9. The European Institute for Transuranium Elements (EURATOM) Karlsruhe

    International Nuclear Information System (INIS)

    1975-01-01

    The objectives of the Institute, its historical and geographical background, its structure, and its operation are described in the first part of this booklet. In the second part, a more detailed account of the scientific and technological work carried out at the Institute is given: fuel science and technology (mainly plutonium) and basic actinide research (mainly transplutonium elements)

  10. Defensive Stakeholder Management in European Universities: An Institutional Logics Perspective

    Science.gov (United States)

    Mampaey, Jelle; Huisman, Jeroen

    2016-01-01

    Earlier studies on stakeholder management in European universities focused on proactive strategies, that is, substantive organizational practices to establish and maintain mutually beneficial exchanges between universities and their stakeholders. We argue that the literature on stakeholder management has to be extended by theorizing defensive…

  11. European inter-institutional impact study of MammaPrint

    NARCIS (Netherlands)

    Cusumano, P. G.; Generali, D.; Ciruelos, E.; Manso, L.; Ghanem, I.; Lifrange, E.; Jerusalem, G.; Klaase, J.; de Snoo, F.; Stork-Sloots, L.; Dekker-Vroling, L.; Holzik, M. Lutke

    Aim: To measure the impact of MammaPrint on adjuvant treatment decisions and to analyze the agreement in treatment decisions between hospitals from 4 European countries for the same patient cohort. Methods: Breast cancer patients were prospectively enrolled and MammaPrint was assessed. Patients'

  12. The effects of institutional change in European soccer

    NARCIS (Netherlands)

    Haan, M.A.; Koning, R.H.; van Witteloostuijn, A.

    2012-01-01

    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

  13. 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

  14. 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…

  15. COMPARATIVE RESEARCH ON PROJECT MANAGEMENT APPROACH IN THE EUROPEAN EDUCATIONAL INSTITUTIONS

    OpenAIRE

    Armenia ANDRONICEANU; Bianca RISTEA

    2015-01-01

    Nowadays, project management is common for many areas and industries, including the educational sector. The international cooperation between educational institutions and the students’ international mobility are built on major projects and programs established through European and national institutions. The aim of this article is to review the best practices of project management implementation in public secondary education. The analysis is focused on three European countries: France, Spain a...

  16. 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.

  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. A Legal Institutional Perspective on the European External Action Service

    DEFF Research Database (Denmark)

    Van Vooren, Bart

    2011-01-01

    the EEAS be drawn into proceedings before the Court of Justice? In answering those questions, this article then examines to which extent the legal-institutional choices on the structure of the EU External Action Service reflects the age-old tension entrenched in EU external relations law: the EU’s nature...

  19. 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?

  20. SEVEN KEY INSTITUTIONS OF THE EUROPEAN UNION- VALIDATED BY THE LISBON TREATY

    Directory of Open Access Journals (Sweden)

    Elena\tIFTIME

    2015-06-01

    Full Text Available The seven institutions of the EU, which the title of this articles announces, structure the institutional basis of the Common European Home, considered to be the emblem of the most dynamic and complex, the most institutionalized and discussed (even controversial regional integration process. Building the Community Europe has began by the establishment of the Communities having 3 political institutions which represented in the evolution of the integration process, the triangle that ensured the coherence and the continuity of the Community actions: Council of Ministers, European Commission and the Assembly to which was added the Court and from 1974 the European Council as an indicative body. The five main institutions have formed the Community institutional system which over time had mainly guidance competences, of decision and direction (Council of Ministers, the Commission and the European Council or control skills ( the European Parliament and the Court of Justice. Since 1975, the institutional structure was strengthened through the creation of a Court of Auditors with general competences of checking accounts and discharge in Community activities. Maastricht Treaty 1992 (1993 raises this body to the rank of Community institution, without substantially altering its powers. The 6 Community institutions were supplemented by validating the status of Community institution of the ECB by the Lisbon Treaty 2007 (2009. ECB together with the national central banks of the Member States whose currency is the euro make up the Eurosystem. Through the Lisbon Treaty, the institutional structure was subjected to a process of improvement and strengthening of the EU which functions currently through the 7 institutions, interdependent, which are in a complementary relationship determined by the common goals which they pursue in Europe and in relations with other parts of the world.

  1. Trust in the institutions of the European Union: A cross-country examination

    OpenAIRE

    Eliyahu V. Sapir and Galina Zapryanova Christine Arnold

    2012-01-01

    Trust in political institutions is one of the key elements which make representative democracies work. Trust creates a connection between citizens and representative political institutions. Democratic governments which enjoy a large degree of trust also tend to have higher degrees of legitimacy and policy efficacy. In Europe’s multi-level governance structure, it is imperative to understand the determinants of trust in the institutions of the European Union. With the increasing salience of ...

  2. Institutional and Socio-Economic Convergence in the European Union

    Directory of Open Access Journals (Sweden)

    Jordi López-Tamayo

    2014-12-01

    Full Text Available The objective of this paper is to analyze convergence in institutional, social, and macroeconomic conditions between EU member states. Our analysis covers the period 1995-2013 and considers the potential impact of the Great Recession. With this aim, we use a composite indicator that combines information from 51 hard and soft indicators, and we estimate convergence equations for the composite indicator and its seven dimensions considering different country groups. The obtained results show evidence of conditional convergence among EU member states but limited evidence of unconditional convergence over the considered period.

  3. 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.

  4. Individual and Institutional Corruption in European and US Healthcare: Overview and Link of Various Corruption Typologies.

    Science.gov (United States)

    Sommersguter-Reichmann, Margit; Wild, Claudia; Stepan, Adolf; Reichmann, Gerhard; Fried, Andrea

    2018-06-01

    In recent years, the fight against healthcare corruption has intensified. Estimates from the European Healthcare Fraud and Corruption Network calculate an approximate €56 billion annual loss to Europe as a result of corruption. To promote understanding of the complexity and interconnection of corrupt activities, we aim to present healthcare-related corruption typologies of the European Union and European Healthcare Fraud and Corruption Network. We subsequently link them to the typology of individual and institutional corruption introduced by Dennis Thompson in the context of investigating misconduct of US Congressional members. According to Thompson, individual corruption is the personal gain of individuals performing duties within an institution in exchange for nurturing private interests, while institutional corruption pertains to the failure of the institution in directing the individual's behaviour towards the achievement of the institution's primary purpose because the institutional design promotes the pursuit of individual goals. Effective anti-corruption activities not only require the enactment of anti-corruption laws but also the monitoring and, where appropriate, revision of institutional frameworks to prevent the undermining of the primary purposes of health systems or institutions. To gain further understanding of the similarities and differences of the three typologies, prime examples of corrupt activities in the health sector in the European Union and USA (along with their potential remedies) are provided. Linking corruption cases to Thompson's typology revealed that many corrupt activities may show elements of both individual and institutional corruption because they are intertwined, partly overlap and may occur jointly. Hence, sanctioning individual actors only does not target the problem.

  5. 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.

  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. Lisbon Treaty – the architect of a new European institutional structure

    Directory of Open Access Journals (Sweden)

    Maria POPESCU

    2013-06-01

    Full Text Available The European Union is today managed by the Lisbon Treaty, which stated, in his time, and rightly so, that is a step towards European integration, both at the institutional and human level, a treaty that succeed, despite difficulties, to move forward the European project that combined his account about half a century. The changes introduced by the Lisbon Treaty have a significant impact on EU governance. Treaty of Lisbon makes substantial changes in the management of the EU, especially with regard to the European Council, the Council of Ministers and the EU's rotating presidency. The main task of the research in this paper is the approach of the provisions of the EU Reform Treaty (Lisbon Treaty in terms of constitutional law. Research conducted prior to permit formulation of a general belief, namely that common European history of all its successes and difficulties demonstrates the viability of the European idea and the correct direction of institutional developments in the EU and the Member States.

  9. 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...

  10. 25 October 2017 - Meeting on a South-East European International Institute for Sustainable Technologies

    CERN Multimedia

    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.

  11. 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

  12. A legal institutional perspective on the European Union External Action Service

    DEFF Research Database (Denmark)

    Van Vooren, Bart

    2010-01-01

    It is beyond doubt that setting up the European External Action Service will have a deep impact on EU external policy making. Both in legal and policy terms, this new player thoroughly changes the institutional balance in EU external relations. The goal of this paper is to examine the legal side...... of that coin, by exploring the legal and institutional nature and position of the EEAS in the EU’s external relations machinery. To that end, it queries the meaning of the EEAS’ sui generis status in the EU institutional set-up: what does it mean to say that the EEAS is ‘functionally autonomous’ from...

  13. F-Word or Blueprint for Institutional Reform? European Integration and the Continued Relevance of Federalism

    Directory of Open Access Journals (Sweden)

    Maximilian Conrad

    2012-12-01

    Full Text Available Federalist thought has historically been an important source of inspiration in European integration. Although the last few decades have witnessed a gradual decline of the concept’s relevance, the most recent developments in the wake of the Eurozone debt crisis have drawn renewed attention to shortcomings in the European Union’s institutional architecture as well as to the feasibility of federal solutions to such institutional shortcomings. This article explores the potential of federalist thought as a blueprint for institutional reform in the EU. Based on a brief introduction to the concept of federalism, the article contextualizes federalism in debates on the democratic deficit, the EU’s sources of legitimacy and the relationship between the union institutions and the member states. If shortcomings in institutional design are the source of the current (and future crises, then closer attention needs to be paid to the costs and benefits of federal reorganization in terms of democracy, legitimacy and sovereignty, particularly from the perspective of small states in the EU. Federal reorganization would not only improve the democratic character of EU decision making, but also strengthen the role of small states in the union. However, it also prompts a number of thorny questions, most importantly regarding the construction of a European demos and its relationship to deeply engrained ideas about the nation state as a more or less natural home of democracy.

  14. 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.

  15. Stimulating translational research: several European life science institutions put their heads together.

    Science.gov (United States)

    Bentires-Alj, Mohamed; Rajan, Abinaya; van Harten, Wim; van Luenen, Henri G A M; Kubicek, Stefan; Andersen, Jesper B; Saarela, Janna; Cook, Simon J; Van Minnebruggen, Geert; Roman-Roman, Sergio; Maurer, Cornelia; Erler, Janine T; Bertero, Michela G

    2015-09-01

    Translational research leaves no-one indifferent and everyone expects a particular benefit. We as EU-LIFE (www.eu-life.eu), an alliance of 13 research institutes in European life sciences, would like to share our experience in an attempt to identify measures to promote translational research without undermining basic exploratory research and academic freedom. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. Biggest challenges in bioinformatics.

    Science.gov (United States)

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-04-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Café' style event.

  3. Biggest challenges in bioinformatics

    OpenAIRE

    Fuller, Jonathan C; Khoueiry, Pierre; Dinkel, Holger; Forslund, Kristoffer; Stamatakis, Alexandros; Barry, Joseph; Budd, Aidan; Soldatos, Theodoros G; Linssen, Katja; Rajput, Abdul Mateen

    2013-01-01

    The third Heidelberg Unseminars in Bioinformatics (HUB) was held in October at Heidelberg University in Germany. HUB brought together around 40 bioinformaticians from academia and industry to discuss the ‘Biggest Challenges in Bioinformatics' in a ‘World Café' style event.

  4. A bioinformatics potpourri.

    Science.gov (United States)

    Schönbach, Christian; Li, Jinyan; Ma, Lan; Horton, Paul; Sjaugi, Muhammad Farhan; Ranganathan, Shoba

    2018-01-19

    The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26-28, 2018.

  5. INSTITUTIONAL BARRIERS TO EFFICIENT POLICY INTERVENTION IN THE EUROPEAN PORT SECTOR

    Directory of Open Access Journals (Sweden)

    Barry UBBELS

    2005-01-01

    Full Text Available Despite the growing role of private involvement in recent port developments, most maritime trade is still largely handled in ports where investments, pricing and other managerial decisions are, to a varying extent, dependent, or at least influenced by public bodies. This paper shows that the extent and type of public intervention differs considerably between ports in the Hamburg-Le Havre range. The wide variety in ownership, financing and management of ports throughout Europe indicates that there is no level playing field at present. Because ports operate in an increasingly competitive environment (intensified by globalisation trends and the completion of the internal market, this may lead to situations of unfair competition. The European Union emphasises the importance of a more harmonised approach of port regulation by national governments (in terms of financing and pricing of infrastructure. Given the differences in (national port management styles and the low levels of transparency, the creation of a level playing field in the European port industry seems far away. This suggests the presence of a major institutional difference in European transport policy that hampers efficient policy intervention.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Traceable size determination of nanoparticles, a comparison among European metrology institutes

    International Nuclear Information System (INIS)

    Meli, Felix; Klein, Tobias; Buhr, Egbert; Frase, Carl Georg; Gleber, Gudrun; Krumrey, Michael; Duta, Alexandru; Duta, Steluta; Korpelainen, Virpi; Bellotti, Roberto; Picotto, Gian Bartolo; Boyd, Robert D; Cuenat, Alexandre

    2012-01-01

    Within the European iMERA-Plus project ‘Traceable Characterisation of Nanoparticles’ various particle measurement procedures were developed and finally a measurement comparison for particle size was carried out among seven laboratories across six national metrology institutes. Seven high quality particle samples made from three different materials and having nominal sizes in the range from 10 to 200 nm were used. The participants applied five fundamentally different measurement methods, atomic force microscopy, dynamic light scattering (DLS), small-angle x-ray scattering, scanning electron microscopy and scanning electron microscopy in transmission mode, and provided a total of 48 independent, traceable results. The comparison reference values were determined as weighted means based on the estimated measurement uncertainties of the participants. The comparison reference values have combined standard uncertainties smaller than 1.4 nm for particles with sizes up to 100 nm. All methods, except DLS, provided consistent results. (paper)

  11. 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.

  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. 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.

  14. 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...... are analysed and important developments in the institutional structure are noted. The internal political economy of distribution channels in Eastern Europe is analysed and the modernisation of distribution systems discussed. Finally, some conclusions are offered and areas for future research suggested....

  15. THE CURRENT INTERNATIONAL FINANCIAL CRISIS AND THE FINANCIAL SUPERVISION INSTITUTIONAL ARRANGEMENTS EFFECTIVENESS IN THE EUROPEAN UNION COUNTRIES

    OpenAIRE

    STOICA Ovidiu; CAPRARU Bogdan

    2012-01-01

    The international financial turmoil rise challenges in evaluating and choosing the optimal financial supervision institutional arrangements in many countries. Our study focuses on the financial supervision institutional architecture and its effectiveness in the European Union during the international financial crisis.We evaluated the effectiveness of the financial supervisory framework by groups of countries, categorised according to the supervisory model. Our analysis demonstrates that the p...

  16. The Institutional vs. the Academic Definition of the Quality of Work Life. What Is the Focus of the European Commission?

    Science.gov (United States)

    Royuela, Vicente; Lopez-Tamayo, Jordi; Surinach, Jordi

    2008-01-01

    In recent years, we have seen how the quality of work life has been focused and defined by the European Commission (EC). In our study we compare the EC definition with the academic one and try to see how close they are. We also analyse the possibility of applying the institutional definition to the Spanish case through the development of specific…

  17. The Making of the Executive Head: The Process of Defining Institutional Leaders in Certain Western European Countries.

    Science.gov (United States)

    Neave, Guy

    1988-01-01

    An examination of the formal procedures by which European university's chief executive is selected and the role he or she fulfills finds many differences among countries. One notable innovation is the election of administrators within the institution. It is suggested that the drive toward professional management may endanger academic collegiality.…

  18. 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

  19. Institutional shifts in inter-municipal service delivery: an analysis of developments in eight Western European countries

    NARCIS (Netherlands)

    Hulst, J.R.; van Montfort, A.J.G.M.; Haveri, A.; Airaksinen, J.; Kelly, J.

    2009-01-01

    Comparative research on inter-municipal cooperation in eight European countries shows that there is a great variety of institutional arrangements for cooperation across the different countries. Also, these arrangements tend to change over time in terms of the scope of cooperation among partners,

  20. 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.

  1. Introduction to bioinformatics.

    Science.gov (United States)

    Can, Tolga

    2014-01-01

    Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.

  2. Institutional environment and job well-being on the governance of the tourism industry: a European study

    Directory of Open Access Journals (Sweden)

    Deybbi Cuéllar\\u2011Molina

    2015-01-01

    Full Text Available The distribution of wealth generated in the tourism industry among the labor force should be considered one out of the facets of the social tourism sustainability. Literature highlights that tourism firms’ practices have an impact on labor well - being. However, it also warns that national institutions may condition the adoption of these practices by firms, and so institutions might become a challenge for well - being. This study analyzes the effect of institutions on well - being, and particularly it differentiates between employees and entrepreneurs as human resources in the tourism industry. The empirical analysis carried out on a sample of 1,352 employees and 302 entrepreneurs located in 27 European countries, confirms the direct effect of national institutions on well - being at work. Because institutions would have affect human resources’ well - being, the tourism authorities should pay attention to the governance of this industry.

  3. 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…

  4. The perspective of European researchers of national occupational safety and health institutes for contributing to a European research agenda: a modified Delphi study.

