WorldWideScience

Sample records for bioinformatics database warehouse

  1. 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

  2. Database Vs Data Warehouse

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Data warehouse technology includes a set of concepts and methods that offer the users useful information for decision making. The necessity to build a data warehouse arises from the necessity to improve the quality of information in the organization. The date proceeding from different sources, having a variety of forms - both structured and unstructured, are filtered according to business rules and are integrated in a single large data collection. Using informatics solutions, managers have understood that data stored in operational systems - including databases, are an informational gold mine that must be exploited. Data warehouses have been developed to answer the increasing demands for complex analysis, which could not be properly achieved with operational databases. The present paper emphasizes some of the criteria that information application developers can use in order to choose between a database solution or a data warehouse one.

  3. 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

  4. Geminivirus data warehouse: a database enriched with machine learning approaches.

    Science.gov (United States)

    Silva, Jose Cleydson F; Carvalho, Thales F M; Basso, Marcos F; Deguchi, Michihito; Pereira, Welison A; Sobrinho, Roberto R; Vidigal, Pedro M P; Brustolini, Otávio J B; Silva, Fabyano F; Dal-Bianco, Maximiller; Fontes, Renildes L F; Santos, Anésia A; Zerbini, Francisco Murilo; Cerqueira, Fabio R; Fontes, Elizabeth P B

    2017-05-05

    The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic losses worldwide. Geminiviruses are divided into nine genera, according to their insect vector, host range, genome organization, and phylogeny reconstruction. Using rolling-circle amplification approaches along with high-throughput sequencing technologies, thousands of full-length geminivirus and satellite genome sequences were amplified and have become available in public databases. As a consequence, many important challenges have emerged, namely, how to classify, store, and analyze massive datasets as well as how to extract information or new knowledge. Data mining approaches, mainly supported by machine learning (ML) techniques, are a natural means for high-throughput data analysis in the context of genomics, transcriptomics, proteomics, and metabolomics. Here, we describe the development of a data warehouse enriched with ML approaches, designated geminivirus.org. We implemented search modules, bioinformatics tools, and ML methods to retrieve high precision information, demarcate species, and create classifiers for genera and open reading frames (ORFs) of geminivirus genomes. The use of data mining techniques such as ETL (Extract, Transform, Load) to feed our database, as well as algorithms based on machine learning for knowledge extraction, allowed us to obtain a database with quality data and suitable tools for bioinformatics analysis. The Geminivirus Data Warehouse (geminivirus.org) offers a simple and user-friendly environment for information retrieval and knowledge discovery related to geminiviruses.

  5. 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...

  6. Optimized Database of Higher Education Management Using Data Warehouse

    Directory of Open Access Journals (Sweden)

    Spits Warnars

    2010-04-01

    Full Text Available The emergence of new higher education institutions has created the competition in higher education market, and data warehouse can be used as an effective technology tools for increasing competitiveness in the higher education market. Data warehouse produce reliable reports for the institution’s high-level management in short time for faster and better decision making, not only on increasing the admission number of students, but also on the possibility to find extraordinary, unconventional funds for the institution. Efficiency comparison was based on length and amount of processed records, total processed byte, amount of processed tables, time to run query and produced record on OLTP database and data warehouse. Efficiency percentages was measured by the formula for percentage increasing and the average efficiency percentage of 461.801,04% shows that using data warehouse is more powerful and efficient rather than using OLTP database. Data warehouse was modeled based on hypercube which is created by limited high demand reports which usually used by high level management. In every table of fact and dimension fields will be inserted which represent the loading constructive merge where the ETL (Extraction, Transformation and Loading process is run based on the old and new files.

  7. Database and Bioinformatics Studies of Probiotics.

    Science.gov (United States)

    Tao, Lin; Wang, Bohua; Zhong, Yafen; Pow, Siok Hoon; Zeng, Xian; Qin, Chu; Zhang, Peng; Chen, Shangying; He, Weidong; Tan, Ying; Liu, Hongxia; Jiang, Yuyang; Chen, Weiping; Chen, Yu Zong

    2017-09-06

    Probiotics have been widely explored for health benefits, animal cares, and agricultural applications. Recent advances in microbiome, microbiota, and microbial dark matter research have fueled greater interests in and paved ways for the study of the mechanisms of probiotics and the discovery of new probiotics from uncharacterized microbial sources. A probiotics database named PROBIO was developed to facilitate these efforts and the need for the information on the known probiotics, which provides the comprehensive information about the probiotic functions of 448 marketed, 167 clinical trial/field trial, and 382 research probiotics for use or being studied for use in humans, animals, and plants. The potential applications of the probiotics data are illustrated by several literature-reported investigations, which have used the relevant information for probing the function and mechanism of the probiotics and for discovering new probiotics. PROBIO can be accessed free of charge at http://bidd2.nus.edu.sg/probio/homepage.htm .

  8. Architectural design of a data warehouse to support operational and analytical queries across disparate clinical databases.

    Science.gov (United States)

    Chelico, John D; Wilcox, Adam; Wajngurt, David

    2007-10-11

    As the clinical data warehouse of the New York Presbyterian Hospital has evolved innovative methods of integrating new data sources and providing more effective and efficient data reporting and analysis need to be explored. We designed and implemented a new clinical data warehouse architecture to handle the integration of disparate clinical databases in the institution. By examining the way downstream systems are populated and streamlining the way data is stored we create a virtual clinical data warehouse that is adaptable to future needs of the organization.