    Science.gov (United States)

    Gagliardi, Diana; Rondinone, Bruna M; Mirabile, Marco; Buresti, Giuliana; Ellwood, Peter; Hery, Michel; Paszkiewicz, Peter; Valenti, Antonio; Iavicoli, Sergio

    2017-06-23

    This study, developed within the frame of the Partnership for European Research on Occupational Safety and Health joint research activities and based on the frame designed by the 2013 European Agency for Safety and Health at Work (EU-OSHA) study, is the first example of using the points of view of European occupational safety and health (OSH) researchers.The objective is to identify priorities for OSH research that may contribute to the achievement of present and future sustainable growth objectives set by the European strategies. The study was carried out using a modified Delphi method with a two-round survey. Each round involved a panel of about 110 researchers representing the network member institutes was selected according to specific criteria, including the ownership of research expertise in at least one of the four macroareas identified by the reference report developed by EU-OSHA in 2013. The study identified some innovative research topics (for example, 'Emerging technological devices' and 'OSH consequences of markets integration') and research priorities (ie, crowdsourcing, e-work, zero-hours contract s ) that are not reflected in previous studies of this nature.The absence of any reference to violence and harassment at work among the researchers' proposals is a major difference from previous similar studies, while topics related to gender issues and electromagnetic fields show a lower importance. The innovative design of a research priorities identification process, which takes advantage of a large, representative and qualified panel of European researchers allowed the definition of a number of research priorities able to support the inclusion of innovative OSH research issues in the scope of the next European research agenda. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  5. The perspective of European researchers of national occupational safety and health institutes for contributing to a European research agenda: a modified Delphi study

    Science.gov (United States)

    Gagliardi, Diana; Rondinone, Bruna M; Mirabile, Marco; Buresti, Giuliana; Ellwood, Peter; Hery, Michel; Paszkiewicz, Peter; Valenti, Antonio; Iavicoli, Sergio

    2017-01-01

    Objectives This study, developed within the frame of the Partnership for European Research on Occupational Safety and Health joint research activities and based on the frame designed by the 2013 European Agency for Safety and Health at Work (EU-OSHA) study, is the first example of using the points of view of European occupational safety and health (OSH) researchers. The objective is to identify priorities for OSH research that may contribute to the achievement of present and future sustainable growth objectives set by the European strategies. Methods The study was carried out using a modified Delphi method with a two-round survey. Each round involved a panel of about 110 researchers representing the network member institutes was selected according to specific criteria, including the ownership of research expertise in at least one of the four macroareas identified by the reference report developed by EU-OSHA in 2013. Results The study identified some innovative research topics (for example, ‘Emerging technological devices’ and ‘OSH consequences of markets integration’) and research priorities (ie, crowdsourcing, e-work, zero-hours contracts) that are not reflected in previous studies of this nature. The absence of any reference to violence and harassment at work among the researchers’ proposals is a major difference from previous similar studies, while topics related to gender issues and electromagnetic fields show a lower importance. Conclusions The innovative design of a research priorities identification process, which takes advantage of a large, representative and qualified panel of European researchers allowed the definition of a number of research priorities able to support the inclusion of innovative OSH research issues in the scope of the next European research agenda. PMID:28645965

  6. 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

  7. A Reinterpretation of Institutional Transformations in European Higher Education: Strategising Pluralistic Organisations in Multiplex Environments

    Science.gov (United States)

    Frolich, Nicoline; Huisman, Jeroen; Slipersaeter, Stig; Stensaker, Bjorn; Botas, Paulo Charles Pimentel

    2013-01-01

    The paper draws on institutional theory with special attention to recent contributions that aim at developing its micro-foundations. We address the question of how individual higher education institutions deal with institutional pluralism. We develop an analytical framework inspired by institutional theory, the sensemaking perspective in…

  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. Ideas, Individuals, and Institutions : Notion and Practices of a European Electricity System

    NARCIS (Netherlands)

    Lagendijk, Vincent

    2018-01-01

    Based upon extensive multi-archival research, this article traces the long lineage of the notion of European electricity network. Since the 1930s engineers and policy makers conceived of a geographical conception for rationalising and optimising electricity supply: a European one. This article

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

    Science.gov (United States)

    2012-12-01

    library/ biblio /publications/2011/fin_report/fin_report_11_en.pdf. 427 Heading 3a: Freedom, security and justice did not exist in the Financial Framework...European Union, 2012. Accessed November 8,2012. http://ec.europa.eu/budget/library/ biblio /publications/2011/fin_report/fin_report_1 1_en.pdf. European

  11. Towards quality, comprehensiveness and excellence. The accreditation project of the Organisation of European Cancer Institutes (OECI)

    NARCIS (Netherlands)

    Saghatchian, Mahasti; Hummel, J. Marjan; Hummel, Henk; Otter, Renee; de Valeriola, Dominique; van Harten, Willem H.; Paradiso, Angelo; Koot, Bert; Ringborg, Ulrik; Tursz, Thomas

    2008-01-01

    There are important gaps in the health status of citizens across Europe, as measured by life expectancy, mortality or morbidity data (Report for the European Commission on the health status of the European Union, 2003). Among the main determinants of the major causes of mortality and morbidity,

  12. 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

  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. 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.

  15. Data mining for bioinformatics applications

    CERN Document Server

    Zengyou, He

    2015-01-01

    Data Mining for Bioinformatics Applications provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems, including problem definition, data collection, data preprocessing, modeling, and validation. The text uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems, containing 45 bioinformatics problems that have been investigated in recent research. For each example, the entire data mining process is described, ranging from data preprocessing to modeling and result validation. Provides valuable information on the data mining methods have been widely used for solving real bioinformatics problems Uses an example-based method to illustrate how to apply data mining techniques to solve real bioinformatics problems Contains 45 bioinformatics problems that have been investigated in recent research.

  16. European Registry of Carotid Artery Stenting: results from a prospective registry of eight high volume EUROPEAN institutions.

    Science.gov (United States)

    Stabile, Eugenio; Garg, Pallav; Cremonesi, Alberto; Bosiers, Marc; Reimers, Bernhard; Setacci, Carlo; Cao, Piergiorgio; Schmidt, Andrej; Sievert, Horst; Peeters, Patrick; Nikas, Dimitry; Werner, Martin; de Donato, Gianmarco; Parlani, Giambattista; Castriota, Fausto; Hornung, Marius; Mauri, Laura; Rubino, Paolo

    2012-08-01

    Carotid endarterectomy (CEA) is the standard revascularization therapy to prevent stroke in patients with carotid artery disease. Carotid artery stenting (CAS) could be considered a potential alternative in patients at high surgical risk. Recent clinical trials have challenged this concept due a relatively high incidence of post-CAS adverse events, which occurred in low volume centers. The aim of this study was to evaluate the outcomes associated with neuroprotected CAS in selected high volume centers. From January 2007 to December 2007, 1,611 patients underwent neuroprotected CAS in eight European Centers. For each patients, clinical, procedural, and one month follow-up data from all patients have been collected. An independent clinical events committee adjudicated the events. Overall in hospital death was 0.06% (one patient), whereas in-hospital stroke was 0.49% (eight patients). Between hospital discharge and 30 days three additional patients died (0.18%) and 10 patients experienced a stroke (0.67%). Overall 30 days mortality was 0.24% (four patients) and stroke incidence 1.12% (18 patients). The 30 day stroke/death rate was 1.36%. CAS is a reasonable alternative to CEA to treat carotid artery atherosclerosis in well-experienced high volume centers. These data suggest that future prospective trials comparing CAS and CEA outcomes should include only centers highly experienced in both treatment modalities. Copyright © 2012 Wiley Periodicals, Inc.

  17. Hostages, free lunches and institutional gaps : the case of the European Currency Union

    OpenAIRE

    Franke, Günter

    2011-01-01

    This paper argues that the strong member states of the European Currency Union are hostages of a financially distressed member state so that they are compelled to provide financial support. Moreover, due to the dynamics of the interaction game, a debt relief is a free lunch for the distressed country. This fosters moral hazard of distressed countries. In the absence of capital market control, European politics do not effectively monitor fiscal politics of member states. The lack of a long ter...

  18. 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.

  19. 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.

  20. International Institutions and Domestic Reform: Equal Pay and British Membership in the European Economic Community.

    Science.gov (United States)

    Frader, Laura Levine

    2018-03-01

    Despite having been overlooked in the standard histories of the UK and the European Community, gender politics and gender policies played a significant role in Britain's applications for membership in the EEC in the 1960s. Joining the European Community required that Britain comply with Article 119 on equal pay for equal work. A combination of domestic feminist and labour movement activism, the commitment of unions and parties, and the internationalization of formal commitments to women's rights constituted internal and external pressures for the passage of an Equal Pay Act in 1970. The article argues that the formal legislative commitment to gender pay equality, changing public attitudes towards women's employment, and European membership impacted further domestic social policy reform and slowly began to shift government attitudes towards gender equality.

  1. COMPARISON OF POPULAR BIOINFORMATICS DATABASES

    OpenAIRE

    Abdulganiyu Abdu Yusuf; Zahraddeen Sufyanu; Kabir Yusuf Mamman; Abubakar Umar Suleiman

    2016-01-01

    Bioinformatics is the application of computational tools to capture and interpret biological data. It has wide applications in drug development, crop improvement, agricultural biotechnology and forensic DNA analysis. There are various databases available to researchers in bioinformatics. These databases are customized for a specific need and are ranged in size, scope, and purpose. The main drawbacks of bioinformatics databases include redundant information, constant change, data spread over m...

  2. Bioinformatics-Aided Venomics

    Directory of Open Access Journals (Sweden)

    Quentin Kaas

    2015-06-01

    Full Text Available Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.

  3. 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

  4. 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

  5. Normative alignment and institutional resilience in legal governance of the European energy transition

    NARCIS (Netherlands)

    Heldeweg, Michiel A.

    2016-01-01

    In the current European energy transition we witness that the recent (and in part still ongoing) shift from energy provision by government enterprises to provision by private corporations (albeit not always fully privatized), is followed by a shift towards energy provision by private collectives

  6. 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...

  7. 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

  8. 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.

  9. Strategic Renewal in Regulatory Environments. How inter- and intra-organisational institutional forces influence European incumbent energy firms

    International Nuclear Information System (INIS)

    Stienstra, M.

    2008-01-01

    How do incumbent firms strategically renew in regulatory environments? Assuming that regulation can both constrain and enable a firm's strategic renewal opportunities, we investigate how and to what extent incumbent firms undertake exploitative and explorative strategic renewal actions in order to remain competitive. Exploitative strategic renewal involves those actions that strengthen or optimise a firm's current resource deployments, whereas explorative strategic renewal relates to actions that generate new sources of value creation for the firm. Based on old institutional theory, new institutional theory, neo-institutional theory and institutional entrepreneurship literature, a multi-level framework that combines selection and adaptation arguments has been developed and applied to investigate strategic renewal behaviour of a sample of European energy incumbents. At industry level of analysis, results show how inter-organisational institutional forces significantly impact firms' choices of exploitative and explorative strategic renewal actions through regulative, normative and cognitive forces. At organisational unit level of analysis, we find that the extent of intra-organisational regulative forces is positively related to exploitative strategic renewal actions. In addition, entrepreneurial proclivity appears to be a catalyst of both exploitative and explorative strategic renewal actions. Finally, our results provide insights how environmental selection and firm level adaptation are interrelated in the context of regulation. The extent of inter-organisational regulative forces positively moderates the relationship between intra-organisational regulative forces and exploitative strategic renewal actions.

  10. Strategic Renewal in Regulatory Environments. How inter- and intra-organisational institutional forces influence European incumbent energy firms

    Energy Technology Data Exchange (ETDEWEB)

    Stienstra, M.

    2008-11-20

    How do incumbent firms strategically renew in regulatory environments? Assuming that regulation can both constrain and enable a firm's strategic renewal opportunities, we investigate how and to what extent incumbent firms undertake exploitative and explorative strategic renewal actions in order to remain competitive. Exploitative strategic renewal involves those actions that strengthen or optimise a firm's current resource deployments, whereas explorative strategic renewal relates to actions that generate new sources of value creation for the firm. Based on old institutional theory, new institutional theory, neo-institutional theory and institutional entrepreneurship literature, a multi-level framework that combines selection and adaptation arguments has been developed and applied to investigate strategic renewal behaviour of a sample of European energy incumbents. At industry level of analysis, results show how inter-organisational institutional forces significantly impact firms' choices of exploitative and explorative strategic renewal actions through regulative, normative and cognitive forces. At organisational unit level of analysis, we find that the extent of intra-organisational regulative forces is positively related to exploitative strategic renewal actions. In addition, entrepreneurial proclivity appears to be a catalyst of both exploitative and explorative strategic renewal actions. Finally, our results provide insights how environmental selection and firm level adaptation are interrelated in the context of regulation. The extent of inter-organisational regulative forces positively moderates the relationship between intra-organisational regulative forces and exploitative strategic renewal actions.

  11. 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...

  12. European Master in Innovation in Nuclear Energy (EMINE). Developed in the frame work of the European Institut of Innovation and Technology, KIC InnoEnergy

    International Nuclear Information System (INIS)

    Ferrié, E.; Carreira, M.; Gudowski, W.; Garrido, F.; Reynier, B.; Dies, J.; Batet, Ll.; Otic, I.; Patte, C.; Darrigues, I.; Fernandez-Olano, P.; Leon, P.T.; Coste-Leconte, S.; Fanjas, Y.; Henriksson, H.

    2014-01-01

    KIC InnoEnergy SE is a European company fostering the integration of education, technology, business and entrepreneurship and strengthening the culture of innovation. The strategic objective is to become the leading engine of innovation in the field of sustainable energy. It has been designated as a one of the first three Knowledge and Innovation Communities by the EIT's Governing Board on 16 December 2009 in Budapest. KIC InnoEnergy addresses sustainable energy as its priority area. KIC InnoEnergy is a world class alliance of top European players with a proven track record. The Consortium consists of 30+ shareholders and additional 50+ partners - companies, research institutes, universities and business schools covering the whole energy mix. They are organised around six regional units, the Co-Location Centres (CC): France, Benelux, Germany, Iberia, Poland Plus and Sweden. On completion of the EMINE programme, a Master of Science degree will be awarded from the universities where studies were performed during year one and year two, i.e. a double-degree. A diploma from KIC InnoEnergy related to innovation and entrepreneurship will also be presented

  13. 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.

  14. Institutional Aspects of European Commission Guidance in the Area of Antitrust Law

    OpenAIRE

    Ben Smulders

    2009-01-01

    From an institutional law perspective, the question arises how to qualify the more than thirty existing communications, notices and guidelines which the Commission has issued in the area of antitrust law.

  15. Recent Japanese and Chinese investments in U.S. and European financial institutions

    OpenAIRE

    Cindy Marks

    2009-01-01

    This Asia Focus report compares some of the more significant investments by Japanese and Chinese financial institutions in both the U.S. and Europe, highlighting trends and offering thoughts on the direction of future investments.

  16. 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.

  17. 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…

  18. 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…

  19. 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.

  20. Executive summary and conclusions from the European Hydration Institute Expert Conference on human hydration, health, and performance.

    Science.gov (United States)

    Benton, D; Braun, H; Cobo, J C; Edmonds, C; Elmadfa, I; El-Sharkawy, A; Feehally, J; Gellert, R; Holdsworth, J; Kapsokefalou, M; Kenney, W L; Leiper, J B; Macdonald, I A; Maffeis, C; Maughan, R J; Shirreffs, S M; Toth-Heyn, P; Watson, P

    2015-09-01

    On April 7-8, 2014, the European Hydration Institute hosted a small group of experts at Castle Combe Manor House, United Kingdom, to discuss a range of issues related to human hydration, health, and performance. The meeting included 18 recognized experts who brought a wealth of experience and knowledge to the topics under review. Eight selected topics were addressed, with the key issues being briefly presented before an in-depth discussion. Presented here is the executive summary and conclusions from this meeting. © The Author(s) 2015. Published by Oxford University Press on behalf of the International Life Sciences Institute. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. Staff Scientist - RNA Bioinformatics | Center for Cancer Research

    Science.gov (United States)

    The newly established RNA Biology Laboratory (RBL) at the Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH) in Frederick, Maryland is recruiting a Staff Scientist with strong expertise in RNA bioinformatics to join the Intramural Research Program’s mission of high impact, high reward science. The RBL is the equivalent of an

  2. HISTORICAL ANALYSIS ON THE APPEARANCE OF THE SUPREME AUDIT INSTITUTIONS IN THE EUROPEAN UNION

    Directory of Open Access Journals (Sweden)

    Ioan Gheorghe Țara

    2014-07-01

    Full Text Available Our scientific approach in the land of Supreme Audit Institutions, begins, as naturally, from the first moment of appearance and of engagement, in order to achieve a succession of the most important historical moments in the evolution of organizations. Under these conditions, our approach pursued by this paper is focused on two main areas: identification of the arising for the first time of the Supreme Audit Institutions and their evolution. We believe that we have no access to a full knowledge of a domain at the present time, as long as we do not know the past, because this is the only way we can build the future. As a result, we begin the journey into the realm of the Supreme Audit Institutions from the ancient times, considering this approach not only a necessity, but our duty, to take it from the beginnings.

  3. 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...

  4. 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.

  5. «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

  6. 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…

  7. Institutional Barriers for Adults' Participation in Higher Education in Thirteen European Countries

    Science.gov (United States)

    Saar, Ellu; Täht, Kadri; Roosalu, Triin

    2014-01-01

    This study focuses on institutional barriers that adult learners experience while participating in higher education programmes. We developed a holistic measure of diversification, accessibility, flexibility and affordability of higher education for adults. Based on pre-economic-crisis data across Europe we then explored the impact of macro-level…

  8. Smart Specialisation in European Regions: Issues of Strategy, Institutions and Implementation

    NARCIS (Netherlands)

    McCann, Philip; Ortega Argiles, Raquel

    2014-01-01

    After reviewing some of the key features of the smart specialisation approach this paper examines issues of strategy and implementation which arise in the light of institutional and macroeconomic context in regional examples from four EU countries. The specific insights provided by this comparative

  9. 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.

  10. 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.

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

    DEFF Research Database (Denmark)

    Manners, Ian

    2013-01-01

    This chapter argues that both the causal elements of domestic/state political leadership, supranational competition, and cosmopolitical normative activism, together with the constitutive element of a ‘normative power’ self image, are important in understanding the EU as a Minervan power. It intro......This chapter argues that both the causal elements of domestic/state political leadership, supranational competition, and cosmopolitical normative activism, together with the constitutive element of a ‘normative power’ self image, are important in understanding the EU as a Minervan power...... multilateralism” embracing the active diplomacy of states, the strengthening of supranational and international institutions, and the engagement with the cosmopolitical and transnational activists that capture the EU as a Minervan power in global institution building....

  12. Organised crime in the European Union: The state of the matter and institutional responses

    Directory of Open Access Journals (Sweden)

    Óscar Jaime-Jiménez

    2010-09-01

    Full Text Available During the past few decades, organised crime has grown considerably as a consequence of political transformations and global economics. The countries of the European Union are very much aware of this situation, and are taking steps to coordinate strategies and boost cooperation in the fight against the problem. This article attempts, firstly, to explain the phenomenon in its present dimensions and in those facets that most affect the EU Member States. The author then goes on to tackle the aspects concerning cooperation, in all its different areas, within the sphere of the EU, before finally carrying out a prospective and proactive examination of the foreseeable evolution of the phenomenon, and the measures necessary to tackle it in all its magnitude.

  13. 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.

  14. 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. PMID:25996054

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

    DEFF Research Database (Denmark)

    Svendsen, Gert Tinggaard

    ' 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....... 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...

  16. 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.

  17. When process mining meets bioinformatics

    NARCIS (Netherlands)

    Jagadeesh Chandra Bose, R.P.; Aalst, van der W.M.P.; Nurcan, S.

    2011-01-01

    Process mining techniques can be used to extract non-trivial process related knowledge and thus generate interesting insights from event logs. Similarly, bioinformatics aims at increasing the understanding of biological processes through the analysis of information associated with biological

  18. 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.

  19. 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 

  20. Public and Private Institutions: Educating Civil Society about European Security Concerns

    Directory of Open Access Journals (Sweden)

    Rafael Bardají

    1997-12-01

    Full Text Available As an specialist in strategic studies and political adviser, the author developes three basic ideas in his speech: 1 the objective necessity of strategic thinking to increase defense awareness, with the goal of ameliorating the relations between civil society and the Armed Forces, and to create a strategic culture to help to make more permeable the Administration decision-making process; 2 public and private institutions have to understand each other, despite the fact that tradition and time pressures do negatively weigh on Administration decision-making; 3 both parts –Administration and specialists in security– have to make the effort of becoming more flexible, on the one hand, and more capable of producing relevant studies in political terms, on the other.

  1. Radioactive waste: institutional determinants of management and disposal policy in three European countries

    International Nuclear Information System (INIS)

    Berkhout, Frans.

    1989-01-01

    The objective of this thesis has been to write a detailed historical account of the policy and practice of radioactive waste management in Britain, Sweden and West Germany, and to draw out implications for theory and public policy. By comparing the evolution of the policy process in three countries it has been possible to develop a better understanding of the particular operational, regulatory and political factors determining policy in each case. The main conclusions are three-fold. First, the presence or absence of commitments to the reprocessing of spent fuel for a wide range of strategic, industrial and legal reasons have been critical to the success in finding an acceptable radwaste management and disposal policy (or strategy). Politically it is not possible to make a clear distinction between radwaste management and policy for the rest of the back-end of the nuclear fuel cycle. Second, because of this complex but intimate relationship to reprocessing policy, the dynamism and consistency of radwaste policies are highly dependent on the industrial and political contexts of the drive to reprocessing. Traditionally a view on reprocessing has been virtually synonymous with a faith or scepticism in the future of nuclear power. Third, the policy process, and indeed its goals was rather unique to national circumstances (the legal and institutional framework, industrial and political structures). This demonstrates one of the principle arguments of the thesis which is that the innovation process for radwaste management and disposal technologies cannot be seen merely as a technical process, but has to be seen as a process of political and institutional negotiations. (author)

  2. 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

  3. 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.

  4. 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.

  5. Generalized Centroid Estimators in Bioinformatics

    Science.gov (United States)

    Hamada, Michiaki; Kiryu, Hisanori; Iwasaki, Wataru; Asai, Kiyoshi

    2011-01-01

    In a number of estimation problems in bioinformatics, accuracy measures of the target problem are usually given, and it is important to design estimators that are suitable to those accuracy measures. However, there is often a discrepancy between an employed estimator and a given accuracy measure of the problem. In this study, we introduce a general class of efficient estimators for estimation problems on high-dimensional binary spaces, which represent many fundamental problems in bioinformatics. Theoretical analysis reveals that the proposed estimators generally fit with commonly-used accuracy measures (e.g. sensitivity, PPV, MCC and F-score) as well as it can be computed efficiently in many cases, and cover a wide range of problems in bioinformatics from the viewpoint of the principle of maximum expected accuracy (MEA). It is also shown that some important algorithms in bioinformatics can be interpreted in a unified manner. Not only the concept presented in this paper gives a useful framework to design MEA-based estimators but also it is highly extendable and sheds new light on many problems in bioinformatics. PMID:21365017

  6. 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…

  7. 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…

  8. 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...

  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. 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.

  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. Bioinformatics in translational drug discovery.

    Science.gov (United States)

    Wooller, Sarah K; Benstead-Hume, Graeme; Chen, Xiangrong; Ali, Yusuf; Pearl, Frances M G

    2017-08-31

    Bioinformatics approaches are becoming ever more essential in translational drug discovery both in academia and within the pharmaceutical industry. Computational exploitation of the increasing volumes of data generated during all phases of drug discovery is enabling key challenges of the process to be addressed. Here, we highlight some of the areas in which bioinformatics resources and methods are being developed to support the drug discovery pipeline. These include the creation of large data warehouses, bioinformatics algorithms to analyse 'big data' that identify novel drug targets and/or biomarkers, programs to assess the tractability of targets, and prediction of repositioning opportunities that use licensed drugs to treat additional indications. © 2017 The Author(s).

  13. 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 Document Server

    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.

  14. 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

    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...

  15. 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).

  16. 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.

  17. 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...

  18. 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

  19. 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…

  20. Bioinformatics of genomic association mapping

    NARCIS (Netherlands)

    Vaez Barzani, Ahmad

    2015-01-01

    In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

  1. A review of bioinformatics training applied to research in molecular medicine, agriculture and biodiversity in Costa Rica and Central America.

    Science.gov (United States)

    Orozco, Allan; Morera, Jessica; Jiménez, Sergio; Boza, Ricardo

    2013-09-01

    Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica's Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region's first Bioinformatics Master's Degree. The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support for Molecular Biology in the region, is providing a foundational stone for the development of Bioinformatics in the area. Central American bioinformaticians have participated in the creation of as well as co-founded the Iberoamerican Bioinformatics Society (SOIBIO). In this article, we review the most recent activities in education and research in Bioinformatics from several regional institutions. These activities have resulted in further advances for Molecular Medicine, Agriculture and Biodiversity research in Costa Rica and the rest of the Central American countries. Finally, we provide summary information on the first Central America Bioinformatics International Congress, as well as the creation of the first Bioinformatics company (Indromics Bioinformatics), spin-off the Academy in Central America and the Caribbean.

  2. 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.

  3. 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

  4. 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...

  5. 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...

  6. Preface to Introduction to Structural Bioinformatics

    NARCIS (Netherlands)

    Feenstra, K. Anton; Abeln, Sanne

    2018-01-01

    While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims to give an introduction into Structural Bioinformatics, which

  7. 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.

  8. Establishing bioinformatics research in the Asia Pacific

    OpenAIRE

    Ranganathan, Shoba; Tammi, Martti; Gribskov, Michael; Tan, Tin Wee

    2006-01-01

    Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-...

  9. 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.

  10. 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.

  11. Establishing bioinformatics research in the Asia Pacific

    Directory of Open Access Journals (Sweden)

    Tammi Martti

    2006-12-01

    Full Text Available Abstract In 1998, the Asia Pacific Bioinformatics Network (APBioNet, Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5th annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand, Penang (Malaysia, Auckland (New Zealand and Busan (South Korea. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community.

  12. Emerging strengths in Asia Pacific bioinformatics.

    Science.gov (United States)

    Ranganathan, Shoba; Hsu, Wen-Lian; Yang, Ueng-Cheng; Tan, Tin Wee

    2008-12-12

    The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

  13. Risk aversion and institutional information disclosure on the European carbon market. A case-study of the 2006 compliance event

    International Nuclear Information System (INIS)

    Chevallier, Julien; Ielpo, Florian; Mercier, Ludovic

    2009-01-01

    This article evaluates the impact of the 2006 compliance event on changes in investors' risk aversion on the European carbon market using the newly available option prices dataset. Thus, we aim at capturing the specific event that occurred on April 2007 as the European Commission disclosed the 2006 verified emissions data. Following the methodology existing for stock indices, we recover empirically risk aversion adjustments on the period 2006-2007 by estimating first the risk-neutral distribution from option prices and second the actual distribution from futures on the European Climate Exchange. Our results show evidence of a dramatic change in the market perception of risk around the 2006 yearly compliance event that has not been assessed yet. (author)

  14. 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.

  15. 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.

  16. Institutional change in European natural gas markets and implications for energy security: Lessons from the German case

    International Nuclear Information System (INIS)

    Westphal, Kirsten

    2014-01-01

    This article focuses on institutional change in the German gas market driven by EU internal market and climate policies. It argues that institutional change has functional externalities for energy security. The German gas market provides a useful case study, as Germany is the biggest continental gas market, a major hub and transport country which has largely privatised, unbundled and separated its natural gas undertakings. Transition is ongoing, tending towards an internal market. Inter/national natural gas economics is in flux. Institutional evolution has repercussions for corporate and market structures, the operating of the system and the realization of transactions. Changes in the institutional framework crucially affect energy security, which is often associated with institutional stability. On the basis of this case study, it is argued herein that the security of natural gas supplies should be reexamined in the context of the developments described above, since overall the institutional changes in natural gas security lag behind the EU’s internal natural gas market development. - Highlights: • EU natural gas market regulation primarily aims to establish competitive markets. • German/EU regulatory approach has externalities for supply security. • Institutional changes and breaks with path dependencies take place in Germany/the EU. • Institutional change results in increasing uncertainty and complexity. • Subsequent change in perceptions and expectations may destabilise trade relations

  17. A history of the collaboration between the European Organisation for Nuclear Research (CERN) and the Joint Institute for Nuclear Research (JINR), and with Soviet research institutes in the USSR 1955-1970

    International Nuclear Information System (INIS)

    Lock, W.O.

    1975-01-01

    The report describes in some detail the origins and development up to 1970 of the collaboration which now exists between the European Organization for Nuclear Research (CERN) and its counterpart the Joint Institute for Nuclear Research (JINR) at Dubna, USSR and also with the Institute for High Energy Physics, Serpukhov, USSR. Part 1 deals with the relations between JINR and CERN, their beginnings and the subsequent development of exchange of scientists, joint Summer Schools, and the organization of Seminars to discuss perspectives in high energy physics. Part 2 describes first the steps which led up to the signing of an Agreement between CERN and the State Committee of the USSR for the Utilization of Atomic Energy, governing collaboration between CERN and the Institute for High Energy Physics at Serpukhov. A brief account is then given of the subsequent installation of equipment built at CERN for the Institute's 76-Gev proton accelerator and the carrying out of joint physics experiments by teams from Western Europe and from the Soviet Union. Part 3 summarizes the origins of collaborative agreements which have been made by CERN with a few other leading Institutes in the Soviet Union. A number of Annexes reproduce some of the relevant documents and letters. (author)

  18. 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...... analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work......Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly...

  19. 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).

  20. 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.

  1. Biology in 'silico': The Bioinformatics Revolution.

    Science.gov (United States)

    Bloom, Mark

    2001-01-01

    Explains the Human Genome Project (HGP) and efforts to sequence the human genome. Describes the role of bioinformatics in the project and considers it the genetics Swiss Army Knife, which has many different uses, for use in forensic science, medicine, agriculture, and environmental sciences. Discusses the use of bioinformatics in the high school…

  2. 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…

  3. 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…

  4. Fuzzy Logic in Medicine and Bioinformatics

    Directory of Open Access Journals (Sweden)

    Angela Torres

    2006-01-01

    Full Text Available The purpose of this paper is to present a general view of the current applications of fuzzy logic in medicine and bioinformatics. We particularly review the medical literature using fuzzy logic. We then recall the geometrical interpretation of fuzzy sets as points in a fuzzy hypercube and present two concrete illustrations in medicine (drug addictions and in bioinformatics (comparison of genomes.

  5. Selective Europeanization

    DEFF Research Database (Denmark)

    Hoch Jovanovic, Tamara; Lynggaard, Kennet

    2014-01-01

    and rules. The article examines the reasons for both resistance and selectiveness to Europeanization of the Danish minority policy through a “path dependency” perspective accentuating decision makers’ reluctance to deviate from existing institutional commitments, even in subsequently significantly altered...... 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...

  6. Rising Strengths Hong Kong SAR in Bioinformatics.

    Science.gov (United States)

    Chakraborty, Chiranjib; George Priya Doss, C; Zhu, Hailong; Agoramoorthy, Govindasamy

    2017-06-01

    Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength. However, several hurdles remain. New government policies will assist computational biologists to overcome these hurdles and further raise the profile of the field. There is a high expectation that bioinformatics in Hong Kong will be a promising area for the next generation.

  7. 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.

  8. 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.

  9. 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.

  10. Bioinformatics clouds for big data manipulation.

    Science.gov (United States)

    Dai, Lin; Gao, Xin; Guo, Yan; Xiao, Jingfa; Zhang, Zhang

    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.

  11. Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods

    Czech Academy of Sciences Publication Activity Database

    Martin, G.; Baurens, F.C.; Droc, G.; Rouard, M.; Cenci, A.; Kilian, A.; Hastie, A.; Doležel, Jaroslav; Aury, J. M.; Alberti, A.; Carreel, F.; D'Hont, A.

    2016-01-01

    Roč. 17, MAR 16 (2016), s. 243 ISSN 1471-2164 Institutional support: RVO:61389030 Keywords : Musa acuminata * Genome assembly * Bioinformatics tool Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.729, year: 2016

  12. The European Nuclear Safety Training and Tutoring Institute (ENSTTI). Annex III [Example of Knowledge Management and Training for TSOs

    International Nuclear Information System (INIS)

    2018-01-01

    ENSTTI is an initiative of members of the ETSON. It was created in 2010 to put in place a high quality training mechanism to meet the training needs of experts at nuclear regulatory authorities and TSOs; to ensure the continuous development of qualified experts in this area; and to foster harmonization of technical practices in nuclear safety, nuclear security and radiation protection. This is achieved through the regular provision of vocational training and tutoring exclusively delivered by senior professionals of European TSOs that take into consideration the latest technical developments and is continuously up-dated and improved by applying a systematic approach to training.

  13. [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

  14. Opening up the black box: drivers and barriers in institutional implementation of the European standards and guidelines

    NARCIS (Netherlands)

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

    2013-01-01

    Over the past twenty years, concerted efforts at assuring the quality of higher education institutions (internally and externally) have acquired the status of prominence, and perhaps overemphasis. While these efforts, as a rule, led to institutionalising quality assurance policies and measures of

  15. Analysing Implementation of the European Standards and Guidelines for Quality Assurance at Institutional Level : Outcomes of the IBAR Project

    NARCIS (Netherlands)

    Westerheijden, Donald F.; Kohoutek, Jan

    2013-01-01

    The IBAR project studied barriers higher education institutions experienced to implementing the ESG part 1. Our paper reports on the major findings of this project. After sketching our conceptual approach, we conclude that the ESG Part 1 seem to be functioning as a codification of many policies and

  16. Opening up the black box : drivers and barriers in institutional implementation of the European standards and guidelines

    NARCIS (Netherlands)

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

    2014-01-01

    Over the past twenty years, concerted efforts at assuring the quality of higher education institutions (internally and externally) have acquired the status of prominence, and perhaps overemphasis. While these efforts, as a rule, led to institutionalising quality assurance policies and measures of

  17. 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,

  18. 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.

  19. Application of machine learning methods in bioinformatics

    Science.gov (United States)

    Yang, Haoyu; An, Zheng; Zhou, Haotian; Hou, Yawen

    2018-05-01

    Faced with the development of bioinformatics, high-throughput genomic technology have enabled biology to enter the era of big data. [1] Bioinformatics is an interdisciplinary, including the acquisition, management, analysis, interpretation and application of biological information, etc. It derives from the Human Genome Project. The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets.[2]. This paper analyzes and compares various algorithms of machine learning and their applications in bioinformatics.

  20. 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

  1. Do We Need A New Constitutionalism for the European Union? An Institutional insight in the Draft Treaty

    OpenAIRE

    Daniela Piana

    2004-01-01

    It could be argued that some historical events are responsible for the recent development of the theoretical debate about the constitutionalism. The first one is the development of a transnational political order, where rules and institutions are created in a new way that seems to represent a rupture with the schemes followed in the international agreements. The second one is the end of the Cold war and the transition to constitutional democracies that has occurred in the countries that belon...

  2. 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

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

    Science.gov (United States)

    Fristensky, Brian

    2007-01-01

    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. PMID:17291351

  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. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    Bioinformatics is an emerging scientific discipline that uses information ... complex biological questions. ... and computer programs for various purposes of primer ..... polymerase chain reaction: Human Immunodeficiency Virus 1 model studies.

  6. 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.

  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. 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...... for interactions between RNA and proteins.Here, we introduce the basic concepts of predicting RNA secondary structure relevant to the further analyses of RNA sequences. We also provide pointers to methods addressing various aspects of RNA bioinformatics and computational RNA biology....

  9. 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.

  10. Dosimetric inter-institutional comparison in European radiotherapy centres: Results of IAEA supported treatment planning system audit.

    Science.gov (United States)

    Gershkevitsh, Eduard; Pesznyak, Csilla; Petrovic, Borislava; Grezdo, Joseph; Chelminski, Krzysztof; do Carmo Lopes, Maria; Izewska, Joanna; Van Dyk, Jacob

    2014-05-01

    One of the newer audit modalities operated by the International Atomic Energy Agency (IAEA) involves audits of treatment planning systems (TPS) in radiotherapy. The main focus of the audit is the dosimetry verification of the delivery of a radiation treatment plan for three-dimensional (3D) conformal radiotherapy using high energy photon beams. The audit has been carried out in eight European countries - Estonia, Hungary, Latvia, Lithuania, Serbia, Slovakia, Poland and Portugal. The corresponding results are presented. The TPS audit reviews the dosimetry, treatment planning and radiotherapy delivery processes using the 'end-to-end' approach, i.e. following the pathway similar to that of the patient, through imaging, treatment planning and dose delivery. The audit is implemented at the national level with IAEA assistance. The national counterparts conduct the TPS audit at local radiotherapy centres through on-site visits. TPS calculated doses are compared with ion chamber measurements performed in an anthropomorphic phantom for eight test cases per algorithm/beam. A set of pre-defined agreement criteria is used to analyse the performance of TPSs. TPS audit was carried out in 60 radiotherapy centres. In total, 190 data sets (combination of algorithm and beam quality) have been collected and reviewed. Dosimetry problems requiring interventions were discovered in about 10% of datasets. In addition, suboptimal beam modelling in TPSs was discovered in a number of cases. The TPS audit project using the IAEA methodology has verified the treatment planning system calculations for 3D conformal radiotherapy in a group of radiotherapy centres in Europe. It contributed to achieving better understanding of the performance of TPSs and helped to resolve issues related to imaging, dosimetry and treatment planning.

  11. 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.

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

    OpenAIRE

    Brazas, Michelle D.; Ouellette, B. F. Francis

    2013-01-01

    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...

  13. Development of Bioinformatics Infrastructure for Genomics Research.

    Science.gov (United States)

    Mulder, Nicola J; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Ahmed, Azza; Ahmed, Rehab; Akanle, Bola; Alibi, Mohamed; Armstrong, Don L; Aron, Shaun; Ashano, Efejiro; Baichoo, Shakuntala; Benkahla, Alia; Brown, David K; Chimusa, Emile R; Fadlelmola, Faisal M; Falola, Dare; Fatumo, Segun; Ghedira, Kais; Ghouila, Amel; Hazelhurst, Scott; Isewon, Itunuoluwa; Jung, Segun; Kassim, Samar Kamal; Kayondo, Jonathan K; Mbiyavanga, Mamana; Meintjes, Ayton; Mohammed, Somia; Mosaku, Abayomi; Moussa, Ahmed; Muhammd, Mustafa; Mungloo-Dilmohamud, Zahra; Nashiru, Oyekanmi; Odia, Trust; Okafor, Adaobi; Oladipo, Olaleye; Osamor, Victor; Oyelade, Jellili; Sadki, Khalid; Salifu, Samson Pandam; Soyemi, Jumoke; Panji, Sumir; Radouani, Fouzia; Souiai, Oussama; Tastan Bishop, Özlem

    2017-06-01

    Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community. H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis. Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for

  14. The Quality of Teaching Staff: Higher Education Institutions' Compliance with the European Standards and Guidelines for Quality Assurance--The Case of Portugal

    Science.gov (United States)

    Cardoso, Sónia; Tavares, Orlanda; Sin, Cristina

    2015-01-01

    In recent years, initiatives for the improvement of teaching quality have been pursued both at European and national levels. Such is the case of the European Standards and Guidelines for Quality Assurance (ESG) and of legislation passed by several European countries, including Portugal, in response to European policy developments driven by the…

  15. Complications and Short-Term Explantation Rate Following Artificial Urinary Sphincter Implantation: Results from a Large Middle European Multi-Institutional Case Series.

    Science.gov (United States)

    Kretschmer, Alexander; Hüsch, Tanja; Thomsen, Frauke; Kronlachner, Dominik; Obaje, Alice; Anding, Ralf; Pottek, Tobias; Rose, Achim; Olianas, Roberto; Friedl, Alexander; Hübner, Wilhelm; Homberg, Roland; Pfitzenmaier, Jesco; Grein, Ulrich; Queissert, Fabian; Naumann, Carsten Maik; Schweiger, Josef; Wotzka, Carola; Nyarangi-Dix, Joanne N; Hofmann, Torben; Seiler, Roland; Haferkamp, Axel; Bauer, Ricarda M

    2016-01-01

    Background/Aims/Objectives: To analyze perioperative complication and short-term explantation rates after perineal or penoscrotal single-cuff and double-cuff artificial urinary sphincter (AUS) implantation in a large middle European multi-institutional patient cohort. 467 male patients with stress urinary incontinence underwent implantation of a perineal single-cuff (n = 152), penoscrotal single-cuff (n = 99), or perineal double-cuff (n = 216) AUS between 2010 and 2012. Postoperative complications and 6-month explantation rates were assessed. For statistical analysis, Fisher's exact test and Kruskal-Wallis rank sum test, and a multiple logistic regression model were used (p AUS, penoscrotal single-cuff implantation led to significantly increased short-term explantation rates (8.6% (perineal) vs. 19.2% (penoscrotal), p = 0.019). The postoperative infection rate was significantly higher after double-cuff compared to single-cuff implantation (6.0% (single-cuff) vs. 13.9% (double-cuff), p = 0.019). The short-term explantation rate after primary double-cuff placement was 6.5% (p = 0.543 vs. perineal single-cuff). In multivariate analysis, the penoscrotal approach (p = 0.004), intraoperative complications (p = 0.005), postoperative bleeding (p = 0.011), and perioperative infection (p < 0.001) were independent risk factors for short-term explantation. Providing data from a large contemporary multi-institutional patient cohort from high-volume and low-volume institutions, our results reflect the current standard of care in middle Europe. We indicate that the penoscrotal approach is an independent risk factor for increased short-term explantation rates. © 2016 S. Karger AG, Basel.