  9. Microsoft Enterprise Consortium: A Resource for Teaching Data Warehouse, Business Intelligence and Database Management Systems

    Science.gov (United States)

    Kreie, Jennifer; Hashemi, Shohreh

    2012-01-01

    Data is a vital resource for businesses; therefore, it is important for businesses to manage and use their data effectively. Because of this, businesses value college graduates with an understanding of and hands-on experience working with databases, data warehouses and data analysis theories and tools. Faculty in many business disciplines try to…

  10. 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 …

  11. Design database for quantitative trait loci (QTL) data warehouse, data mining, and meta-analysis.

    Science.gov (United States)

    Hu, Zhi-Liang; Reecy, James M; Wu, Xiao-Lin

    2012-01-01

    A database can be used to warehouse quantitative trait loci (QTL) data from multiple sources for comparison, genomic data mining, and meta-analysis. A robust database design involves sound data structure logistics, meaningful data transformations, normalization, and proper user interface designs. This chapter starts with a brief review of relational database basics and concentrates on issues associated with curation of QTL data into a relational database, with emphasis on the principles of data normalization and structure optimization. In addition, some simple examples of QTL data mining and meta-analysis are included. These examples are provided to help readers better understand the potential and importance of sound database design.

  12. 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...

  13. 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...

  14. Databases and Associated Bioinformatic Tools in Studies of Food Allergens, Epitopes and Haptens – a Review

    Directory of Open Access Journals (Sweden)

    Bucholska Justyna

    2018-06-01

    Full Text Available Allergies and/or food intolerances are a growing problem of the modern world. Diffi culties associated with the correct diagnosis of food allergies result in the need to classify the factors causing allergies and allergens themselves. Therefore, internet databases and other bioinformatic tools play a special role in deepening knowledge of biologically-important compounds. Internet repositories, as a source of information on different chemical compounds, including those related to allergy and intolerance, are increasingly being used by scientists. Bioinformatic methods play a signifi cant role in biological and medical sciences, and their importance in food science is increasing. This study aimed at presenting selected databases and tools of bioinformatic analysis useful in research on food allergies, allergens (11 databases, epitopes (7 databases, and haptens (2 databases. It also presents examples of the application of computer methods in studies related to allergies.

  15. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

    Science.gov (United States)

    Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos; Bastian, Frederic; Bergmann, Sven; Bougueleret, Lydie; Bucher, Philipp; Delorenzi, Mauro; Lane, Lydie; Le Mercier, Philippe; Lisacek, Frédérique; Michielin, Olivier; Palagi, Patricia M; Rougemont, Jacques; Schwede, Torsten; von Mering, Christian; van Nimwegen, Erik; Walther, Daniel; Xenarios, Ioannis; Zavolan, Mihaela; Zdobnov, Evgeny M; Zoete, Vincent; Appel, Ron D

    2014-07-01

    The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. 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.

  17. Preliminary Study of Bioinformatics Patents and Their Classifications Registered in the KIPRIS Database.

    Science.gov (United States)

    Park, Hyun-Seok

    2012-12-01

    Whereas a vast amount of new information on bioinformatics is made available to the public through patents, only a small set of patents are cited in academic papers. A detailed analysis of registered bioinformatics patents, using the existing patent search system, can provide valuable information links between science and technology. However, it is extremely difficult to select keywords to capture bioinformatics patents, reflecting the convergence of several underlying technologies. No single word or even several words are sufficient to identify such patents. The analysis of patent subclasses can provide valuable information. In this paper, I did a preliminary study of the current status of bioinformatics patents and their International Patent Classification (IPC) groups registered in the Korea Intellectual Property Rights Information Service (KIPRIS) database.

  18. A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

    Directory of Open Access Journals (Sweden)

    Geraint Duck

    Full Text Available Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT, though some are instead seeing rapid growth (e.g., the GO, R. We find a striking imbalance in resource usage with the top 5% of resource names (133 names accounting for 47% of total usage, and over 70% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here: http://dx.doi.org/10.6084/m9.figshare.1281371.

  19. Music Warehouses

    DEFF Research Database (Denmark)

    Deliege, Francois; Pedersen, Torben Bach

    2006-01-01

    Music Information Retrieval has received increasing attention from both the industrial and the research communities in recent years. Many audio extraction techniques providing content-based music information have been developed, sparking the need for intelligent storage and retrieval facilities....... This paper proposes to satisfy this need by extending technology from business-oriented data warehouses to so-called music warehouses that integrate a large variety of music-related information, including both low-level features and high-level musical information. Music warehouses thus help to close...... the “semantic gap” by supporting integrated querying of these two kinds of music data. This paper presents a number of new challenges for the database community that must be taken up to meet the particular demands of music warehouses....

  20. The OAuth 2.0 Web Authorization Protocol for the Internet Addiction Bioinformatics (IABio) Database.

    Science.gov (United States)

    Choi, Jeongseok; Kim, Jaekwon; Lee, Dong Kyun; Jang, Kwang Soo; Kim, Dai-Jin; Choi, In Young

    2016-03-01

    Internet addiction (IA) has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet. In addition, bioinformatics databases, especially genetic databases, require a high level of security and should be designed based on medical information standards. In this respect, our study proposes the OAuth standard protocol for database access authorization. The proposed IA Bioinformatics (IABio) database system is based on internet user authentication, which is a guideline for medical information standards, and uses OAuth 2.0 for access control technology. This study designed and developed the system requirements and configuration. The OAuth 2.0 protocol is expected to establish the security of personal medical information and be applied to genomic research on IA.

  1. The OAuth 2.0 Web Authorization Protocol for the Internet Addiction Bioinformatics (IABio Database

    Directory of Open Access Journals (Sweden)

    Jeongseok Choi

    2016-03-01

    Full Text Available Internet addiction (IA has become a widespread and problematic phenomenon as smart devices pervade society. Moreover, internet gaming disorder leads to increases in social expenditures for both individuals and nations alike. Although the prevention and treatment of IA are getting more important, the diagnosis of IA remains problematic. Understanding the neurobiological mechanism of behavioral addictions is essential for the development of specific and effective treatments. Although there are many databases related to other addictions, a database for IA has not been developed yet. In addition, bioinformatics databases, especially genetic databases, require a high level of security and should be designed based on medical information standards. In this respect, our study proposes the OAuth standard protocol for database access authorization. The proposed IA Bioinformatics (IABio database system is based on internet user authentication, which is a guideline for medical information standards, and uses OAuth 2.0 for access control technology. This study designed and developed the system requirements and configuration. The OAuth 2.0 protocol is expected to establish the security of personal medical information and be applied to genomic research on IA.