  16. 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.

  17. 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.

    Science.gov (United States)

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

    2010-02-01

    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 and technical for treatment delivery and quality assurance. These are reviewed for four categories of solutions; kV CT and kV CBCT (cone-beam CT) as well as MV CT and MV CBCT. It will also provide a framework and checklist to consider the capability and functionality of these systems as well as the resources needed for implementation. Two different but typical clinical cases (tonsillar and prostate cancer) using 3DCT-IGRT are illustrated with workflow processes via feedback questionnaires from several large clinical centres currently utilizing these systems. The feedback from these clinical centres 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 on clinicians, physicists and radiation therapy technologists interested in IGRT. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

  18. Synergy between Medical Informatics and Bioinformatics: Facilitating Genomic Medicine for Future Health Care

    Czech Academy of Sciences Publication Activity Database

    Martin-Sanchez, F.; Iakovidis, I.; Norager, S.; Maojo, V.; de Groen, P.; Van der Lei, J.; Jones, T.; Abraham-Fuchs, K.; Apweiler, R.; Babic, A.; Baud, R.; Breton, V.; Cinquin, P.; Doupi, P.; Dugas, M.; Eils, R.; Engelbrecht, R.; Ghazal, P.; Jehenson, P.; Kulikowski, C.; Lampe, K.; De Moor, G.; Orphanoudakis, S.; Rossing, N.; Sarachan, B.; Sousa, A.; Spekowius, G.; Thireos, G.; Zahlmann, G.; Zvárová, Jana; Hermosilla, I.; Vicente, F. J.

    2004-01-01

    Roč. 37, - (2004), s. 30-42 ISSN 1532-0464 Institutional research plan: CEZ:AV0Z1030915 Keywords : bioinformatics * medical informatics * genomics * genomic medicine * biomedical informatics Subject RIV: BD - Theory of Information Impact factor: 1.013, year: 2004

  19. Translational Bioinformatics and Clinical Research (Biomedical) Informatics.

    Science.gov (United States)

    Sirintrapun, S Joseph; Zehir, Ahmet; Syed, Aijazuddin; Gao, JianJiong; Schultz, Nikolaus; Cheng, Donavan T

    2015-06-01

    Translational bioinformatics and clinical research (biomedical) informatics are the primary domains related to informatics activities that support translational research. Translational bioinformatics focuses on computational techniques in genetics, molecular biology, and systems biology. Clinical research (biomedical) informatics involves the use of informatics in discovery and management of new knowledge relating to health and disease. This article details 3 projects that are hybrid applications of translational bioinformatics and clinical research (biomedical) informatics: The Cancer Genome Atlas, the cBioPortal for Cancer Genomics, and the Memorial Sloan Kettering Cancer Center clinical variants and results database, all designed to facilitate insights into cancer biology and clinical/therapeutic correlations. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

    Abstract Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab Contact: jeffrey.t.chang@uth.tmc.edu PMID:28052928

  1. The GMOD Drupal Bioinformatic Server Framework

    Science.gov (United States)

    Papanicolaou, Alexie; Heckel, David G.

    2010-01-01

    Motivation: 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). Results: 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. Conclusion: 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. Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com Contact: alexie@butterflybase.org PMID:20971988

  2. 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.

  3. The stability and growth pact in European Monetary Union. Institutional and economic foundations and a game-theoretical-experimental contribution to the credibility of sanctioning excessive deficits

    International Nuclear Information System (INIS)

    Sutter, M.

    1999-03-01

    At the summit of the European Union (EU) in Amsterdam in June 1997, the Stability and Growth Pact has been concluded in order to ensure sound public finances in European Monetary Union (EMU). The pact's aim is to safeguard the compliance of EMU-member states with one of the Maastricht Treaty's fiscal convergence criteria, namely the requirement to hold a country's overall net deficit below 3 % of its GDP. Compliance within EMU shall be achieved by monetary sanctions against countries with an excessive deficit. Because the excessive deficit procedure, as laid down in the Maastricht Treaty, was rather loose, the stability and growth pact was formulated to clarify and speed up this procedure. The pact's effectiveness will essentially depend upon how strictly it will be applied. So far, the voting procedures in the EU-Council, which are crucial for sanctioning excessive deficits, has not been the subject of a detailed study in the literature on the pact. An analysis of the distribution of voting power when voting on an excessive deficit reveals that it is rather easy to bloc the imposition of sanctions, especially for relatively large EU-states and for those EMU-members opposing the imposition of sanctions. In addition to the institutional handicaps of the pact one can expect reciprocal voting behavior in the pact, which will further reduce the probability that a country with an excessive deficit in EMU will actually have to pay a fine. An experimental study into voting behavior in relatively small groups confirms this result. (author)

  4. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    reaction (PCR), oligo hybridization and DNA sequencing. Proper primer design is actually one of the most important factors/steps in successful DNA sequencing. Various bioinformatics programs are available for selection of primer pairs from a template sequence. The plethora programs for PCR primer design reflects the.

  5. "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).…

  6. 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:…

  7. 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...

  8. 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…

  9. 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...

  10. 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…

  11. Bioboxes: standardised containers for interchangeable bioinformatics software.

    Science.gov (United States)

    Belmann, Peter; Dröge, Johannes; Bremges, Andreas; McHardy, Alice C; Sczyrba, Alexander; Barton, Michael D

    2015-01-01

    Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable.

  12. 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 ...

  13. SPECIES DATABASES AND THE BIOINFORMATICS REVOLUTION.

    Science.gov (United States)

    Biological databases are having a growth spurt. Much of this results from research in genetics and biodiversity, coupled with fast-paced developments in information technology. The revolution in bioinformatics, defined by Sugden and Pennisi (2000) as the "tools and techniques for...

  14. 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

  15. Turkey and European Security Institutions

    Science.gov (United States)

    2009-03-01

    Korean War, when Turkey sent troops in support of the United Nations defense of South Korea. As a Muslim country, Turkey’s cooperation with the United...history of Turkish cinema : “Valley of the Wolves Iraq.” The United States military deemed the film and its viewers potentially dangerous enough that

  16. 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.

  17. 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

  18. Shared Bioinformatics Databases within the Unipro UGENE Platform

    Directory of Open Access Journals (Sweden)

    Protsyuk Ivan V.

    2015-03-01

    Full Text Available Unipro UGENE is an open-source bioinformatics toolkit that integrates popular tools along with original instruments for molecular biologists within a unified user interface. Nowadays, most bioinformatics desktop applications, including UGENE, make use of a local data model while processing different types of data. Such an approach causes an inconvenience for scientists working cooperatively and relying on the same data. This refers to the need of making multiple copies of certain files for every workplace and maintaining synchronization between them in case of modifications. Therefore, we focused on delivering a collaborative work into the UGENE user experience. Currently, several UGENE installations can be connected to a designated shared database and users can interact with it simultaneously. Such databases can be created by UGENE users and be used at their discretion. Objects of each data type, supported by UGENE such as sequences, annotations, multiple alignments, etc., can now be easily imported from or exported to a remote storage. One of the main advantages of this system, compared to existing ones, is the almost simultaneous access of client applications to shared data regardless of their volume. Moreover, the system is capable of storing millions of objects. The storage itself is a regular database server so even an inexpert user is able to deploy it. Thus, UGENE may provide access to shared data for users located, for example, in the same laboratory or institution. UGENE is available at: http://ugene.net/download.html.

  19. 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

  20. European Community.

    Science.gov (United States)

    1987-05-01

    The European Community was established in 1951 to reconcile France and Germany after World War II and to make possible the eventual federation of Europe. By 1986, there were 12 member countries: France, Italy, Belgium, the Federal Republic of Germany, Luxembourg, the Netherlands, Denmark, Ireland, the United Kingdom, Greece, Spain, and Portugal. Principal areas of concern are internal and external trade, agriculture, monetary coordination, fisheries, common industrial and commercial policies, assistance, science and research, and common social and regional policies. The European Community has a budget of US$34.035 billion/year, funded by customs duties and 1.4% of each member's value-added tax. The treaties establishing the European Community call for members to form a common market, a common customs tariff, and common agricultural, transport, economic, and nuclear policies. Major European Community institutions include the Commission, Council of Ministers, European Parliament, Court of Justice, and Economic and Social Committee. The Community is the world's largest trading unit, accounting for 15% of world trade. The 2 main goals of the Community's industrial policy are to create an open internal market and to promote technological innovation in order to improve international competitiveness. The European Community aims to contribute to the economic and social development of Third World countries as well.

  1. 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…

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. The growing need for microservices in bioinformatics.

    Science.gov (United States)

    Williams, Christopher L; Sica, Jeffrey C; Killen, Robert T; Balis, Ulysses G J

    2016-01-01

    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. Bioinformatics relies on nimble IT framework which can adapt to changing requirements. To present a well-established software design and deployment strategy as a solution for current challenges within bioinformatics. Use of the microservices framework is an effective methodology for the fabrication and

  8. The growing need for microservices in bioinformatics

    Science.gov (United States)

    Williams, Christopher L.; Sica, Jeffrey C.; Killen, Robert T.; Balis, Ulysses G. J.

    2016-01-01

    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 is an effective

  9. Bioinformatics of cardiovascular miRNA biology.

    Science.gov (United States)

    Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

    2015-12-01

    MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Comprehensive decision tree models in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Gregor Stiglic

    Full Text Available PURPOSE: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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

  11. 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

  12. Penalized feature selection and classification in bioinformatics

    OpenAIRE

    Ma, Shuangge; Huang, Jian

    2008-01-01

    In bioinformatics studies, supervised classification with high-dimensional input variables is frequently encountered. Examples routinely arise in genomic, epigenetic and proteomic studies. Feature selection can be employed along with classifier construction to avoid over-fitting, to generate more reliable classifier and to provide more insights into the underlying causal relationships. In this article, we provide a review of several recently developed penalized feature selection and classific...

  13. 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...

  14. Adapting bioinformatics curricula for big data.

    Science.gov (United States)

    Greene, Anna C; Giffin, Kristine A; Greene, Casey S; Moore, Jason H

    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. © The Author 2015. Published by Oxford University Press.

  15. 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. PMID:25050811

  16. Application of Bioinformatics in Chronobiology Research

    Directory of Open Access Journals (Sweden)

    Robson da Silva Lopes

    2013-01-01

    Full Text Available Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through “omics” projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. European Identity and European Citizenship: the Case of Missing Polis?

    Czech Academy of Sciences Publication Activity Database

    Šejvl, Michal

    2008-01-01

    Roč. 2, č. 2 (2008), s. 49-56 ISSN 1789-1035 Institutional research plan: CEZ:AV0Z70680506 Keywords : the European integration * law of citizenship * European identity Subject RIV: AG - Legal Sciences

  2. 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.

  3. Modern bioinformatics meets traditional Chinese medicine.

    Science.gov (United States)

    Gu, Peiqin; Chen, Huajun

    2014-11-01

    Traditional Chinese medicine (TCM) is gaining increasing attention with the emergence of integrative medicine and personalized medicine, characterized by pattern differentiation on individual variance and treatments based on natural herbal synergism. Investigating the effectiveness and safety of the potential mechanisms of TCM and the combination principles of drug therapies will bridge the cultural gap with Western medicine and improve the development of integrative medicine. Dealing with rapidly growing amounts of biomedical data and their heterogeneous nature are two important tasks among modern biomedical communities. Bioinformatics, as an emerging interdisciplinary field of computer science and biology, has become a useful tool for easing the data deluge pressure by automating the computation processes with informatics methods. Using these methods to retrieve, store and analyze the biomedical data can effectively reveal the associated knowledge hidden in the data, and thus promote the discovery of integrated information. Recently, these techniques of bioinformatics have been used for facilitating the interactional effects of both Western medicine and TCM. The analysis of TCM data using computational technologies provides biological evidence for the basic understanding of TCM mechanisms, safety and efficacy of TCM treatments. At the same time, the carrier and targets associated with TCM remedies can inspire the rethinking of modern drug development. This review summarizes the significant achievements of applying bioinformatics techniques to many aspects of the research in TCM, such as analysis of TCM-related '-omics' data and techniques for analyzing biological processes and pharmaceutical mechanisms of TCM, which have shown certain potential of bringing new thoughts to both sides. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  4. Multiobjective optimization in bioinformatics and computational biology.

    Science.gov (United States)

    Handl, Julia; Kell, Douglas B; Knowles, Joshua

    2007-01-01

    This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

  5. 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.

  6. 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.

  7. 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...... institutional investors in two Scandinavian countries with diminutive legal and cultural distance in general. Research Findings/Insights: Using data on shareholder proposals from Danish and Swedish annual general meetings from 2006 throughout 2010, we find that institutional investors are approximately....../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....

  8. 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…

  9. OpenHelix: bioinformatics education outside of a different box.

    Science.gov (United States)

    Williams, Jennifer M; Mangan, Mary E; Perreault-Micale, Cynthia; Lathe, Scott; Sirohi, Neeraj; Lathe, Warren C

    2010-11-01

    The amount of biological data is increasing rapidly, and will continue to increase as new rapid technologies are developed. Professionals in every area of bioscience will have data management needs that require publicly available bioinformatics resources. Not all scientists desire a formal bioinformatics education but would benefit from more informal educational sources of learning. Effective bioinformatics education formats will address a broad range of scientific needs, will be aimed at a variety of user skill levels, and will be delivered in a number of different formats to address different learning styles. Informal sources of bioinformatics education that are effective are available, and will be explored in this review.

  10. RISE OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY IN INDIA: A LOOK THROUGH PUBLICATIONS

    Directory of Open Access Journals (Sweden)

    Anjali Srivastava

    2017-09-01

    Full Text Available Computational biology and bioinformatics have been part and parcel of biomedical research for few decades now. However, the institutionalization of bioinformatics research took place with the establishment of Distributed Information Centres (DISCs in the research institutions of repute in various disciplines by the Department of Biotechnology, Government of India. Though, at initial stages, this endeavor was mainly focused on providing infrastructure for using information technology and internet based communication and tools for carrying out computational biology and in-silico assisted research in varied arena of research starting from disease biology to agricultural crops, spices, veterinary science and many more, the natural outcome of establishment of such facilities resulted into new experiments with bioinformatics tools. Thus, Biotechnology Information Systems (BTIS grew into a solid movement and a large number of publications started coming out of these centres. In the end of last century, bioinformatics started developing like a full-fledged research subject. In the last decade, a need was felt to actually make a factual estimation of the result of this endeavor of DBT which had, by then, established about two hundred centres in almost all disciplines of biomedical research. In a bid to evaluate the efforts and outcome of these centres, BTIS Centre at CSIR-CDRI, Lucknow was entrusted with collecting and collating the publications of these centres. However, when the full data was compiled, the DBT task force felt that the study must include Non-BTIS centres also so as to expand the report to have a glimpse of bioinformatics publications from the country.

  11. Introduction: European climate leadership

    NARCIS (Netherlands)

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

    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

  12. European Analytical Column

    DEFF Research Database (Denmark)

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

    2009-01-01

    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...

  13. Widening participation would be key in enhancing bioinformatics and genomics research in Africa

    Directory of Open Access Journals (Sweden)

    Thomas K. Karikari

    2015-09-01

    Full Text Available Bioinformatics and genome science (BGS are gradually gaining roots in Africa, contributing to studies that are leading to improved understanding of health, disease, agriculture and food security. While a few African countries have established foundations for research and training in these areas, BGS appear to be limited to only a few institutions in specific African countries. However, improving the disciplines in Africa will require pragmatic efforts to expand training and research partnerships to scientists in yet-unreached institutions. Here, we discuss the need to expand BGS programmes in Africa, and propose mechanisms to do so.

  14. On the substantial contribution of "contempt" as a folk affect concept to the history of the European popular institution of charivari.

    Science.gov (United States)

    Neagota, Bogdan; Benga, Ileana; Benga, Oana

    2017-01-01

    The integration of the folk affect concept of "contempt" into the analysis of the complex institution known generally as charivari is mutually beneficial for both ethno-anthropology (which may thus access inner causes for disputed social and collective behaviors) and evolutionary psychology (which may thus study the length of tradition together with the width of the institution spread, serving the same social functions).

  15. 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.

  16. Bioinformatics for Next Generation Sequencing Data

    Directory of Open Access Journals (Sweden)

    Alberto Magi

    2010-09-01

    Full Text Available The emergence of next-generation sequencing (NGS platforms imposes increasing demands on statistical methods and bioinformatic tools for the analysis and the management of the huge amounts of data generated by these technologies. Even at the early stages of their commercial availability, a large number of softwares already exist for analyzing NGS data. These tools can be fit into many general categories including alignment of sequence reads to a reference, base-calling and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection and genome browsing. This manuscript aims to guide readers in the choice of the available computational tools that can be used to face the several steps of the data analysis workflow.

  17. Combining multiple decisions: applications to bioinformatics

    International Nuclear Information System (INIS)

    Yukinawa, N; Ishii, S; Takenouchi, T; Oba, S

    2008-01-01

    Multi-class classification is one of the fundamental tasks in bioinformatics and typically arises in cancer diagnosis studies by gene expression profiling. This article reviews two recent approaches to multi-class classification by combining multiple binary classifiers, which are formulated based on a unified framework of error-correcting output coding (ECOC). The first approach is to construct a multi-class classifier in which each binary classifier to be aggregated has a weight value to be optimally tuned based on the observed data. In the second approach, misclassification of each binary classifier is formulated as a bit inversion error with a probabilistic model by making an analogy to the context of information transmission theory. Experimental studies using various real-world datasets including cancer classification problems reveal that both of the new methods are superior or comparable to other multi-class classification methods

  18. 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.

  19. 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.

  20. 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...

  1. Evaluating an Inquiry-Based Bioinformatics Course Using Q Methodology

    Science.gov (United States)

    Ramlo, Susan E.; McConnell, David; Duan, Zhong-Hui; Moore, Francisco B.

    2008-01-01

    Faculty at a Midwestern metropolitan public university recently developed a course on bioinformatics that emphasized collaboration and inquiry. Bioinformatics, essentially the application of computational tools to biological data, is inherently interdisciplinary. Thus part of the challenge of creating this course was serving the needs and…

  2. Bioinformatics education dissemination with an evolutionary problem solving perspective.

    Science.gov (United States)

    Jungck, John R; Donovan, Samuel S; Weisstein, Anton E; Khiripet, Noppadon; Everse, Stephen J

    2010-11-01

    Bioinformatics is central to biology education in the 21st century. With the generation of terabytes of data per day, the application of computer-based tools to stored and distributed data is fundamentally changing research and its application to problems in medicine, agriculture, conservation and forensics. In light of this 'information revolution,' undergraduate biology curricula must be redesigned to prepare the next generation of informed citizens as well as those who will pursue careers in the life sciences. The BEDROCK initiative (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting together) has fostered an international community of bioinformatics educators. The initiative's goals are to: (i) Identify and support faculty who can take leadership roles in bioinformatics education; (ii) Highlight and distribute innovative approaches to incorporating evolutionary bioinformatics data and techniques throughout undergraduate education; (iii) Establish mechanisms for the broad dissemination of bioinformatics resource materials and teaching models; (iv) Emphasize phylogenetic thinking and problem solving; and (v) Develop and publish new software tools to help students develop and test evolutionary hypotheses. Since 2002, BEDROCK has offered more than 50 faculty workshops around the world, published many resources and supported an environment for developing and sharing bioinformatics education approaches. The BEDROCK initiative builds on the established pedagogical philosophy and academic community of the BioQUEST Curriculum Consortium to assemble the diverse intellectual and human resources required to sustain an international reform effort in undergraduate bioinformatics education.