  2. Envirofacts Data Warehouse

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Envirofacts Data Warehouse contains information from select EPA Environmental program office databases and provides access about environmental activities that...

  3. Database Are Not Toasters: A Framework for Comparing Data Warehouse Appliances

    Science.gov (United States)

    Trajman, Omer; Crolotte, Alain; Steinhoff, David; Nambiar, Raghunath Othayoth; Poess, Meikel

    The success of Business Intelligence (BI) applications depends on two factors, the ability to analyze data ever more quickly and the ability to handle ever increasing volumes of data. Data Warehouse (DW) and Data Mart (DM) installations that support BI applications have historically been built using traditional architectures either designed from the ground up or based on customized reference system designs. The advent of Data Warehouse Appliances (DA) brings packaged software and hardware solutions that address performance and scalability requirements for certain market segments. The differences between DAs and custom installations make direct comparisons between them impractical and suggest the need for a targeted DA benchmark. In this paper we review data warehouse appliances by surveying thirteen products offered today. We assess the common characteristics among them and propose a classification for DA offerings. We hope our results will help define a useful benchmark for DAs.

  4. Importance of databases of nucleic acids for bioinformatic analysis focused to genomics

    Science.gov (United States)

    Jimenez-Gutierrez, L. R.; Barrios-Hernández, C. J.; Pedraza-Ferreira, G. R.; Vera-Cala, L.; Martinez-Perez, F.

    2016-08-01

    Recently, bioinformatics has become a new field of science, indispensable in the analysis of millions of nucleic acids sequences, which are currently deposited in international databases (public or private); these databases contain information of genes, RNA, ORF, proteins, intergenic regions, including entire genomes from some species. The analysis of this information requires computer programs; which were renewed in the use of new mathematical methods, and the introduction of the use of artificial intelligence. In addition to the constant creation of supercomputing units trained to withstand the heavy workload of sequence analysis. However, it is still necessary the innovation on platforms that allow genomic analyses, faster and more effectively, with a technological understanding of all biological processes.

  5. 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.

  6. 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.

  7. Envirofacts Data Warehouse

    Science.gov (United States)

    The Envirofacts Data Warehouse contains information from select EPA Environmental program office databases and provides access about environmental activities that may affect air, water, and land anywhere in the United States. The Envirofacts Warehouse supports its own web enabled tools as well as a host of other EPA applications.

  8. A bioinformatics pipeline to build a knowledge database for in silico antibody engineering.

    Science.gov (United States)

    Zhao, Shanrong; Lu, Jin

    2011-04-01

    A challenge to antibody engineering is the large number of positions and nature of variation and opposing concerns of introducing unfavorable biochemical properties. While large libraries are quite successful in identifying antibodies with improved binding or activity, still only a fraction of possibilities can be explored and that would require considerable effort. The vast array of natural antibody sequences provides a potential wealth of information on (1) selecting hotspots for variation, and (2) designing mutants to mimic natural variations seen in hotspots. The human immune system can generate an enormous diversity of immunoglobulins against an almost unlimited range of antigens by gene rearrangement of a limited number of germline variable, diversity and joining genes followed by somatic hypermutation and antigen selection. All the antibody sequences in NCBI database can be assigned to different germline genes. As a result, a position specific scoring matrix for each germline gene can be constructed by aligning all its member sequences and calculating the amino acid frequencies for each position. The position specific scoring matrix for each germline gene characterizes "hotspots" and the nature of variations, and thus reduces the sequence space of exploration in antibody engineering. We have developed a bioinformatics pipeline to conduct analysis of human antibody sequences, and generated a comprehensive knowledge database for in silico antibody engineering. The pipeline is fully automatic and the knowledge database can be refreshed anytime by re-running the pipeline. The refresh process is fast, typically taking 1min on a Lenovo ThinkPad T60 laptop with 3G memory. Our knowledge database consists of (1) the individual germline gene usage in generation of natural antibodies; (2) the CDR length distributions; and (3) the position specific scoring matrix for each germline gene. The knowledge database provides comprehensive support for antibody engineering

  9. Development of prostate cancer research database with the clinical data warehouse technology for direct linkage with electronic medical record system.

    Science.gov (United States)

    Choi, In Young; Park, Seungho; Park, Bumjoon; Chung, Byung Ha; Kim, Choung-Soo; Lee, Hyun Moo; Byun, Seok-Soo; Lee, Ji Youl

    2013-01-01

    In spite of increased prostate cancer patients, little is known about the impact of treatments for prostate cancer patients and outcome of different treatments based on nationwide data. In order to obtain more comprehensive information for Korean prostate cancer patients, many professionals urged to have national system to monitor the quality of prostate cancer care. To gain its objective, the prostate cancer database system was planned and cautiously accommodated different views from various professions. This prostate cancer research database system incorporates information about a prostate cancer research including demographics, medical history, operation information, laboratory, and quality of life surveys. And, this system includes three different ways of clinical data collection to produce a comprehensive data base; direct data extraction from electronic medical record (EMR) system, manual data entry after linking EMR documents like magnetic resonance imaging findings and paper-based data collection for survey from patients. We implemented clinical data warehouse technology to test direct EMR link method with St. Mary's Hospital system. Using this method, total number of eligible patients were 2,300 from 1997 until 2012. Among them, 538 patients conducted surgery and others have different treatments. Our database system could provide the infrastructure for collecting error free data to support various retrospective and prospective studies.

  10. BioDWH: a data warehouse kit for life science data integration.

    Science.gov (United States)

    Töpel, Thoralf; Kormeier, Benjamin; Klassen, Andreas; Hofestädt, Ralf

    2008-08-25

    This paper presents a novel bioinformatics data warehouse software kit that integrates biological information from multiple public life science data sources into a local database management system. It stands out from other approaches by providing up-to-date integrated knowledge, platform and database independence as well as high usability and customization. This open source software can be used as a general infrastructure for integrative bioinformatics research and development. The advantages of the approach are realized by using a Java-based system architecture and object-relational mapping (ORM) technology. Finally, a practical application of the system is presented within the emerging area of medical bioinformatics to show the usefulness of the approach. The BioDWH data warehouse software is available for the scientific community at http://sourceforge.net/projects/biodwh/.

  11. Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases.

    Science.gov (United States)

    Llorens, Carlos; Futami, Ricardo; Renaud, Gabriel; Moya, Andrés

    2009-01-27

    Clan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements. Recent findings describing various pools of single-domain nonviral host peptidases, in prokaryotes and eukaryotes, indicate that the diversity of clan AA is larger than previously thought. The ensuing approach to investigate this enzyme group is by studying its phylogeny. However, clan AA is a difficult case to study due to the low similarity and different rates of evolution. This work is an ongoing attempt to investigate the different clan AA families to understand the cause of their diversity. In this paper, we describe in-progress database and bioinformatic flowchart designed to characterize the clan AA protein domain based on all possible protein families through ancestral reconstructions, sequence logos, and hidden markov models (HMMs). The flowchart includes the characterization of a major consensus sequence based on 6 amino acid patterns with correspondence with Andreeva's model, the structural template describing the clan AA peptidase fold. The set of tools is work in progress we have organized in a database within the GyDB project, referred to as Clan AA Reference Database http://gydb.uv.es/gydb/phylogeny.php?tree=caard. The pre-existing classification combined with the evolutionary history of LTR retroelements permits a consistent taxonomical collection of sequence logos and HMMs. This set is useful for gene annotation but also a reference to evaluate the diversity of, and the relationships among, the different families. Comparisons among HMMs suggest a common ancestor for all dimeric clan AA peptidases that is halfway between single-domain nonviral peptidases and those coded by Ty3/Gypsy LTR retroelements. Sequence logos reveal how all clan AA families follow similar protein domain architecture related to the peptidase fold. In particular, each family nucleates a particular consensus motif in the

  12. Contextualizing Data Warehouses with Documents

    DEFF Research Database (Denmark)

    Perez, Juan Manuel; Berlanga, Rafael; Aramburu, Maria Jose

    2008-01-01

    warehouse with a document warehouse, resulting in a contextualized warehouse. Thus, the user first selects an analysis context by supplying some keywords. Then, the analysis is performed on a novel type of OLAP cube, called an R-cube, which is materialized by retrieving and ranking the documents......Current data warehouse and OLAP technologies are applied to analyze the structured data that companies store in databases. The context that helps to understand data over time is usually described separately in text-rich documents. This paper proposes to integrate the traditional corporate data...

  13. Data Warehouse Architecture for DSS Applciations

    Directory of Open Access Journals (Sweden)

    V. J. Anand

    1996-11-01

    Full Text Available A data warehouse facilitates the integration of disparate operational databases in an enterprise into a single store. The warehouse then provides knowledge workers with easy access to historical, summarized and other forms of aggregated data. A major flaw in present warehouse architectures is the de-coupling of the warehouse database from its underlying operational databases. This creates two problems: the difficulty in updating the warehouse and the inability to provide users with a drill-down feature from warehouse to current data. We propose an architecture that is based on a federated database system extended to incorporate a materialized warehouse. A federated database provides the basic mechanism to tightly couple heterogeneous databases, which in this case are the operational and warehouse databases. The warehouse database is a special component in the federation, made up of historical data, external data and materialized views of the operational data. This approach enables users to access historical and current data when required, and provides a method of maintaining the warehouse as an integrated view of the underlying operational data sources.

  14. A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

    Science.gov (United States)

    Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

    2018-01-01

    Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have

  15. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Ussery, David

    2004-01-01

    and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently......, these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web...

  16. miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal

    Science.gov (United States)

    Chen, Liang; Heikkinen, Liisa; Wang, ChangLiang; Yang, Yang; Knott, K Emily

    2018-01-01

    Abstract Hundreds of bioinformatics tools have been developed for MicroRNA (miRNA) investigations including those used for identification, target prediction, structure and expression profile analysis. However, finding the correct tool for a specific application requires the tedious and laborious process of locating, downloading, testing and validating the appropriate tool from a group of nearly a thousand. In order to facilitate this process, we developed a novel database portal named miRToolsGallery. We constructed the portal by manually curating > 950 miRNA analysis tools and resources. In the portal, a query to locate the appropriate tool is expedited by being searchable, filterable and rankable. The ranking feature is vital to quickly identify and prioritize the more useful from the obscure tools. Tools are ranked via different criteria including the PageRank algorithm, date of publication, number of citations, average of votes and number of publications. miRToolsGallery provides links and data for the comprehensive collection of currently available miRNA tools with a ranking function which can be adjusted using different criteria according to specific requirements. Database URL: http://www.mirtoolsgallery.org

  17. DICOM Data Warehouse: Part 2

    OpenAIRE

    Langer, Steve G.

    2015-01-01

    In 2010, the DICOM Data Warehouse (DDW) was launched as a data warehouse for DICOM meta-data. Its chief design goals were to have a flexible database schema that enabled it to index standard patient and study information, modality specific tags (public and private), and create a framework to derive computable information (derived tags) from the former items. Furthermore, it was to map the above information to an internally standard lexicon that enables a non-DICOM savvy programmer to write st...

  18. The Cardiac Safety Research Consortium electrocardiogram warehouse: thorough QT database specifications and principles of use for algorithm development and testing.