  3. 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 ...

  4. 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 ...

  5. 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…

  6. 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…

  7. 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 ...

  8. 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 ...

  9. 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.

  10. Is there room for ethics within bioinformatics education?

    Science.gov (United States)

    Taneri, Bahar

    2011-07-01

    When bioinformatics education is considered, several issues are addressed. At the undergraduate level, the main issue revolves around conveying information from two main and different fields: biology and computer science. At the graduate level, the main issue is bridging the gap between biology students and computer science students. However, there is an educational component that is rarely addressed within the context of bioinformatics education: the ethics component. Here, a different perspective is provided on bioinformatics education, and the current status of ethics is analyzed within the existing bioinformatics programs. Analysis of the existing undergraduate and graduate programs, in both Europe and the United States, reveals the minimal attention given to ethics within bioinformatics education. Given that bioinformaticians speedily and effectively shape the biomedical sciences and hence their implications for society, here redesigning of the bioinformatics curricula is suggested in order to integrate the necessary ethics education. Unique ethical problems awaiting bioinformaticians and bioinformatics ethics as a separate field of study are discussed. In addition, a template for an "Ethics in Bioinformatics" course is provided.

  11. 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.

  12. 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.

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

    Science.gov (United States)

    Mulder, Nicola; Schwartz, Russell; Brazas, Michelle D; Brooksbank, Cath; Gaeta, Bruno; Morgan, Sarah L; Pauley, Mark A; Rosenwald, Anne; Rustici, Gabriella; Sierk, Michael; Warnow, Tandy; Welch, Lonnie

    2018-02-01

    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.

  14. 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

  15. 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

  16. A generally applicable lightweight method for calculating a value structure for tools and services in bioinformatics infrastructure projects.

    Science.gov (United States)

    Mayer, Gerhard; Quast, Christian; Felden, Janine; Lange, Matthias; Prinz, Manuel; Pühler, Alfred; Lawerenz, Chris; Scholz, Uwe; Glöckner, Frank Oliver; Müller, Wolfgang; Marcus, Katrin; Eisenacher, Martin

    2017-10-30

    Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific 'service provision units' is introduced together with the factors influencing them and the main underlying assumptions for these 'value influencing factors'. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared. © The Author 2017. Published by Oxford University Press.

  17. EDUCast@fccn: An example of European cooperation to implement the production of AV content in Higher Education Institutions in Portugal

    OpenAIRE

    Samuel Martins; Hugo Ribeiro; Rui Ribeiro; Nelson Dias

    2012-01-01

    The specific logistics of each Higher Education Institution (HEI) in Portugal and the specific teaching of each academic community are some of the major challenges faced by technical staff, administrative staff and educational support staff of these institutions when trying to find an appropriate solution for the provision of audiovisual content. In this sense, it was developed since 2010 an innovative partnership initiated by the Portuguese Foundation for National Scientific Computing (FCCN)...

  18. European Research Reloaded : Cooperation and Integration Among Europeanized States

    NARCIS (Netherlands)

    Holzhacker, Ron; Haverland, Markus

    2006-01-01

    European integration has had an ever deepening impact on the member states. The first wave of research concerned the process of institution building and policy developments at the European Union (EU) level. The second wave, on Europeanization used the resulting integration as an explanatory factor

  19. 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.

  20. PATRIC, the bacterial bioinformatics database and analysis resource

    Science.gov (United States)

    Wattam, Alice R.; Abraham, David; Dalay, Oral; Disz, Terry L.; Driscoll, Timothy; Gabbard, Joseph L.; Gillespie, Joseph J.; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K.; Olson, Robert; Overbeek, Ross; Pusch, Gordon D.; Shukla, Maulik; Schulman, Julie; Stevens, Rick L.; Sullivan, Daniel E.; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J.C.; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W.

    2014-01-01

    The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue. PMID:24225323

  1. PATRIC, the bacterial bioinformatics database and analysis resource.

    Science.gov (United States)

    Wattam, Alice R; Abraham, David; Dalay, Oral; Disz, Terry L; Driscoll, Timothy; Gabbard, Joseph L; Gillespie, Joseph J; Gough, Roger; Hix, Deborah; Kenyon, Ronald; Machi, Dustin; Mao, Chunhong; Nordberg, Eric K; Olson, Robert; Overbeek, Ross; Pusch, Gordon D; Shukla, Maulik; Schulman, Julie; Stevens, Rick L; Sullivan, Daniel E; Vonstein, Veronika; Warren, Andrew; Will, Rebecca; Wilson, Meredith J C; Yoo, Hyun Seung; Zhang, Chengdong; Zhang, Yan; Sobral, Bruno W

    2014-01-01

    The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10,000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.

  2. 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

  3. Bioinformatics research in the Asia Pacific: a 2007 update.

    Science.gov (United States)

    Ranganathan, Shoba; Gribskov, Michael; Tan, Tin Wee

    2008-01-01

    We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.

  4. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.

    Science.gov (United States)

    Brazas, Michelle D; Ouellette, B F Francis

    2016-06-01

    Bioinformatics.ca has been hosting continuing education programs in introductory and advanced bioinformatics topics in Canada since 1999 and has trained more than 2,000 participants to date. These workshops have been adapted over the years to keep pace with advances in both science and technology as well as the changing landscape in available learning modalities and the bioinformatics training needs of our audience. Post-workshop surveys have been a mandatory component of each workshop and are used to ensure appropriate adjustments are made to workshops to maximize learning. However, neither bioinformatics.ca nor others offering similar training programs have explored the long-term impact of bioinformatics continuing education training. Bioinformatics.ca recently initiated a look back on the impact its workshops have had on the career trajectories, research outcomes, publications, and collaborations of its participants. Using an anonymous online survey, bioinformatics.ca analyzed responses from those surveyed and discovered its workshops have had a positive impact on collaborations, research, publications, and career progression.

  5. 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.

  6. 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.

  7. Bioinformatics in cancer therapy and drug design

    International Nuclear Information System (INIS)

    Horbach, D.Y.; Usanov, S.A.

    2005-01-01

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  8. Bioinformatics in cancer therapy and drug design

    Energy Technology Data Exchange (ETDEWEB)

    Horbach, D Y [International A. Sakharov environmental univ., Minsk (Belarus); Usanov, S A [Inst. of bioorganic chemistry, National academy of sciences of Belarus, Minsk (Belarus)

    2005-05-15

    One of the mechanisms of external signal transduction (ionizing radiation, toxicants, stress) to the target cell is the existence of membrane and intracellular proteins with intrinsic tyrosine kinase activity. No wonder that etiology of malignant growth links to abnormalities in signal transduction through tyrosine kinases. The epidermal growth factor receptor (EGFR) tyrosine kinases play fundamental roles in development, proliferation and differentiation of tissues of epithelial, mesenchymal and neuronal origin. There are four types of EGFR: EGF receptor (ErbB1/HER1), ErbB2/Neu/HER2, ErbB3/HER3 and ErbB4/HER4. Abnormal expression of EGFR, appearance of receptor mutants with changed ability to protein-protein interactions or increased tyrosine kinase activity have been implicated in the malignancy of different types of human tumors. Bioinformatics is currently using in investigation on design and selection of drugs that can make alterations in structure or competitively bind with receptors and so display antagonistic characteristics. (authors)

  9. 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.

  10. Parallel evolutionary computation in bioinformatics applications.

    Science.gov (United States)

    Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

    2013-05-01

    A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  11. 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....

  12. An Overview of Bioinformatics Tools and Resources in Allergy.

    Science.gov (United States)

    Fu, Zhiyan; Lin, Jing

    2017-01-01

    The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.

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

    NARCIS (Netherlands)

    Killaspy, Helen; King, Michael; Wright, Christine; White, Sarah; McCrone, Paul; Kallert, Thomas; Cervilla, Jorge; Raboch, Jiri; Onchev, Georgi; Mezzina, Roberto; Wiersma, Durk; Kiejna, Andrzej; Ploumpidis, Dimitris; Caldas de Almeida, Jose Miguel

    2009-01-01

    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

  14. Round Table: Integrating radiation protection research in the EU - European Joint Programme and participation of the Slovak Republic and Czech Republic national institutions in it

    International Nuclear Information System (INIS)

    Duranova, T.; Bohunova, J.; Raskop, W.; Schneider, T.; Liland, A.; Andronopoulos, S.; Mustonen, R.

    2014-01-01

    Activities of the NERIS-TP association are described. The NERIS ICRP Workshop, held in Bratislava, Slovak Republic in February 6-8, 2012, was organized by VUJE in cooperation with ICRP aiming to provide a forum for discussion and sharing of experiences on the implementation of the ICRP Recommendations. International, European and national perspectives were presented. 88 specialists from 51 organizations from 26 countries participated in the workshop. The final Dissemination Workshop 'Strengthening the Preparedness at National and Territorial Level Using New Tools and Methods - Stakeholders Experiences', was conducted in Oslo from 22 to 24 January 2014. International organisations such as HERCA, EC DG Research, IAEA, OECD/NEA, and NGOs such as NTW (Nuclear Transparency Watch) and GMF (Group of European Municipalities with Nuclear Facilities) as well as representatives of the OPERRA project participated in the workshop and particular panels. 82 experts and stakeholders participated in the workshop, representing twenty countries. Notably, participants from Japanese organisations provided first feedback from the management of the consequences of the Fukushima accident. (authors)

  15. IMRT credentialing for prospective trials using institutional virtual phantoms: results of a joint European Organization for the Research and Treatment of Cancer and Radiological Physics Center project

    International Nuclear Information System (INIS)

    Weber, Damien C; Vallet, Veronique; Molineu, Andrea; Melidis, Christos; Teglas, Vanda; Naudy, Suzanne; Moeckli, Raphael; Followill, David S; Hurkmans, Coen W

    2014-01-01

    Intensity-modulated radiotherapy (IMRT) credentialing for a EORTC study was performed using an anthropomorphic head phantom from the Radiological Physics Center (RPC; RPC PH ). Institutions were retrospectively requested to irradiate their institutional phantom (INST PH ) using the same treatment plan in the framework of a Virtual Phantom Project (VPP) for IMRT credentialing. CT data set of the institutional phantom and measured 2D dose matrices were requested from centers and sent to a dedicated secure EORTC uploader. Data from the RPC PH and INST PH were thereafter centrally analyzed and inter-compared by the QA team using commercially available software (RIT; ver.5.2; Colorado Springs, USA). Eighteen institutions participated to the VPP. The measurements of 6 (33%) institutions could not be analyzed centrally. All other centers passed both the VPP and the RPC ±7%/4 mm credentialing criteria. At the 5%/5 mm gamma criteria (90% of pixels passing), 11(92%) as compared to 12 (100%) centers pass the credentialing process with RPC PH and INST PH (p = 0.29), respectively. The corresponding pass rate for the 3%/3 mm gamma criteria (90% of pixels passing) was 2 (17%) and 9 (75%; p = 0.01), respectively. IMRT dosimetry gamma evaluations in a single plane for a H&N prospective trial using the INST PH measurements showed agreement at the gamma index criteria of ±5%/5 mm (90% of pixels passing) for a small number of VPP measurements. Using more stringent, criteria, the RPC PH and INST PH comparison showed disagreement. More data is warranted and urgently required within the framework of prospective studies

  16. 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

  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. Development of a cloud-based Bioinformatics Training Platform.

    Science.gov (United States)

    Revote, Jerico; Watson-Haigh, Nathan S; Quenette, Steve; Bethwaite, Blair; McGrath, Annette; Shang, Catherine A

    2017-05-01

    The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP. © The Author 2016. Published by Oxford University Press.

  19. An Adaptive Hybrid Multiprocessor technique for bioinformatics sequence alignment

    KAUST Repository

    Bonny, Talal; Salama, Khaled N.; Zidan, Mohammed A.

    2012-01-01

    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

  20. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

    Science.gov (United States)

    Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

    2016-09-29

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.

  1. 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 ...

  2. Best practices in bioinformatics training for life scientists.

    KAUST Repository

    Via, Allegra; Blicher, Thomas; Bongcam-Rudloff, Erik; Brazas, Michelle D; Brooksbank, Cath; Budd, Aidan; De Las Rivas, Javier; Dreyer, Jacqueline; Fernandes, Pedro L; van Gelder, Celia; Jacob, Joachim; Jimenez, Rafael C; Loveland, Jane; Moran, Federico; Mulder, Nicola; Nyrö nen, Tommi; Rother, Kristian; Schneider, Maria Victoria; Attwood, Teresa K

    2013-01-01

    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

  3. Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

    Science.gov (United States)

    Diaz Acosta, B.

    2011-01-01

    The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

  4. Bioinformatics tools for development of fast and cost effective simple ...

    African Journals Online (AJOL)

    Bioinformatics tools for development of fast and cost effective simple sequence repeat ... comparative mapping and exploration of functional genetic diversity in the ... Already, a number of computer programs have been implemented that aim at ...

  5. Social closure and discriminatory practices related to the Roma minority in the Czech Republic through the perspective of national and European institutions

    Directory of Open Access Journals (Sweden)

    Lucie Cviklová

    2011-01-01

    Full Text Available While differentiating among notions of social exclusion, social closure and bridging social capital, the article analyses the evolution of cultural and social borders between the Czech majority on the one hand and the Roma minority on the other. Special attention has been paid to current legal practices concerning discrimination which have shifted the burden of proof in favor of ethnic minorities and have introduced cleavages between the processes of direct and indirect discrimination. It is explained that the unequal access to elementary education has been crucial in generating social exclusion of the minority. In relation to this, the landmark decision of the European Court of Human Rights is discussed, as it particularly highlights the importance of educational segregation of Roma people in Czech schools for children with learning disabilities.

  6. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Science.gov (United States)

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  7. PubData: search engine for bioinformatics databases worldwide

    OpenAIRE

    Vand, Kasra; Wahlestedt, Thor; Khomtchouk, Kelly; Sayed, Mohammed; Wahlestedt, Claes; Khomtchouk, Bohdan

    2016-01-01

    We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the use...

  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. 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.

  11. An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.

    Science.gov (United States)

    Gerstein, Mark; Greenbaum, Dov; Cheung, Kei; Miller, Perry L

    2007-02-01

    Computational biology and bioinformatics (CBB), the terms often used interchangeably, represent a rapidly evolving biological discipline. With the clear potential for discovery and innovation, and the need to deal with the deluge of biological data, many academic institutions are committing significant resources to develop CBB research and training programs. Yale formally established an interdepartmental Ph.D. program in CBB in May 2003. This paper describes Yale's program, discussing the scope of the field, the program's goals and curriculum, as well as a number of issues that arose in implementing the program. (Further updated information is available from the program's website, www.cbb.yale.edu.)

  12. 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

  13. The European Social Survey and European research policy

    DEFF Research Database (Denmark)

    Kropp, Kristoffer

    2017-01-01

    This article analyses the history of the European Social Survey (ESS) and its relationship to changes in European research policy, using Bourdieu’s field-analytical approach. It argues that the success of the ESS relied on three interwoven processes that we can understand theoretically in terms...... of the establishment of homological structures and the formation of conjunctural alliances between the field of European social-scientific research and the field of European policy. The three interwoven processes that I depict are: first, the production of a European field of social research, connected to both...... European and national scientific institutions; second, the establishment of European Union (EU) institutions and organisations that were able to identify and link up with social researchers; and third, the formation of conjunctural alliances between the two fields (social science and EU research policy...

  14. 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......Discourse analysis as a methodology is perhaps not readily associated with substantive causality claims. At the same time the study of discourses is very much the study of conceptions of causal relations among a set, or sets, of agents. Within Europeanization research we have seen endeavours......, it suggests that discourse analysis and the study of causality are by no means opposites. The study of Europeanization discourses may even be seen as an essential step in the move towards claims of causality in Europeanization research. This chapter deals with the question of how we may move from the study...

  15. 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?

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

    Science.gov (United States)

    2012-01-01

    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 Virtual Machines, allowing the

  17. 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

  18. 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.

  19. 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.

  20. European Integration and Postcolonial Sovereignty Games

    DEFF Research Database (Denmark)

    observation, textual, legal and institutional analysis for a new theoretical approach to understanding the strategic possibilities and subjectivity of non-sovereign entities in international politics. Bringing together research on European integration and postcolonial theory, European Integration...

  1. Documenting the emergence of bio-ontologies: or, why researching bioinformatics requires HPSSB.

    Science.gov (United States)

    Leonelli, Sabina

    2010-01-01

    This paper reflects on the analytic challenges emerging from the study of bioinformatic tools recently created to store and disseminate biological data, such as databases, repositories, and bio-ontologies. I focus my discussion on the Gene Ontology, a term that defines three entities at once: a classification system facilitating the distribution and use of genomic data as evidence towards new insights; an expert community specialised in the curation of those data; and a scientific institution promoting the use of this tool among experimental biologists. These three dimensions of the Gene Ontology can be clearly distinguished analytically, but are tightly intertwined in practice. I suggest that this is true of all bioinformatic tools: they need to be understood simultaneously as epistemic, social, and institutional entities, since they shape the knowledge extracted from data and at the same time regulate the organisation, development, and communication of research. This viewpoint has one important implication for the methodologies used to study these tools; that is, the need to integrate historical, philosophical, and sociological approaches. I illustrate this claim through examples of misunderstandings that may result from a narrowly disciplinary study of the Gene Ontology, as I experienced them in my own research.

  2. Bioinformatics in the Netherlands: the value of a nationwide community.

    Science.gov (United States)

    van Gelder, Celia W G; Hooft, Rob W W; van Rijswijk, Merlijn N; van den Berg, Linda; Kok, Ruben G; Reinders, Marcel; Mons, Barend; Heringa, Jaap

    2017-09-15

    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 supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly. © The Author 2017. Published by Oxford University Press.

  3. 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.

  4. Genomics and bioinformatics resources for translational science in Rosaceae.

    Science.gov (United States)

    Jung, Sook; Main, Dorrie

    2014-01-01

    Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

  5. 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.

  6. Best practices in bioinformatics training for life scientists

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...... 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...

  7. European Union

    International Nuclear Information System (INIS)

    Schaller, K.