    Science.gov (United States)

    Kligfield, Paul; Green, Cynthia L; Mortara, Justin; Sager, Philip; Stockbridge, Norman; Li, Michael; Zhang, Joanne; George, Samuel; Rodriguez, Ignacio; Bloomfield, Daniel; Krucoff, Mitchell W

    2010-12-01

    This document examines the formation, structure, and principles guiding the use of electrocardiogram (ECG) data sets obtained during thorough QT studies that have been derived from the ECG Warehouse of the Cardiac Safety Research Consortium (CSRC). These principles are designed to preserve the fairness and public interest of access to these data, commensurate with the mission of the CSRC. The data sets comprise anonymized XML formatted digitized ECGs and descriptive variables from placebo and positive control arms of individual studies previously submitted on a proprietary basis to the US Food and Drug Administration by pharmaceutical sponsors. Sponsors permit the release of these studies into the public domain through the CSRC on behalf of the Food and Drug Administration's Critical Path Initiative and public health interest. For algorithm research protocols submitted to and approved by CSRC, unblinded "training" ECG data sets are provided for algorithm development and for initial evaluation, whereas separate blinded "testing" data sets are used for formal algorithm evaluation in cooperation with the CSRC according to methods detailed in this document. Copyright © 2010 Mosby, Inc. All rights reserved.

  19. Combining information from a clinical data warehouse and a pharmaceutical database to generate a framework to detect comorbidities in electronic health records.

    Science.gov (United States)

    Sylvestre, Emmanuelle; Bouzillé, Guillaume; Chazard, Emmanuel; His-Mahier, Cécil; Riou, Christine; Cuggia, Marc

    2018-01-24

    Medical coding is used for a variety of activities, from observational studies to hospital billing. However, comorbidities tend to be under-reported by medical coders. The aim of this study was to develop an algorithm to detect comorbidities in electronic health records (EHR) by using a clinical data warehouse (CDW) and a knowledge database. We enriched the Theriaque pharmaceutical database with the French national Comorbidities List to identify drugs associated with at least one major comorbid condition and diagnoses associated with a drug indication. Then, we compared the drug indications in the Theriaque database with the ICD-10 billing codes in EHR to detect potentially missing comorbidities based on drug prescriptions. Finally, we improved comorbidity detection by matching drug prescriptions and laboratory test results. We tested the obtained algorithm by using two retrospective datasets extracted from the Rennes University Hospital (RUH) CDW. The first dataset included all adult patients hospitalized in the ear, nose, throat (ENT) surgical ward between October and December 2014 (ENT dataset). The second included all adult patients hospitalized at RUH between January and February 2015 (general dataset). We reviewed medical records to find written evidence of the suggested comorbidities in current or past stays. Among the 22,132 Common Units of Dispensation (CUD) codes present in the Theriaque database, 19,970 drugs (90.2%) were associated with one or several ICD-10 diagnoses, based on their indication, and 11,162 (50.4%) with at least one of the 4878 comorbidities from the comorbidity list. Among the 122 patients of the ENT dataset, 75.4% had at least one drug prescription without corresponding ICD-10 code. The comorbidity diagnoses suggested by the algorithm were confirmed in 44.6% of the cases. Among the 4312 patients of the general dataset, 68.4% had at least one drug prescription without corresponding ICD-10 code. The comorbidity diagnoses suggested by the

  20. An Empirical Analysis of Humanitarian Warehouse Locations

    Directory of Open Access Journals (Sweden)

    Sander de Leeuw

    2016-06-01

    Full Text Available The purpose of this paper is to empirically verify characteristics of current warehouse locations of humanitarian organizations (based on public information and to relate those to the model developed by Richardson, de Leeuw and Dullaert (2016. This paper is based on desk research. Public data such as (annual reports and databases are used to determine the features of the location in empirical terms. We find that a significant proportion of our sample co-locates their products at UNHRD premises. This suggests that organizations prefer to cluster their warehouse activities, particularly when there is no fee involved for using the warehouse (as is the case in the UNHRD network. The geographic map of the current warehouses, together with the quantified location factors, provides an overview of the current warehouse locations. We found that the characteristics of the current warehouse locations are aligned with literature on location selection factors. Current location can be characterized by infrastructure characteristics (in particular closeness to airport and safety concerns and by the low occurrence of disasters. Other factors that were considered by us but were not supported by empirical evidence were labor quality and availability as well as the political environment. In our study we were only able to use a limited sample of warehouses. We also focused our research on countries where two or more organizations have their warehouses located. We did not account for warehouse sizes or the kinds of products stored in our analysis.

  1. Warehouse Sanitation Workshop Handbook.

    Science.gov (United States)

    Food and Drug Administration (DHHS/PHS), Washington, DC.

    This workshop handbook contains information and reference materials on proper food warehouse sanitation. The materials have been used at Food and Drug Administration (FDA) food warehouse sanitation workshops, and are selected by the FDA for use by food warehouse operators and for training warehouse sanitation employees. The handbook is divided…

  2. Conceptual Data Warehouse Structures

    DEFF Research Database (Denmark)

    Bækgaard, Lars

    1998-01-01

    changing information needs. We show how the event-entity-relationship model (EVER) can be used for schema design and query formulation in data warehouses. Our work is based on a layered data warehouse architecture in which a global data warehouse is used for flexible long-term organization and storage......We analyze some of the problems related to conceptual modeling in data warehousing environments. The long-term data warehousing challenge is flexibility rather than efficiency. The reason is that most warehouses will contain growing collections of historical data that are supposed to satisfy...... of all warehouse data whereas local data warehouses are used for efficient query formulation and answering. In order to support flexible modeling of global warehouses we use a flexible version of EVER for global schema design. In order to support efficient query formulation in local data warehouses we...

  3. Automation in Warehouse Development

    CERN Document Server

    Verriet, Jacques

    2012-01-01

    The warehouses of the future will come in a variety of forms, but with a few common ingredients. Firstly, human operational handling of items in warehouses is increasingly being replaced by automated item handling. Extended warehouse automation counteracts the scarcity of human operators and supports the quality of picking processes. Secondly, the development of models to simulate and analyse warehouse designs and their components facilitates the challenging task of developing warehouses that take into account each customer’s individual requirements and logistic processes. Automation in Warehouse Development addresses both types of automation from the innovative perspective of applied science. In particular, it describes the outcomes of the Falcon project, a joint endeavour by a consortium of industrial and academic partners. The results include a model-based approach to automate warehouse control design, analysis models for warehouse design, concepts for robotic item handling and computer vision, and auton...