    1995-01-01

    Different instruments used by European Commission of the European Union for financial support radioactive waste management activities in the Russian Federation are outlined. Three particular programmes in the area are described

  8. The Evolution of European Security: From Confrontation to Cooperation

    Science.gov (United States)

    2013-03-01

    Vasconcelos , (Paris: The European Union Institute for Security Studies, 2009), 41. 60 Ibid. 61 European Union Home Page, “Common Security and...of ESDP,” in What Ambitions for European Defense in 2020?, 2nd ed., ed. Álvaro de Vasconcelos (Paris: The European Union Institute for Security

  9. Integr8: enhanced inter-operability of European molecular biology databases.

    Science.gov (United States)

    Kersey, P J; Morris, L; Hermjakob, H; Apweiler, R

    2003-01-01

    The increasing production of molecular biology data in the post-genomic era, and the proliferation of databases that store it, require the development of an integrative layer in database services to facilitate the synthesis of related information. The solution of this problem is made more difficult by the absence of universal identifiers for biological entities, and the breadth and variety of available data. Integr8 was modelled using UML (Universal Modelling Language). Integr8 is being implemented as an n-tier system using a modern object-oriented programming language (Java). An object-relational mapping tool, OJB, is being used to specify the interface between the upper layers and an underlying relational database. The European Bioinformatics Institute is launching the Integr8 project. Integr8 will be an automatically populated database in which we will maintain stable identifiers for biological entities, describe their relationships with each other (in accordance with the central dogma of biology), and store equivalences between identified entities in the source databases. Only core data will be stored in Integr8, with web links to the source databases providing further information. Integr8 will provide the integrative layer of the next generation of bioinformatics services from the EBI. Web-based interfaces will be developed to offer gene-centric views of the integrated data, presenting (where known) the links between genome, proteome and phenotype.

  10. 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

  11. 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.

  12. 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.

  13. Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

    Science.gov (United States)

    Lima, Andre O. S.; Garces, Sergio P. S.

    2006-01-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

  14. 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

  15. Bioinformatic tools and guideline for PCR primer design | Abd ...

    African Journals Online (AJOL)

    Bioinformatics has become an essential tool not only for basic research but also for applied research in biotechnology and biomedical sciences. Optimal primer sequence and appropriate primer concentration are essential for maximal specificity and efficiency of PCR. A poorly designed primer can result in little or no ...

  16. 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...

  17. 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…

  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. Bioinformatics for Undergraduates: Steps toward a Quantitative Bioscience Curriculum

    Science.gov (United States)

    Chapman, Barbara S.; Christmann, James L.; Thatcher, Eileen F.

    2006-01-01

    We describe an innovative bioinformatics course developed under grants from the National Science Foundation and the California State University Program in Research and Education in Biotechnology for undergraduate biology students. The project has been part of a continuing effort to offer students classroom experiences focused on principles and…

  20. 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

  1. 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. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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

    Indian Academy of Sciences (India)

    Rapid cloning and bioinformatic analysis of spinach Y chromosome- specific EST sequences. Chuan-Liang Deng, Wei-Li Zhang, Ying Cao, Shao-Jing Wang, ... Arabidopsis thaliana mRNA for mitochondrial half-ABC transporter (STA1 gene). 389 2.31E-13. 98.96. SP3−12. Betula pendula histidine kinase 3 (HK3) mRNA, ...

  3. 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.

  4. A comparison of the treatment recommendations for neurogenic lower urinary tract dysfunction in the national institute for health and care excellence, European Association of Urology and international consultations on incontinence guidelines.

    Science.gov (United States)

    Jaggi, Ashley; Drake, Marcus; Siddiqui, Emad; Fatoye, Francis

    2018-04-17

    Healthcare guidelines are an important vehicle in establishing up-to-date evidence based medicine (EBM) in clinical practice. Due to varying development processes, clinical guidelines created by different institutions can often contain contrasting recommendations. This can have implications for optimal and standardized patient care across management settings. The similarities and differences of treatment recommendations made in the National Institute for Health and Care Excellence (NICE), The European Association of Urology (EAU), and the International Consultation on Continence (ICI) guidelines for neurogenic lower urinary tract dysfunction (NLUTD) were assessed. The guidelines generally agree on their approach to conservative management, including behavioral therapies, and catheterization techniques. There was discrepancy on the benefit of using an alpha blocker in NLUTD and bladder outlet obstruction (BOO) and administering Botulinum toxin A (Onabotulinum-A) in NLUTD. The highest degree of divergence was seen in recommendations for surgical treatments, where the EAU made gender-specific recommendations, and gave continent urinary diversion higher preference than given in the NICE and ICI guidelines. In the absence of high-quality clinical evidence, many of the recommendations made across all three guidelines are based on expert opinion. NICE, the EAU and ICI have similarities but they place differing emphasis on costs and expert opinion, which translated in notably different recommendations. It is evident that increased research efforts, possibly in the form of prospective registries, pragmatic trials, and resource utilization studies are necessary to improve the underlying evidence base for NLUTD, and subsequently the strength and concordance of recommendations across guidelines. © 2018 Wiley Periodicals, Inc.

  5. Bioclipse: an open source workbench for chemo- and bioinformatics

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

    Full Text Available Abstract Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL, an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

  6. 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

  7. BioWarehouse: a bioinformatics database warehouse toolkit.

    Science.gov (United States)

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

    2006-03-23

    This article addresses the problem of interoperation of heterogeneous bioinformatics databases. 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. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

  8. 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.

  9. 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 …

  10. "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.

  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. Are Central European countries’ financial institutions embedded?

    NARCIS (Netherlands)

    Jong, E. de; Hooijdonk, C.J.J. van

    2010-01-01

    The fall of the Iron Curtain in 1989 was one of the causes of an increased interest in the relation between economics and culture. An important idea of this literature is that social and economic systems will function properly if they are embedded in a corresponding value system. Although some

  13. 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

  14. 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'…

  15. 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.…

  16. 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.

  17. 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

  18. The European energy community is now

    International Nuclear Information System (INIS)

    Andoura, Sami; Buzek, Jerzy; Delors, Jacques; Vitorino, Antonio

    2013-01-01

    On the eve of the European Council on 22 May dealing with energy issues, the Jacques Delors Institute publishes a Tribune calling for the implementation of a positive agenda for the European energy policy and the definition of the concrete bases of a genuine European Energy

  19. 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.].

  20. 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...

  1. Meeting review: 2002 O'Reilly Bioinformatics Technology Conference.

    Science.gov (United States)

    Counsell, Damian

    2002-01-01

    At the end of January I travelled to the States to speak at and attend the first O'Reilly Bioinformatics Technology Conference. It was a large, well-organized and diverse meeting with an interesting history. Although the meeting was not a typical academic conference, its style will, I am sure, become more typical of meetings in both biological and computational sciences.Speakers at the event included prominent bioinformatics researchers such as Ewan Birney, Terry Gaasterland and Lincoln Stein; authors and leaders in the open source programming community like Damian Conway and Nat Torkington; and representatives from several publishing companies including the Nature Publishing Group, Current Science Group and the President of O'Reilly himself, Tim O'Reilly. There were presentations, tutorials, debates, quizzes and even a 'jam session' for musical bioinformaticists.

  2. 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.

  3. Rise and demise of bioinformatics? Promise and progress.

    Directory of Open Access Journals (Sweden)

    Christos A Ouzounis

    Full Text Available The field of bioinformatics and computational biology has gone through a number of transformations during the past 15 years, establishing itself as a key component of new biology. This spectacular growth has been challenged by a number of disruptive changes in science and technology. Despite the apparent fatigue of the linguistic use of the term itself, bioinformatics has grown perhaps to a point beyond recognition. We explore both historical aspects and future trends and argue that as the field expands, key questions remain unanswered and acquire new meaning while at the same time the range of applications is widening to cover an ever increasing number of biological disciplines. These trends appear to be pointing to a redefinition of certain objectives, milestones, and possibly the field itself.

  4. 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.

  5. Bioinformatics and Microarray Data Analysis on the Cloud.

    Science.gov (United States)

    Calabrese, Barbara; Cannataro, Mario

    2016-01-01

    High-throughput platforms such as microarray, mass spectrometry, and next-generation sequencing are producing an increasing volume of omics data that needs large data storage and computing power. Cloud computing offers massive scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and thus, it may represent the key technology for facing those issues. In fact, in the recent years it has been adopted for the deployment of different bioinformatics solutions and services both in academia and in the industry. Although this, cloud computing presents several issues regarding the security and privacy of data, that are particularly important when analyzing patients data, such as in personalized medicine. This chapter reviews main academic and industrial cloud-based bioinformatics solutions; with a special focus on microarray data analysis solutions and underlines main issues and problems related to the use of such platforms for the storage and analysis of patients data.

  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. 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.  .

  8. 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.

  9. 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...

  10. Neonatal Informatics: Transforming Neonatal Care Through Translational Bioinformatics

    Science.gov (United States)

    Palma, Jonathan P.; Benitz, William E.; Tarczy-Hornoch, Peter; Butte, Atul J.; Longhurst, Christopher A.

    2012-01-01

    The future of neonatal informatics will be driven by the availability of increasingly vast amounts of clinical and genetic data. The field of translational bioinformatics is concerned with linking and learning from these data and applying new findings to clinical care to transform the data into proactive, predictive, preventive, and participatory health. As a result of advances in translational informatics, the care of neonates will become more data driven, evidence based, and personalized. PMID:22924023

  11. Kubernetes as an approach for solving bioinformatic problems.

    OpenAIRE

    Markstedt, Olof

    2017-01-01

    The cluster orchestration tool Kubernetes enables easy deployment and reproducibility of life science research by utilizing the advantages of the container technology. The container technology allows for easy tool creation, sharing and runs on any Linux system once it has been built. The applicability of Kubernetes as an approach to run bioinformatic workflows was evaluated and resulted in some examples of how Kubernetes and containers could be used within the field of life science and how th...

  12. 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.

  13. p3d – Python module for structural bioinformatics

    Directory of Open Access Journals (Sweden)

    Fufezan Christian

    2009-08-01

    Full Text Available Abstract Background 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. Results 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. Conclusion p3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language.

  14. mORCA: sailing bioinformatics world with mobile devices.

    Science.gov (United States)

    Díaz-Del-Pino, Sergio; Falgueras, Juan; Perez-Wohlfeil, Esteban; Trelles, Oswaldo

    2018-03-01

    Nearly 10 years have passed since the first mobile apps appeared. Given the fact that bioinformatics is a web-based world and that mobile devices are endowed with web-browsers, it seemed natural that bioinformatics would transit from personal computers to mobile devices but nothing could be further from the truth. The transition demands new paradigms, designs and novel implementations. Throughout an in-depth analysis of requirements of existing bioinformatics applications we designed and deployed an easy-to-use web-based lightweight mobile client. Such client is able to browse, select, compose automatically interface parameters, invoke services and monitor the execution of Web Services using the service's metadata stored in catalogs or repositories. mORCA is available at http://bitlab-es.com/morca/app as a web-app. It is also available in the App store by Apple and Play Store by Google. The software will be available for at least 2 years. ortrelles@uma.es. Source code, final web-app, training material and documentation is available at http://bitlab-es.com/morca. © The Author(s) 2017. Published by Oxford University Press.

  15. 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.

  16. Combining medical informatics and bioinformatics toward tools for personalized medicine.

    Science.gov (United States)

    Sarachan, B D; Simmons, M K; Subramanian, P; Temkin, J M

    2003-01-01

    Key bioinformatics and medical informatics research areas need to be identified to advance knowledge and understanding of disease risk factors and molecular disease pathology in the 21 st century toward new diagnoses, prognoses, and treatments. Three high-impact informatics areas are identified: predictive medicine (to identify significant correlations within clinical data using statistical and artificial intelligence methods), along with pathway informatics and cellular simulations (that combine biological knowledge with advanced informatics to elucidate molecular disease pathology). Initial predictive models have been developed for a pilot study in Huntington's disease. An initial bioinformatics platform has been developed for the reconstruction and analysis of pathways, and work has begun on pathway simulation. A bioinformatics research program has been established at GE Global Research Center as an important technology toward next generation medical diagnostics. We anticipate that 21 st century medical research will be a combination of informatics tools with traditional biology wet lab research, and that this will translate to increased use of informatics techniques in the clinic.

  17. 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.

  18. 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.

  19. Bioinformatics process management: information flow via a computational journal

    Directory of Open Access Journals (Sweden)

    Lushington Gerald

    2007-12-01

    Full Text Available Abstract This paper presents the Bioinformatics Computational Journal (BCJ, a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.

  20. The European Union: Challenges and Perspectives

    Directory of Open Access Journals (Sweden)

    Botescu Ion

    2017-01-01

    If to all these we add the protectionist measures that the new president of the United States wishes to implement, as well as some deterioration in the European Union credibility generated by Brexit, the bureaucratic aspects that characterize the European institutions, etc., we can outline the context of the European Union, which requires a series of measures to ensure the progress of the European Union as a whole and, in particular, the effective integration of each Community country.

  1. The European Crisis Management: An Organizational Narrative

    OpenAIRE

    Patrícia Kaplánová

    2016-01-01

    The debate of scholars in the field of international relations in last years has put the European Union’s role into the consideration. The European Foreign and Security Policy has positioned itself through its development to the constructive and normative line of research of world politics. With this respect, this article examines a character of crisis management of the European Common Foreign Policy based on the institutional development. Besides the European Union does not po...

  2. Analysis of the European Food Industry

    OpenAIRE

    Banse, Martin; McDonald, Scott; Joint Research Centre; Institute for Prospective Technological Studies; Kaditi, Eleni

    2008-01-01

    This report is based on a study assigned to the Centre for European Policy Studies (CEPS) by the European Commission¿s Joint Research Centre, Institute for Prospective Technological Studies (JRC-IPTS) to investigate recent developments in the European food industry and the impact of foreign direct investment (FDI) and trade flows on the food industry in the EU-25. The report illustrates trends in and the structure of the European food industry. Past and possible future developments are ana...

  3. 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.

  4. 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"...

  5. Video Bioinformatics Analysis of Human Embryonic Stem Cell Colony Growth

    Science.gov (United States)

    Lin, Sabrina; Fonteno, Shawn; Satish, Shruthi; Bhanu, Bir; Talbot, Prue

    2010-01-01

    Because video data are complex and are comprised of many images, mining information from video material is difficult to do without the aid of computer software. Video bioinformatics is a powerful quantitative approach for extracting spatio-temporal data from video images using computer software to perform dating mining and analysis. In this article, we introduce a video bioinformatics method for quantifying the growth of human embryonic stem cells (hESC) by analyzing time-lapse videos collected in a Nikon BioStation CT incubator equipped with a camera for video imaging. In our experiments, hESC colonies that were attached to Matrigel were filmed for 48 hours in the BioStation CT. To determine the rate of growth of these colonies, recipes were developed using CL-Quant software which enables users to extract various types of data from video images. To accurately evaluate colony growth, three recipes were created. The first segmented the image into the colony and background, the second enhanced the image to define colonies throughout the video sequence accurately, and the third measured the number of pixels in the colony over time. The three recipes were run in sequence on video data collected in a BioStation CT to analyze the rate of growth of individual hESC colonies over 48 hours. To verify the truthfulness of the CL-Quant recipes, the same data were analyzed manually using Adobe Photoshop software. When the data obtained using the CL-Quant recipes and Photoshop were compared, results were virtually identical, indicating the CL-Quant recipes were truthful. The method described here could be applied to any video data to measure growth rates of hESC or other cells that grow in colonies. In addition, other video bioinformatics recipes can be developed in the future for other cell processes such as migration, apoptosis, and cell adhesion. PMID:20495527

  6. [Pharmacogenetics II. Research molecular methods, bioinformatics and ethical concerns].

    Science.gov (United States)

    Daudén, E

    2007-01-01

    Pharmacogenetics refers to the study of the individual pharmacological response based on the genotype. Its objective is to optimize treatment in an individual basis, thereby creating a more efficient and safe personalized therapy. In the second part of this review, the molecular methods of study in pharmacogenetics, including microarray technology or DNA chips, are discussed. Among them we highlight the microarrays used to determine the gene expression that detect specific RNA sequences, and the microarrays employed to determine the genotype that detect specific DNA sequences, including polymorphisms, particularly single nucleotide polymorphisms (SNPs). The relationship between pharmacogenetics, bioinformatics and ethical concerns is reviewed.

  7. MicroRNA from tuberculosis RNA: A bioinformatics study

    OpenAIRE

    Wiwanitkit, Somsri; Wiwanitkit, Viroj

    2012-01-01

    The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

  8. Biowep: a workflow enactment portal for bioinformatics applications.

    Science.gov (United States)

    Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

    2007-03-08

    The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of

  9. Biowep: a workflow enactment portal for bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Romano Paolo

    2007-03-01

    Full Text Available Abstract Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS, can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. Results We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. Conclusion We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical

  10. Application of bioinformatics on the detection of pathogens by Pcr

    International Nuclear Information System (INIS)

    Rezig, Slim; Sakhri, Saber

    2007-01-01

    Salmonellas are the main responsible agent for the frequent food-borne gastrointestinal diseases. Their detection using classical methods are laborious and their results take a lot of time to be revealed. In this context, we tried to set up a revealing technique of the invA virulence gene, found in the majority of Salmonella species. After amplification with PCR using specific primers created and verified by bioinformatics programs, two couples of primers were set up and they appeared to be very specific and sensitive for the detection of invA gene. (Author)

  11. New Directions in Statistical Physics: Econophysics, Bioinformatics, and Pattern Recognition

    International Nuclear Information System (INIS)

    Grassberger, P

    2004-01-01

    This book contains 18 contributions from different authors. Its subtitle 'Econophysics, Bioinformatics, and Pattern Recognition' says more precisely what it is about: not so much about central problems of conventional statistical physics like equilibrium phase transitions and critical phenomena, but about its interdisciplinary applications. After a long period of specialization, physicists have, over the last few decades, found more and more satisfaction in breaking out of the limitations set by the traditional classification of sciences. Indeed, this classification had never been strict, and physicists in particular had always ventured into other fields. Helmholtz, in the middle of the 19th century, had considered himself a physicist when working on physiology, stressing that the physics of animate nature is as much a legitimate field of activity as the physics of inanimate nature. Later, Max Delbrueck and Francis Crick did for experimental biology what Schroedinger did for its theoretical foundation. And many of the experimental techniques used in chemistry, biology, and medicine were developed by a steady stream of talented physicists who left their proper discipline to venture out into the wider world of science. The development we have witnessed over the last thirty years or so is different. It started with neural networks where methods could be applied which had been developed for spin glasses, but todays list includes vehicular traffic (driven lattice gases), geology (self-organized criticality), economy (fractal stochastic processes and large scale simulations), engineering (dynamical chaos), and many others. By staying in the physics departments, these activities have transformed the physics curriculum and the view physicists have of themselves. In many departments there are now courses on econophysics or on biological physics, and some universities offer degrees in the physics of traffic or in econophysics. In order to document this change of attitude

  12. Engineering Institute

    Science.gov (United States)

    Projects Past Projects Publications NSEC » Engineering Institute Engineering Institute Multidisciplinary engineering research that integrates advanced modeling and simulations, novel sensing systems and new home of Engineering Institute Contact Institute Director Charles Farrar (505) 665-0860 Email UCSD EI

  13. SeqHound: biological sequence and structure database as a platform for bioinformatics research

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2002-10-01

    Full Text Available Abstract Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.

  14. 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...

  15. Network of Research Infrastructures for European Seismology (NERIES)—Web Portal Developments for Interactive Access to Earthquake Data on a European Scale

    OpenAIRE

    A. Spinuso; L. Trani; S. Rives; P. Thomy; F. Euchner; Danijel Schorlemmer; Joachim Saul; Andres Heinloo; R. Bossu; T. van Eck

    2009-01-01

    The Network of Research Infrastructures for European Seismology (NERIES) is European Commission (EC) project whose focus is networking together seismological observatories and research institutes into one integrated European infrastructure that provides access to data and data products for research. Seismological institutes and organizations in European and Mediterranean countries maintain large, geographically distributed data archives, therefore this scenario suggested a design approach bas...

  16. European hadrons

    International Nuclear Information System (INIS)

    Anon.