  4. GALT protein database, a bioinformatics resource for the management and analysis of structural features of a galactosemia-related protein and its mutants.

    Science.gov (United States)

    d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

    2009-06-01

    We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type I. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.

  5. Automation in Warehouse Development

    NARCIS (Netherlands)

    Hamberg, R.; Verriet, J.

    2012-01-01

    The warehouses of the future will come in a variety of forms, but with a few common ingredients. Firstly, human operational handling of items in warehouses is increasingly being replaced by automated item handling. Extended warehouse automation counteracts the scarcity of human operators and

  6. 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).

  7. RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database.

    Science.gov (United States)

    Field, Helen I; Fenyö, David; Beavis, Ronald C

    2002-01-01

    RADARS, a rapid, automated, data archiving and retrieval software system for high-throughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent processing. The system automatically takes unprocessed data files, identifies proteins via in silico database searching, then stores the processed data and search results in a relational database suitable for customized reporting. The system is robust, used in 24/7 operation, accessible to multiple users of an intranet through a web browser, may be monitored by Virtual Private Network, and is secure. RADARS is scalable for use on one or many computers, and is suited to multiple processor systems. It can incorporate any local database in FASTA format, and can search protein and DNA databases online. A key feature is a suite of visualisation tools (many available gratis), allowing facile manipulation of spectra, by hand annotation, reanalysis, and access to all procedures. We also described the use of Sonar MS/MS, a novel, rapid search engine requiring 40 MB RAM per process for searches against a genomic or EST database translated in all six reading frames. RADARS reduces the cost of analysis by its efficient algorithms: Sonar MS/MS can identifiy proteins without accurate knowledge of the parent ion mass and without protein tags. Statistical scoring methods provide close-to-expert accuracy and brings robust data analysis to the non-expert user.

  8. XWeB: The XML Warehouse Benchmark

    Science.gov (United States)

    Mahboubi, Hadj; Darmont, Jérôme

    With the emergence of XML as a standard for representing business data, new decision support applications are being developed. These XML data warehouses aim at supporting On-Line Analytical Processing (OLAP) operations that manipulate irregular XML data. To ensure feasibility of these new tools, important performance issues must be addressed. Performance is customarily assessed with the help of benchmarks. However, decision support benchmarks do not currently support XML features. In this paper, we introduce the XML Warehouse Benchmark (XWeB), which aims at filling this gap. XWeB derives from the relational decision support benchmark TPC-H. It is mainly composed of a test data warehouse that is based on a unified reference model for XML warehouses and that features XML-specific structures, and its associate XQuery decision support workload. XWeB's usage is illustrated by experiments on several XML database management systems.

  9. Development of a medical informatics data warehouse.

    Science.gov (United States)

    Wu, Cai

    2006-01-01

    This project built a medical informatics data warehouse (MedInfo DDW) in an Oracle database to analyze medical information which has been collected through Baylor Family Medicine Clinic (FCM) Logician application. The MedInfo DDW used Star Schema with dimensional model, FCM database as operational data store (ODS); the data from on-line transaction processing (OLTP) were extracted and transferred to a knowledge based data warehouse through SQLLoad, and the patient information was analyzed by using on-line analytic processing (OLAP) in Crystal Report.

  10. Evaluation of warehouse workers productivity

    OpenAIRE

    Štěpánková, Anna

    2015-01-01

    The aim of this diploma thesis is to create a new system to measure and evaluate the productivity of warehouse processes in Euromedia books wholesale warehouse. The Warehouse management system (WMS) is implemented in the warehouse, so the company has information about processes within warehouse. However, the system does not have any tool to measure and report the productivity of individual workers and shifts. So the manager of the warehouse does not have enough data for efficient human resour...

  11. Building a Data Warehouse.

    Science.gov (United States)

    Levine, Elliott

    2002-01-01

    Describes how to build a data warehouse, using the Schools Interoperability Framework (www.sifinfo.org), that supports data-driven decision making and complies with the Freedom of Information Act. Provides several suggestions for building and maintaining a data warehouse. (PKP)

  12. Aptamer Bioinformatics

    Directory of Open Access Journals (Sweden)

    Andrew B. Kinghorn

    2017-11-01

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

  13. Intelligent environmental data warehouse

    International Nuclear Information System (INIS)

    Ekechukwu, B.

    1998-01-01

    Making quick and effective decisions in environment management are based on multiple and complex parameters, a data warehouse is a powerful tool for the over all management of massive environmental information. Selecting the right data from a warehouse is an important factor consideration for end-users. This paper proposed an intelligent environmental data warehouse system. It consists of data warehouse to feed an environmental researchers and managers with desire environmental information needs to their research studies and decision in form of geometric and attribute data for study area, and a metadata for the other sources of environmental information. In addition, the proposed intelligent search engine works according to a set of rule, which enables the system to be aware of the environmental data wanted by the end-user. The system development process passes through four stages. These are data preparation, warehouse development, intelligent engine development and internet platform system development. (author)

  14. Developing a standardized healthcare cost data warehouse.

    Science.gov (United States)

    Visscher, Sue L; Naessens, James M; Yawn, Barbara P; Reinalda, Megan S; Anderson, Stephanie S; Borah, Bijan J

    2017-06-12

    Research addressing value in healthcare requires a measure of cost. While there are many sources and types of cost data, each has strengths and weaknesses. Many researchers appear to create study-specific cost datasets, but the explanations of their costing methodologies are not always clear, causing their results to be difficult to interpret. Our solution, described in this paper, was to use widely accepted costing methodologies to create a service-level, standardized healthcare cost data warehouse from an institutional perspective that includes all professional and hospital-billed services for our patients. The warehouse is based on a National Institutes of Research-funded research infrastructure containing the linked health records and medical care administrative data of two healthcare providers and their affiliated hospitals. Since all patients are identified in the data warehouse, their costs can be linked to other systems and databases, such as electronic health records, tumor registries, and disease or treatment registries. We describe the two institutions' administrative source data; the reference files, which include Medicare fee schedules and cost reports; the process of creating standardized costs; and the warehouse structure. The costing algorithm can create inflation-adjusted standardized costs at the service line level for defined study cohorts on request. The resulting standardized costs contained in the data warehouse can be used to create detailed, bottom-up analyses of professional and facility costs of procedures, medical conditions, and patient care cycles without revealing business-sensitive information. After its creation, a standardized cost data warehouse is relatively easy to maintain and can be expanded to include data from other providers. Individual investigators who may not have sufficient knowledge about administrative data do not have to try to create their own standardized costs on a project-by-project basis because our data