    1986-01-01

    The European Hadron Facility (EHF) is a project for particle and nuclear physics in the 1990s which would consist of a fast cycling high intensity proton synchrotron of about 30 GeV primary energy and providing a varied spectrum of intense high quality secondary beams (polarized protons, pions, muons, kaons, antiprotons, neutrinos). The physics case of this project has been studied over the last two years by a European group of particle and nuclear physicists (EHF Study Group), whilst the conceptual design for the accelerator complex was worked out (and is still being worked on) by an international group of machine experts (EHF Design Study Group). Both aspects have been discussed in recent years in a series of working parties, topical seminars, and workshops held in Freiburg, Trieste, Heidelberg, Karlsruhe, Les Rasses and Villigen. This long series of meetings culminated in the International Conference on a European Hadron Facility held in Mainz from 10-14 March

  17. 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.

  18. 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.

  19. 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.

  20. 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. .

  1. 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).

  2. 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.

  3. 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.

  4. mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.

    Science.gov (United States)

    Bokulich, Nicholas A; Rideout, Jai Ram; Mercurio, William G; Shiffer, Arron; Wolfe, Benjamin; Maurice, Corinne F; Dutton, Rachel J; Turnbaugh, Peter J; Knight, Rob; Caporaso, J Gregory

    2016-01-01

    Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e.g., raw sequence data) for each mock community data set. mockrobiota does not supply physical sample materials directly, but the data set metadata included for each mock community indicate whether physical sample materials are available. At the time of this writing, mockrobiota contains 11 mock community data sets with known species compositions, including bacterial, archaeal, and eukaryotic mock communities, analyzed by high-throughput marker gene sequencing. IMPORTANCE The availability of standard and public mock community data will facilitate ongoing method optimizations, comparisons across studies that share source data, and greater transparency and access and eliminate redundancy. These are also valuable resources for bioinformatics teaching and training. This dynamic resource is intended to expand and evolve to meet the changing needs of the omics community.

  5. The constitutional momentum of European contract law (II): The DCFR and the European constitutional order

    OpenAIRE

    Mak, C.

    2009-01-01

    This paper analyses the potential impact of the recently published Draft Common Frame of Reference for European contract law (DCFR) on the European constitutional process. Looking at the combination of characteristics of codification and aspects of constitutionalism reflected in the DCFR, it is submitted that the further harmonisation of European contract law may contribute to the definition of the European constitutional order both on the institutional level (regarding the forms in which Eur...

  6. 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.

  7. YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

    Science.gov (United States)

    Colangelo, Christopher M; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L; Carriero, Nicholas J; Gulcicek, Erol E; Lam, TuKiet T; Wu, Terence; Bjornson, Robert D; Bruce, Can; Nairn, Angus C; Rinehart, Jesse; Miller, Perry L; Williams, Kenneth R

    2015-02-01

    We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  8. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

    Directory of Open Access Journals (Sweden)

    Evelina Y. Basenko

    2018-03-01

    Full Text Available FungiDB (fungidb.org is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD, The Broad Institute, Joint Genome Institute (JGI, Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.. This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records.

  9. The European Union in International Financial Governance

    Directory of Open Access Journals (Sweden)

    Niamh Moloney

    2017-01-01

    Full Text Available This article considers the role of the European Union in international financial governance after the institutional reforms it undertook in connection with the global financial crisis. It suggests that the new administrative actors that support the governance of the European Union's single financial market, notably the European Supervisory Authorities, have the potential to reshape how the European Union engages with international financial governance. It finds that the European Union’s effectiveness in influencing international financial governance—and the effectiveness of international financial governance more generally—is likely to strengthen as a result.

  10. Theories and myths of European foreign policy

    DEFF Research Database (Denmark)

    Manners, Ian James

    2014-01-01

    interactions of European international organizations, and the behaviour of European non-governmental actors working through the above agents as part of transnational and globalizing activism. The chapter adopts a pan-European approach in analysing EFP at the interfaces of these international, supranational...... the international, supranational and transnational policy processes of European states and institutions in relation to the rest of the world. In this respect, the study of EFP includes an analysis of the engagements of European states in international and multilateral diplomacy, the interregional and multipolar...... activity, whether international, supranational or transnational, in order to identify common patterns....

  11. European standards and regulation - CEN/CENELEC

    Energy Technology Data Exchange (ETDEWEB)

    Caballero, J. [AENOR, Madrid (Spain)

    1997-02-27

    An overview is given of the European Standards structure, as well as the general Directives and Regulations related to the Heating, Ventilation and Air Conditioning Sector. The importance of standardisation, both on quality and as a strategic tool for manufacturers, is stressed. Participation in the elaboration of standards makes it possible to reflect a manufacturer`s technology in the standards. Voluntary standardisation can be used as a differentiating element. European standards for the HVAC sector are being elaborated by the European Standardisation Committee (CEN), the European Electrotechnical Standardisation Committee (CENELEC) and by the European Telecommunication Institute (ETSI)

  12. 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...

  13. Play the European card

    International Nuclear Information System (INIS)

    Majewski, O.

    1999-01-01

    Dr. Otto Majewski, Chief Executive Officer of the Bayernwerk AG utility, in his capacity as Chairman of the European Nuclear Council pointed out at ENC 98 in Nice that national energy policies constituted a major danger to the use of nuclear power. At the same time, he indicated ways and means by which to evade that danger. The decisions taken in Sweden and in the Federal Republic of Germany to opt out of the use of nuclear power show that national energy policies can seriously jeopardize the use of nuclear power. Bayernwerk CEO Dr. Majewski urged nuclear power plant operators to counteract these tendencies by playing the European card. Nuclear power anyway was a classical topic of European cooperation which, in the past, had resulted in higher safety standards and in the development of the EPR. It should also be attempted, by working on European institutions, to strengthen the use of nuclear power, even on a national level. He invoked economic arguments against nuclear opponents, especially the preservation of competitiveness by means of lower electricity prices, and arguments of climate protection. (orig.) [de

  14. Chinese outbound to tourism : new challenges for european tourism

    OpenAIRE

    Andreu, Rosario; Claver, Enrique; Quer, Diego

    2013-01-01

    The growth of China’s outbound tourism is a source of both threats and opportunities for European countries. Therefore, European tourism institutions and companies should focus their attention on this emerging market. The objective of this paper is to analyze the consequences that the boom in Chinese tourism could have for European tourism. A critical analysis provides the basis for actions and measures that the main European tourism institutions and companies should adopt i...

  15. Chinese outbound tourism: new challenges for European tourism

    OpenAIRE

    Andreu, Rosario; Claver-Cortés, Enrique; Quer, Diego

    2013-01-01

    The growth of China’s outbound tourism is a source of both threats and opportunities for European countries. Therefore, European tourism institutions and companies should focus their attention on this emerging market. The objective of this paper is to analyze the consequences that the boom in Chinese tourism could have for European tourism. A critical analysis provides the basis for actions and measures that the main European tourism institutions and companies should adopt in order to face th...

  16. 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

  17. Experimental Spaces and Institutional Innovation

    DEFF Research Database (Denmark)

    Cartel, Melodie; Boxenbaum, Eva

    and procedures that connect the prototype to the organizational field, hence increasing the likelihood of institutional innovation. We develop a process model of institutional institutionalization that, through temporal interactions between distancing work and anchoring work, enables the generation......This paper examines processes involved in designing experimental spaces for institutional innovation. Through a qualitative, process-oriented analysis of an experimental space related to the institutional innovation of carbon markets in Europe, we show how key actors in the European electricity...... sector deliberately designed an experimental space and engaged a range of stakeholders in experimenting incognito with a carbon market model. A mirror image of their prototype later appeared as European policy. Our findings show that the key actors engaged in two forms of institutional work, distancing...

  18. European Nuclear Features

    International Nuclear Information System (INIS)

    Barre, B.; Gonzalez, E.; Diaz Diaz, J.L.; Jimenez, J.L.; Velarde, G.; Navarro, J.M.; Hittner, D.; Dominguez, M.T.; Bollini, G.; Martin, A.; Suarez, J.; Traini, E.; Lang-Lenton, J.

    2004-01-01

    ''European Nuclear Features - ENF'' is a joint publication of the three specialized technical journals, Nuclear Espana (Spain), Revue General Nucleaire (France), and atw - International Journal of Nuclear Power (Germany). The ENF support the international Europeen exchange of information and news about energy and nuclear power. News items, comments, and scientific and technical contributions will cover important aspects of the field. The second issue of ENF contains contributions about theses topics, among others: Institutional and Political Changes in the EU. - CIEMAT Department of Nuclear Fission: A General Overview. - Inertial Fusion Energy at DENIM. - High Temperature Reactors. European Research Programme. - On Site Assistance to Khmelnitsky NPP 1 and 2 (Ukraine). - Dismantling and Decommissioning of Vandellos I. (orig.)

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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...

  4. Bioinformatics and the Politics of Innovation in the Life Sciences

    Science.gov (United States)

    Zhou, Yinhua; Datta, Saheli; Salter, Charlotte

    2016-01-01

    The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation. PMID:27546935

  5. 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.

  6. Meta-learning framework applied in bioinformatics inference system design.

    Science.gov (United States)

    Arredondo, Tomás; Ormazábal, Wladimir

    2015-01-01

    This paper describes a meta-learner inference system development framework which is applied and tested in the implementation of bioinformatic inference systems. These inference systems are used for the systematic classification of the best candidates for inclusion in bacterial metabolic pathway maps. This meta-learner-based approach utilises a workflow where the user provides feedback with final classification decisions which are stored in conjunction with analysed genetic sequences for periodic inference system training. The inference systems were trained and tested with three different data sets related to the bacterial degradation of aromatic compounds. The analysis of the meta-learner-based framework involved contrasting several different optimisation methods with various different parameters. The obtained inference systems were also contrasted with other standard classification methods with accurate prediction capabilities observed.

  7. Achievements and challenges in structural bioinformatics and computational biophysics.

    Science.gov (United States)

    Samish, Ilan; Bourne, Philip E; Najmanovich, Rafael J

    2015-01-01

    The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. © The Author 2014. Published by Oxford University Press.

  8. ISEV position paper: extracellular vesicle RNA analysis and bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew F. Hill

    2013-12-01

    Full Text Available Extracellular vesicles (EVs are the collective term for the various vesicles that are released by cells into the extracellular space. Such vesicles include exosomes and microvesicles, which vary by their size and/or protein and genetic cargo. With the discovery that EVs contain genetic material in the form of RNA (evRNA has come the increased interest in these vesicles for their potential use as sources of disease biomarkers and potential therapeutic agents. Rapid developments in the availability of deep sequencing technologies have enabled the study of EV-related RNA in detail. In October 2012, the International Society for Extracellular Vesicles (ISEV held a workshop on “evRNA analysis and bioinformatics.” Here, we report the conclusions of one of the roundtable discussions where we discussed evRNA analysis technologies and provide some guidelines to researchers in the field to consider when performing such analysis.

  9. Establishing a master's degree programme in bioinformatics: challenges and opportunities.

    Science.gov (United States)

    Sahinidis, N V; Harandi, M T; Heath, M T; Murphy, L; Snir, M; Wheeler, R P; Zukoski, C F

    2005-12-01

    The development of the Bioinformatics MS degree program at the University of Illinois, the challenges and opportunities associated with such a process, and the current structure of the program is described. This program has departed from earlier University practice in significant ways. Despite the existence of several interdisciplinary programs at the University, a few of which grant degrees, this is the first interdisciplinary program that grants degrees and formally recognises departmental specialisation areas. The program, which is not owned by any particular department but by the Graduate College itself, is operated in a franchise-like fashion via several departmental concentrations. With four different colleges and many more departments involved in establishing and operating the program, the logistics of the operation are of considerable complexity but result in significant interactions across the entire campus.

  10. The web server of IBM's Bioinformatics and Pattern Discovery group.

    Science.gov (United States)

    Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel; Shibuya, Tetsuo

    2003-07-01

    We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

  11. Bioinformatics Tools for the Discovery of New Nonribosomal Peptides

    DEFF Research Database (Denmark)

    Leclère, Valérie; Weber, Tilmann; Jacques, Philippe

    2016-01-01

    -dimensional structure of the peptides can be compared with the structural patterns of all known NRPs. The presented workflow leads to an efficient and rapid screening of genomic data generated by high throughput technologies. The exploration of such sequenced genomes may lead to the discovery of new drugs (i......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 deciphering of the domain architecture of the nonribosomal peptide synthetases (NRPSs). In the next step, candidate peptides synthesized by these NRPSs are predicted in silico, considering the specificity of incorporated monomers together with their isomery. To assess their novelty, the two...

  12. Single-Cell Transcriptomics Bioinformatics and Computational Challenges

    Directory of Open Access Journals (Sweden)

    Lana Garmire

    2016-09-01

    Full Text Available The emerging single-cell RNA-Seq (scRNA-Seq technology holds the promise to revolutionize our understanding of diseases and associated biological processes at an unprecedented resolution. It opens the door to reveal the intercellular heterogeneity and has been employed to a variety of applications, ranging from characterizing cancer cells subpopulations to elucidating tumor resistance mechanisms. Parallel to improving experimental protocols to deal with technological issues, deriving new analytical methods to reveal the complexity in scRNA-Seq data is just as challenging. Here we review the current state-of-the-art bioinformatics tools and methods for scRNA-Seq analysis, as well as addressing some critical analytical challenges that the field faces.

  13. A bioinformatics roadmap for the human vaccines project.

    Science.gov (United States)

    Scheuermann, Richard H; Sinkovits, Robert S; Schenkelberg, Theodore; Koff, Wayne C

    2017-06-01

    Biomedical research has become a data intensive science in which high throughput experimentation is producing comprehensive data about biological systems at an ever-increasing pace. The Human Vaccines Project is a new public-private partnership, with the goal of accelerating development of improved vaccines and immunotherapies for global infectious diseases and cancers by decoding the human immune system. To achieve its mission, the Project is developing a Bioinformatics Hub as an open-source, multidisciplinary effort with the overarching goal of providing an enabling infrastructure to support the data processing, analysis and knowledge extraction procedures required to translate high throughput, high complexity human immunology research data into biomedical knowledge, to determine the core principles driving specific and durable protective immune responses.

  14. BioRuby: bioinformatics software for the Ruby programming language.

    Science.gov (United States)

    Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

    2010-10-15

    The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

  15. DNA mimic proteins: functions, structures, and bioinformatic analysis.

    Science.gov (United States)

    Wang, Hao-Ching; Ho, Chun-Han; Hsu, Kai-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J

    2014-05-13

    DNA mimic proteins have DNA-like negative surface charge distributions, and they function by occupying the DNA binding sites of DNA binding proteins to prevent these sites from being accessed by DNA. DNA mimic proteins control the activities of a variety of DNA binding proteins and are involved in a wide range of cellular mechanisms such as chromatin assembly, DNA repair, transcription regulation, and gene recombination. However, the sequences and structures of DNA mimic proteins are diverse, making them difficult to predict by bioinformatic search. To date, only a few DNA mimic proteins have been reported. These DNA mimics were not found by searching for functional motifs in their sequences but were revealed only by structural analysis of their charge distribution. This review highlights the biological roles and structures of 16 reported DNA mimic proteins. We also discuss approaches that might be used to discover new DNA mimic proteins.

  16. The study of the European Union from outside: European integration studies in Norway and Iceland 1990-2010

    OpenAIRE

    Eliassen, Kjell; Marino, Marit Sjøvaag; Bergmann, Eirikur

    2012-01-01

    This is a working paper version of a paper written for SENT - The Network of European Studies. The aim of this chapter is to map the research on European integration carried out by Norwegian and Icelandic researchers and research institutions in the period 1990–2010. This study covers research of central aspects of the European Union itself: institutions, decision-making processes, policies, actors and the relationship to other countries, global and regional institutions and local and regiona...

  17. Institutional entrepreneurship:

    DEFF Research Database (Denmark)

    Gretzinger, Susanne

    2018-01-01

    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...... 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...... 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....

  18. Bioinformatics Database Tools in Analysis of Genetics of Neurodevelopmental Disorders

    Directory of Open Access Journals (Sweden)

    Dibyashree Mallik

    2017-10-01

    Full Text Available Bioinformatics tools are recently used in various sectors of biology. Many questions regarding Neurodevelopmental disorder which arises as a major health issue recently can be solved by using various bioinformatics databases. Schizophrenia is such a mental disorder which is now arises as a major threat in young age people because it is mostly seen in case of people during their late adolescence or early adulthood period. Databases like DISGENET, GWAS, PHARMGKB, and DRUGBANK have huge repository of genes associated with schizophrenia. We found a lot of genes are being associated with schizophrenia, but approximately 200 genes are found to be present in any of these databases. After further screening out process 20 genes are found to be highly associated with each other and are also a common genes in many other diseases also. It is also found that they all are serves as a common targeting gene in many antipsychotic drugs. After analysis of various biological properties, molecular function it is found that these 20 genes are mostly involved in biological regulation process and are having receptor activity. They are belonging mainly to receptor protein class. Among these 20 genes CYP2C9, CYP3A4, DRD2, HTR1A, HTR2A are shown to be a main targeting genes of most of the antipsychotic drugs and are associated with  more than 40% diseases. The basic findings of the present study enumerated that a suitable combined drug can be design by targeting these genes which can be used for the better treatment of schizophrenia.

  19. The european ALARA network

    International Nuclear Information System (INIS)

    Croueail, P.; Lefaure, C.; Croft, J.

    2000-01-01

    Throughout the 1980s and early 1990s the European Commission sponsored projects on the understanding and practical implementation of the ALARA principle. These projects helped ensure that ALARA was integrated into many organisations radiation protection programmes, particularly in the nuclear industry. However there was still much to be done in the non-nuclear sector, as well as for the management of internal exposure. Therefore, the European Commission decided to set up, as of the first January 1996, a European ALARA Network (EAN) whose main goals are to: Further promote ALARA within non nuclear industry, research and the nuclear cycle; Provide a means for feedback experience and the exchange and dissemination of good radiological protection practices in these areas; Initiate proposals for research projects and workshops on topics dealing with optimisation of radiological protection for all types of occupational exposure. The Network has a Steering Committee of experts from 11 countries, with CEPN being the co-ordinator. Twice yearly, the EAN products for the international community a European ALARA Newsletter that reaches several thousand individuals or institutions, mainly in Europe. Each year since 1997, the EAN has organised an ALARA workshop attended by 60 to 80 experts from about ten countries. The first three Workshops were devoted to: ALARA and Decommissioning (1997, Saclay, France), Good Radiation Practices in Industry and Research (1998, Chilton, United Kingdam), and ALARA and Internal Exposure (1999, Munich, Germany). Each of these Workshops gave rise to sets of recommendations to the European Commission which included proposals for further research, modification of regulations, and actions to support feedback experience within the member states. (author)

  20. 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....

  1. The European Logarithmic Microprocessor

    Czech Academy of Sciences Publication Activity Database

    Coleman, J. N.; Softley, C. I.; Kadlec, Jiří; Matoušek, R.; Tichý, Milan; Pohl, Zdeněk; Heřmánek, Antonín; Benschop, N. F.

    2008-01-01

    Roč. 57, č. 4 (2008), s. 532-546 ISSN 0018-9340 Grant - others:Evropská komise(BE) ESPRIT 33544 Institutional research plan: CEZ:AV0Z10750506 Source of funding: R - rámcový projekt EK Keywords : Processor architecture * arithmetic unit * logarithmic arithmetic Subject RIV: JC - Computer Hardware ; Software Impact factor: 2.611, year: 2008 http://library.utia.cas.cz/separaty/2008/ZS/kadlec-the%20european%20logarithmic%20microprocessor.pdf

  2. European Corporate Law

    DEFF Research Database (Denmark)

    Dorresteijn, Adriaan; Teichmann, Christoph; Werlauff, Erik

    , and the United Kingdom are taken into account; Italy is now included in this new edition. As in earlier editions, the authors demonstrate that analysis and comparison of national corporate laws yield highly valuable general principles and observations, not least because business organizations, wherever located...... 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...