  15. Chronic Condition Data Warehouse

    Data.gov (United States)

    U.S. Department of Health & Human Services — The CMS Chronic Condition Data Warehouse (CCW) provides researchers with Medicare and Medicaid beneficiary, claims, and assessment data linked by beneficiary across...

  16. Public Refrigerated Warehouses

    Data.gov (United States)

    Department of Homeland Security — The International Association of Refrigerated Warehouses (IARW) came into existence in 1891 when a number of conventional warehousemen took on the demands of storing...

  17. HRSA Data Warehouse

    Data.gov (United States)

    U.S. Department of Health & Human Services — The HRSA Data Warehouse is the go-to source for data, maps, reports, locators, and dashboards on HRSA's public health programs. This website provides a wide variety...

  18. The development of health care data warehouses to support data mining.

    Science.gov (United States)

    Lyman, Jason A; Scully, Kenneth; Harrison, James H

    2008-03-01

    Clinical data warehouses offer tremendous benefits as a foundation for data mining. By serving as a source for comprehensive clinical and demographic information on large patient populations, they streamline knowledge discovery efforts by providing standard and efficient mechanisms to replace time-consuming and expensive original data collection, organization, and processing. Building effective data warehouses requires knowledge of and attention to key issues in database design, data acquisition and processing, and data access and security. In this article, the authors provide an operational and technical definition of data warehouses, present examples of data mining projects enabled by existing data warehouses, and describe key issues and challenges related to warehouse development and implementation.

  19. DICOM Data Warehouse: Part 2.

    Science.gov (United States)

    Langer, Steve G

    2016-06-01

    In 2010, the DICOM Data Warehouse (DDW) was launched as a data warehouse for DICOM meta-data. Its chief design goals were to have a flexible database schema that enabled it to index standard patient and study information, modality specific tags (public and private), and create a framework to derive computable information (derived tags) from the former items. Furthermore, it was to map the above information to an internally standard lexicon that enables a non-DICOM savvy programmer to write standard SQL queries and retrieve the equivalent data from a cohort of scanners, regardless of what tag that data element was found in over the changing epochs of DICOM and ensuing migration of elements from private to public tags. After 5 years, the original design has scaled astonishingly well. Very little has changed in the database schema. The knowledge base is now fluent in over 90 device types. Also, additional stored procedures have been written to compute data that is derivable from standard or mapped tags. Finally, an early concern is that the system would not be able to address the variability DICOM-SR objects has been addressed. As of this writing the system is indexing 300 MR, 600 CT, and 2000 other (XA, DR, CR, MG) imaging studies per day. The only remaining issue to be solved is the case for tags that were not prospectively indexed-and indeed, this final challenge may lead to a noSQL, big data, approach in a subsequent version.

  20. Data Linkage from Clinical to Study Databases via an R Data Warehouse User Interface. Experiences from a Large Clinical Follow-up Study.

    Science.gov (United States)

    Kaspar, Mathias; Ertl, Maximilian; Fette, Georg; Dietrich, Georg; Toepfer, Martin; Angermann, Christiane; Störk, Stefan; Puppe, Frank

    2016-08-05

    Data that needs to be documented for clinical studies has often been acquired and documented in clinical routine. Usually this data is manually transferred to Case Report Forms (CRF) and/or directly into an electronic data capture (EDC) system. To enhance the documentation process of a large clinical follow-up study targeting patients admitted for acutely decompensated heart failure by accessing the data created during routine and study visits from a hospital information system (HIS) and by transferring it via a data warehouse (DWH) into the study's EDC system. This project is based on the clinical DWH developed at the University of Würzburg. The DWH was extended by several new data domains including data created by the study team itself. An R user interface was developed for the DWH that allows to access its source data in all its detail, to transform data as comprehensively as possible by R into study-specific variables and to support the creation of data and catalog tables. A data flow was established that starts with labeling patients as study patients within the HIS and proceeds with updating the DWH with this label and further data domains at a daily rate. Several study-specific variables were defined using the implemented R user interface of the DWH. This system was then used to export these variables as data tables ready for import into our EDC system. The data tables were then used to initialize the first 296 patients within the EDC system by pseudonym, visit and data values. Afterwards, these records were filled with clinical data on heart failure, vital parameters and time spent on selected wards. This solution focuses on the comprehensive access and transformation of data for a DWH-EDC system linkage. Using this system in a large clinical study has demonstrated the feasibility of this approach for a study with a complex visit schedule.

  1. Security Data Warehouse Application

    Science.gov (United States)

    Vernon, Lynn R.; Hennan, Robert; Ortiz, Chris; Gonzalez, Steve; Roane, John

    2012-01-01

    The Security Data Warehouse (SDW) is used to aggregate and correlate all JSC IT security data. This includes IT asset inventory such as operating systems and patch levels, users, user logins, remote access dial-in and VPN, and vulnerability tracking and reporting. The correlation of this data allows for an integrated understanding of current security issues and systems by providing this data in a format that associates it to an individual host. The cornerstone of the SDW is its unique host-mapping algorithm that has undergone extensive field tests, and provides a high degree of accuracy. The algorithm comprises two parts. The first part employs fuzzy logic to derive a best-guess host assignment using incomplete sensor data. The second part is logic to identify and correct errors in the database, based on subsequent, more complete data. Host records are automatically split or merged, as appropriate. The process had to be refined and thoroughly tested before the SDW deployment was feasible. Complexity was increased by adding the dimension of time. The SDW correlates all data with its relationship to time. This lends support to forensic investigations, audits, and overall situational awareness. Another important feature of the SDW architecture is that all of the underlying complexities of the data model and host-mapping algorithm are encapsulated in an easy-to-use and understandable Perl language Application Programming Interface (API). This allows the SDW to be quickly augmented with additional sensors using minimal coding and testing. It also supports rapid generation of ad hoc reports and integration with other information systems.