  3. BioStar: an online question & answer resource for the bioinformatics community

    Science.gov (United States)

    Although the era of big data has produced many bioinformatics tools and databases, using them effectively often requires specialized knowledge. Many groups lack bioinformatics expertise, and frequently find that software documentation is inadequate and local colleagues may be overburdened or unfamil...

  4. Comparative Proteome Bioinformatics: Identification of Phosphotyrosine Signaling Proteins in the Unicellular Protozoan Ciliate Tetrahymena

    DEFF Research Database (Denmark)

    Gammeltoft, Steen; Christensen, Søren Tvorup; Joachimiak, Marcin

    2005-01-01

    Tetrahymena, bioinformatics, cilia, evolution, signaling, TtPTK1, PTK, Grb2, SH-PTP 2, Plcy, Src, PTP, PI3K, SH2, SH3, PH......Tetrahymena, bioinformatics, cilia, evolution, signaling, TtPTK1, PTK, Grb2, SH-PTP 2, Plcy, Src, PTP, PI3K, SH2, SH3, PH...

  5. Bioinformatics Methods for Interpreting Toxicogenomics Data: The Role of Text-Mining

    NARCIS (Netherlands)

    Hettne, K.M.; Kleinjans, J.; Stierum, R.H.; Boorsma, A.; Kors, J.A.

    2014-01-01

    This chapter concerns the application of bioinformatics methods to the analysis of toxicogenomics data. The chapter starts with an introduction covering how bioinformatics has been applied in toxicogenomics data analysis, and continues with a description of the foundations of a specific

  6. Making Bioinformatics Projects a Meaningful Experience in an Undergraduate Biotechnology or Biomedical Science Programme

    Science.gov (United States)

    Sutcliffe, Iain C.; Cummings, Stephen P.

    2007-01-01

    Bioinformatics has emerged as an important discipline within the biological sciences that allows scientists to decipher and manage the vast quantities of data (such as genome sequences) that are now available. Consequently, there is an obvious need to provide graduates in biosciences with generic, transferable skills in bioinformatics. We present…

  7. Green Fluorescent Protein-Focused Bioinformatics Laboratory Experiment Suitable for Undergraduates in Biochemistry Courses

    Science.gov (United States)

    Rowe, Laura

    2017-01-01

    An introductory bioinformatics laboratory experiment focused on protein analysis has been developed that is suitable for undergraduate students in introductory biochemistry courses. The laboratory experiment is designed to be potentially used as a "stand-alone" activity in which students are introduced to basic bioinformatics tools and…

  8. Teaching Bioinformatics and Neuroinformatics by Using Free Web-Based Tools

    Science.gov (United States)

    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…

  9. Exploring Cystic Fibrosis Using Bioinformatics Tools: A Module Designed for the Freshman Biology Course

    Science.gov (United States)

    Zhang, Xiaorong

    2011-01-01

    We incorporated a bioinformatics component into the freshman biology course that allows students to explore cystic fibrosis (CF), a common genetic disorder, using bioinformatics tools and skills. Students learn about CF through searching genetic databases, analyzing genetic sequences, and observing the three-dimensional structures of proteins…

  10. A Portable Bioinformatics Course for Upper-Division Undergraduate Curriculum in Sciences

    Science.gov (United States)

    Floraino, Wely B.

    2008-01-01

    This article discusses the challenges that bioinformatics education is facing and describes a bioinformatics course that is successfully taught at the California State Polytechnic University, Pomona, to the fourth year undergraduate students in biological sciences, chemistry, and computer science. Information on lecture and computer practice…

  11. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  12. Incorporating a Collaborative Web-Based Virtual Laboratory in an Undergraduate Bioinformatics Course

    Science.gov (United States)

    Weisman, David

    2010-01-01

    Face-to-face bioinformatics courses commonly include a weekly, in-person computer lab to facilitate active learning, reinforce conceptual material, and teach practical skills. Similarly, fully-online bioinformatics courses employ hands-on exercises to achieve these outcomes, although students typically perform this work offsite. Combining a…

  13. Bioinformatics in High School Biology Curricula: A Study of State Science Standards

    Science.gov (United States)

    Wefer, Stephen H.; Sheppard, Keith

    2008-01-01

    The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics…

  14. Integration of Bioinformatics into an Undergraduate Biology Curriculum and the Impact on Development of Mathematical Skills

    Science.gov (United States)

    Wightman, Bruce; Hark, Amy T.

    2012-01-01

    The development of fields such as bioinformatics and genomics has created new challenges and opportunities for undergraduate biology curricula. Students preparing for careers in science, technology, and medicine need more intensive study of bioinformatics and more sophisticated training in the mathematics on which this field is based. In this…

  15. PayDIBI: Pay-as-you-go data integration for bioinformatics

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

    Background: Scientific research in bio-informatics is often data-driven and supported by biolog- ical databases. In a growing number of research projects, researchers like to ask questions that require the combination of information from more than one database. Most bio-informatics papers do not

  16. 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,

  17. Konference European Studies: between Globalisation and Regionalism

    Czech Academy of Sciences Publication Activity Database

    Laštovková, Jitka

    2006-01-01

    Roč. 42, č. 5 (2006), s. 1009-1010 ISSN 0038-0288. [European Studies: between Globalisation and Regionalism. Šiauliai, 12.05.2006-03.05.2006] Institutional research plan: CEZ:AV0Z70280505 Keywords : conference * European identitiy * globalization Subject RIV: AO - Sociology, Demography Impact factor: 0.128, year: 2006

  18. 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 OBOR OECD: Law

  19. A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

    Science.gov (United States)

    Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

    2012-07-01

    The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

  20. 9th International Conference on Practical Applications of Computational Biology and Bioinformatics

    CERN Document Server

    Rocha, Miguel; Fdez-Riverola, Florentino; Paz, Juan

    2015-01-01

    This proceedings presents recent practical applications of Computational Biology and  Bioinformatics. It contains the proceedings of the 9th International Conference on Practical Applications of Computational Biology & Bioinformatics held at University of Salamanca, Spain, at June 3rd-5th, 2015. The International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB) is an annual international meeting dedicated to emerging and challenging applied research in Bioinformatics and Computational Biology. Biological and biomedical research are increasingly driven by experimental techniques that challenge our ability to analyse, process and extract meaningful knowledge from the underlying data. The impressive capabilities of next generation sequencing technologies, together with novel and ever evolving distinct types of omics data technologies, have put an increasingly complex set of challenges for the growing fields of Bioinformatics and Computational Biology. The analysis o...

  1. Extending Asia Pacific bioinformatics into new realms in the "-omics" era.

    Science.gov (United States)

    Ranganathan, Shoba; Eisenhaber, Frank; Tong, Joo Chuan; Tan, Tin Wee

    2009-12-03

    The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics (InCoB), Sept. 7-11, 2009 at Biopolis, Singapore. Besides bringing together scientists from the field of bioinformatics in this region, InCoB has actively engaged clinicians and researchers from the area of systems biology, to facilitate greater synergy between these two groups. InCoB2009 followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India), Hong Kong and Taipei (Taiwan), with InCoB2010 scheduled to be held in Tokyo, Japan, Sept. 26-28, 2010. The Workshop on Education in Bioinformatics and Computational Biology (WEBCB) and symposia on Clinical Bioinformatics (CBAS), the Singapore Symposium on Computational Biology (SYMBIO) and training tutorials were scheduled prior to the scientific meeting, and provided ample opportunity for in-depth learning and special interest meetings for educators, clinicians and students. We provide a brief overview of the peer-reviewed bioinformatics manuscripts accepted for publication in this supplement, grouped into thematic areas. In order to facilitate scientific reproducibility and accountability, we have, for the first time, introduced minimum information criteria for our pubilcations, including compliance to a Minimum Information about a Bioinformatics Investigation (MIABi). As the regional research expertise in bioinformatics matures, we have delineated a minimum set of bioinformatics skills required for addressing the computational challenges of the "-omics" era.

  2. Deprivation and non-institutional political participation

    DEFF Research Database (Denmark)

    Ejrnæs, Anders

    2017-01-01

    This article examines how the relationship between perceived economic deprivation (PED) and non-institutional forms of political activity interacted with institutional trust during the economic crisis in 24 European countries. Using multi-level regression analysis, two broad questions are addressed......: (1) does PED have an impact on the level of non-institutional political participation among European citizens? And (2) does the level of institutional trust within countries have an impact on the relationship between PED and political activity among European citizens? The empirical analyses are based...... the opposite correlation on an individual level within the countries. Second, the analysis provides evidence that the institutional context shapes the connection between PED and political participation on the individual level. In countries with a high level of institutional trust, economically deprived...

  3. 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

  4. Colonial Institutions

    DEFF Research Database (Denmark)

    McAtackney, Laura; Palmer, Russell

    2016-01-01

    and the USA which reveal that the study of colonial institutions should not be limited to the functional life of these institutions—or solely those that take the form of monumental architecture—but should include the long shadow of “imperial debris” (Stoler 2008) and immaterial institutions....

  5. European Utility Requirements: European nuclear energy

    International Nuclear Information System (INIS)

    Komsi, M.; Patrakka, E.

    1997-01-01

    The work procedure and the content of the European Utility Requirements (EUR) concerning the future LWRs is described in the article. European Utility Requirements, produced by utilities in a number of European countries, is a document specifying the details relating to engineered safety, operating performance, reliability and economics of the reactors to be built by manufacturers for the European market

  6. 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...... and force employment remained distinct and varied in Europe, and yet, what facilitates their convergence at the European Union level into the ambiguous notion of crisis management? We argue that an important answer to these questions is endogenous to the military: both role conceptions and organizational...

  7. Institutional upbringing

    DEFF Research Database (Denmark)

    Gulløv, Eva

    2008-01-01

    In the chapter, I discuss the role day care institutions play in the construction of the idea of proper childhood in Denmark. Drawing on findings from research on ethnic minority children in two Danish day care institutions, I begin with a discussion of how childcare institutions act as civilising...... agents, empowered with the legitimate right to define and control normality and proper ways of behaving oneself. I aim to show how institutions come to define the normal child and proper childhood in accordance with current efforts toward reinventing national culture, exemplified by legislation requiring...... 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....

  8. A web services choreography scenario for interoperating bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Cheung David W

    2004-03-01

    Full Text Available Abstract Background Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1 the platforms on which the applications run are heterogeneous, 2 their web interface is not machine-friendly, 3 they use a non-standard format for data input and output, 4 they do not exploit standards to define application interface and message exchange, and 5 existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. Results To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates

  9. Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades.

    Science.gov (United States)

    Wren, Jonathan D

    2016-09-01

    To analyze the relative proportion of bioinformatics papers and their non-bioinformatics counterparts in the top 20 most cited papers annually for the past two decades. When defining bioinformatics papers as encompassing both those that provide software for data analysis or methods underlying data analysis software, we find that over the past two decades, more than a third (34%) of the most cited papers in science were bioinformatics papers, which is approximately a 31-fold enrichment relative to the total number of bioinformatics papers published. More than half of the most cited papers during this span were bioinformatics papers. Yet, the average 5-year JIF of top 20 bioinformatics papers was 7.7, whereas the average JIF for top 20 non-bioinformatics papers was 25.8, significantly higher (P papers, bioinformatics journals tended to have higher Gini coefficients, suggesting that development of novel bioinformatics resources may be somewhat 'hit or miss'. That is, relative to other fields, bioinformatics produces some programs that are extremely widely adopted and cited, yet there are fewer of intermediate success. jdwren@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Identification of key genes and molecular mechanisms associated with dedifferentiated liposarcoma based on bioinformatic methods

    Directory of Open Access Journals (Sweden)

    Yu H

    2017-06-01

    Full Text Available Hongliang Yu,1 Dong Pei,2 Longyun Chen,2 Xiaoxiang Zhou,2 Haiwen Zhu2 1Department of Radiation Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 2Department of Radiation Oncology, Yancheng Third People’s Hospital, Yancheng, Jiangsu, People’s Republic of China Background: Dedifferentiated liposarcoma (DDLPS is one of the most deadly types of soft tissue sarcoma. To date, there have been few studies dedicated to elucidating the molecular mechanisms behind the disease; therefore, the molecular mechanisms behind this malignancy remain largely unknown.Materials and methods: Microarray profiles of 46 DDLPS samples and nine normal fat controls were extracted from Gene Expression Omnibus (GEO. Quality control for these microarray profiles was performed before analysis. Hierarchical clustering and principal component analysis were used to distinguish the general differences in gene expression between DDLPS samples and the normal fat controls. Differentially expressed genes (DEGs were identified using the Limma package in R. Next, the enriched Gene Ontology (GO terms and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways were obtained using the online tool DAVID (http://david.abcc.ncifcrf.gov/. A protein–protein interaction (PPI network was constructed using the STRING database and Cytoscape software. Furthermore, the hub genes within the PPI network were identified.Results: All 55 microarray profiles were confirmed to be of high quality. The gene expression pattern of DDLPS samples was significantly different from that of normal fat controls. In total, 700 DEGs were identified, and 83 enriched GO terms and three KEGG pathways were obtained. Specifically, within the DEGs of DDLPS samples, several pathways were identified as being significantly enriched, including the PPAR signaling pathway, cell cycle pathway, and pyruvate metabolism pathway

  11. Buying in to bioinformatics: an introduction to commercial sequence analysis software.

    Science.gov (United States)

    Smith, David Roy

    2015-07-01

    Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. © The Author 2014. Published by Oxford University Press.

  12. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  13. Institutions and structures as barriers?

    DEFF Research Database (Denmark)

    Diop-Christensen, Anna; Pavlopoulos, Dimitris

    2016-01-01

    This study investigated the effect of institutions on the unemployment duration gap between non-EU immigrants and native-born in 12 European countries. Going further than the existing literature, our study encompassed unemployment duration, distinguishing between exits to inactivity, primary and ...

  14. High-throughput bioinformatics with the Cyrille2 pipeline system

    Directory of Open Access Journals (Sweden)

    de Groot Joost CW

    2008-02-01

    Full Text Available Abstract Background Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible. Results We have developed a generic pipeline system called Cyrille2. The system is modular in design and consists of three functionally distinct parts: 1 a web based, graphical user interface (GUI that enables a pipeline operator to manage the system; 2 the Scheduler, which forms the functional core of the system and which tracks what data enters the system and determines what jobs must be scheduled for execution, and; 3 the Executor, which searches for scheduled jobs and executes these on a compute cluster. Conclusion The Cyrille2 system is an extensible, modular system, implementing the stated requirements. Cyrille2 enables easy creation and execution of high throughput, flexible bioinformatics pipelines.

  15. Progress and challenges in bioinformatics approaches for enhancer identification

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2017-02-03

    Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.

  16. Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

    Directory of Open Access Journals (Sweden)

    Zhuofei Xu

    Full Text Available As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.

  17. WeBIAS: a web server for publishing bioinformatics applications.

    Science.gov (United States)

    Daniluk, Paweł; Wilczyński, Bartek; Lesyng, Bogdan

    2015-11-02

    One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well as impairs actual usefulness to the scientific community at large. In this note we present WeBIAS-a simple, self-contained solution to make command-line programs accessible through web forms. It comprises a web portal capable of serving several applications and backend schedulers which carry out computations. The server handles user registration and authentication, stores queries and results, and provides a convenient administrator interface. WeBIAS is implemented in Python and available under GNU Affero General Public License. It has been developed and tested on GNU/Linux compatible platforms covering a vast majority of operational WWW servers. Since it is written in pure Python, it should be easy to deploy also on all other platforms supporting Python (e.g. Windows, Mac OS X). Documentation and source code, as well as a demonstration site are available at http://bioinfo.imdik.pan.pl/webias . WeBIAS has been designed specifically with ease of installation and deployment of services in mind. Setting up a simple application requires minimal effort, yet it is possible to create visually appealing, feature-rich interfaces for query submission and presentation of results.

  18. Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

    Science.gov (United States)

    Graña, Osvaldo; López-Fernández, Hugo; Fdez-Riverola, Florentino; González Pisano, David; Glez-Peña, Daniel

    2018-04-15

    High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data. Bicycle analyzes whole genome bisulfite sequencing data, targeted bisulfite sequencing data and hydroxymethylation data. To show how bicycle overtakes other available pipelines, we compared them on a defined number of features that are summarized in a table. We also tested bicycle with both simulated and real datasets, to show its level of performance, and compared it to different state-of-the-art methylation analysis pipelines. Bicycle is publicly available under GNU LGPL v3.0 license at http://www.sing-group.org/bicycle. Users can also download a customized Ubuntu LiveCD including bicycle and other bisulfite sequencing data pipelines compared here. In addition, a docker image with bicycle and its dependencies, which allows a straightforward use of bicycle in any platform (e.g. Linux, OS X or Windows), is also available. ograna@cnio.es or dgpena@uvigo.es. Supplementary data are available at Bioinformatics online.

  19. Accurate Prediction of Coronary Artery Disease Using Bioinformatics Algorithms

    Directory of Open Access Journals (Sweden)

    Hajar Shafiee

    2016-06-01

    Full Text Available Background and Objectives: Cardiovascular disease is one of the main causes of death in developed and Third World countries. According to the statement of the World Health Organization, it is predicted that death due to heart disease will rise to 23 million by 2030. According to the latest statistics reported by Iran’s Minister of health, 3.39% of all deaths are attributed to cardiovascular diseases and 19.5% are related to myocardial infarction. The aim of this study was to predict coronary artery disease using data mining algorithms. Methods: In this study, various bioinformatics algorithms, such as decision trees, neural networks, support vector machines, clustering, etc., were used to predict coronary heart disease. The data used in this study was taken from several valid databases (including 14 data. Results: In this research, data mining techniques can be effectively used to diagnose different diseases, including coronary artery disease. Also, for the first time, a prediction system based on support vector machine with the best possible accuracy was introduced. Conclusion: The results showed that among the features, thallium scan variable is the most important feature in the diagnosis of heart disease. Designation of machine prediction models, such as support vector machine learning algorithm can differentiate between sick and healthy individuals with 100% accuracy.

  20. Exploiting graphics processing units for computational biology and bioinformatics.

    Science.gov (United States)

    Payne, Joshua L; Sinnott-Armstrong, Nicholas A; Moore, Jason H

    2010-09-01

    Advances in the video gaming industry have led to the production of low-cost, high-performance graphics processing units (GPUs) that possess more memory bandwidth and computational capability than central processing units (CPUs), the standard workhorses of scientific computing. With the recent release of generalpurpose GPUs and NVIDIA's GPU programming language, CUDA, graphics engines are being adopted widely in scientific computing applications, particularly in the fields of computational biology and bioinformatics. The goal of this article is to concisely present an introduction to GPU hardware and programming, aimed at the computational biologist or bioinformaticist. To this end, we discuss the primary differences between GPU and CPU architecture, introduce the basics of the CUDA programming language, and discuss important CUDA programming practices, such as the proper use of coalesced reads, data types, and memory hierarchies. We highlight each of these topics in the context of computing the all-pairs distance between instances in a dataset, a common procedure in numerous disciplines of scientific computing. We conclude with a runtime analysis of the GPU and CPU implementations of the all-pairs distance calculation. We show our final GPU implementation to outperform the CPU implementation by a factor of 1700.