  2. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

    Science.gov (United States)

    Smith, Richard N; Aleksic, Jelena; Butano, Daniela; Carr, Adrian; Contrino, Sergio; Hu, Fengyuan; Lyne, Mike; Lyne, Rachel; Kalderimis, Alex; Rutherford, Kim; Stepan, Radek; Sullivan, Julie; Wakeling, Matthew; Watkins, Xavier; Micklem, Gos

    2012-12-01

    InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. Freely available from http://www.intermine.org under the LGPL license. g.micklem@gen.cam.ac.uk Supplementary data are available at Bioinformatics online.

  3. 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.

  4. TRUNCATULIX--a data warehouse for the legume community.

    Science.gov (United States)

    Henckel, Kolja; Runte, Kai J; Bekel, Thomas; Dondrup, Michael; Jakobi, Tobias; Küster, Helge; Goesmann, Alexander

    2009-02-11

    Databases for either sequence, annotation, or microarray experiments data are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, data from different sources develop their full capacities only when combined. The idea of a data warehouse directly adresses this problem and solves it by integrating all required data into one single database - hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula, there is currently no such single data warehouse that integrates all freely available gene sequences, the corresponding gene expression data, and annotation information. Thus, we created the data warehouse TRUNCATULIX, an integrative database of Medicago truncatula sequence and expression data. The TRUNCATULIX data warehouse integrates five public databases for gene sequences, and gene annotations, as well as a database for microarray expression data covering raw data, normalized datasets, and complete expression profiling experiments. It can be accessed via an AJAX-based web interface using a standard web browser. For the first time, users can now quickly search for specific genes and gene expression data in a huge database based on high-quality annotations. The results can be exported as Excel, HTML, or as csv files for further usage. The integration of sequence, annotation, and gene expression data from several Medicago truncatula databases in TRUNCATULIX provides the legume community with access to data and data mining capability not previously available. TRUNCATULIX is freely available at http://www.cebitec.uni-bielefeld.de/truncatulix/.

  5. Usage of data warehouse for analysing software's bugs

    Science.gov (United States)

    Živanov, Danijel; Krstićev, Danijela Boberić; Mirković, Duško

    2017-07-01

    We analysed the database schema of Bugzilla system and taking into account user's requirements for reporting, we presented a dimensional model for the data warehouse which will be used for reporting software defects. The idea proposed in this paper is not to throw away Bugzilla system because it certainly has many strengths, but to make integration of Bugzilla and the proposed data warehouse. Bugzilla would continue to be used for recording bugs that occur during the development and maintenance of software while the data warehouse would be used for storing data on bugs in an appropriate form, which is more suitable for analysis.

  6. Building the Readiness Data Warehouse

    National Research Council Canada - National Science Library

    Tysor, Sue

    2000-01-01

    .... This is the role of the data warehouse. The data warehouse will deliver business intelligence based on operational data, decision support data and external data to all business units in the organization...

  7. 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.

  8. HEALTH CARE DATA WAREHOUSE SYSTEM ARCHITECTURE FOR INFLUENZA (FLU) DISEASES

    OpenAIRE

    Rajib Dutta

    2013-01-01

    Data Warehouse is the most reliable technology used by the company for planning, forecasting and management. Critical business management data was contained in several unrelated and disconnected databases, both internally managed and from external sources. Client was unable to view the data from an integrated viewpoint. The data warehousing is one of the best technique to integrate data. This paper presents the Influenza (Flu) diseases specific data warehouse architecture for h...

  9. Building data warehouse in Metropolia University of Applied Sciences

    OpenAIRE

    Tikka, Antti

    2013-01-01

    Universities use many different data systems that store data in different databases. To get maximum benefit from this precious data it is necessary to build a data warehouse. In this building project data from different sources is integrated and processed to form that can be easily used in reporting and analyzing.There are two different widespread data warehouse architectures: Inmon’s and Kimball’s. Metropolia started first with Inmon’s architecture. There were many problems and after many ye...

  10. A clinician friendly data warehouse oriented toward narrative reports: Dr. Warehouse.

    Science.gov (United States)

    Garcelon, Nicolas; Neuraz, Antoine; Salomon, Rémi; Faour, Hassan; Benoit, Vincent; Delapalme, Arthur; Munnich, Arnold; Burgun, Anita; Rance, Bastien

    2018-04-01

    Clinical data warehouses are often oriented toward integration and exploration of coded data. However narrative reports are of crucial importance for translational research. This paper describes Dr. Warehouse®, an open source data warehouse oriented toward clinical narrative reports and designed to support clinicians' day-to-day use. Dr. Warehouse relies on an original database model to focus on documents in addition to facts. Besides classical querying functionalities, the system provides an advanced search engine and Graphical User Interfaces adapted to the exploration of text. Dr. Warehouse is dedicated to translational research with cohort recruitment capabilities, high throughput phenotyping and patient centric views (including similarity metrics among patients). These features leverage Natural Language Processing based on the extraction of UMLS® concepts, as well as negation and family history detection. A survey conducted after 6 months of use at the Necker Children's Hospital shows a high rate of satisfaction among the users (96.6%). During this period, 122 users performed 2837 queries, accessed 4,267 patients' records and included 36,632 patients in 131 cohorts. The source code is available at this github link https://github.com/imagine-bdd/DRWH. A demonstration based on PubMed abstracts is available at https://imagine-plateforme-bdd.fr/dwh_pubmed/. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  11. DATA WAREHOUSES SECURITY IMPLEMENTATION

    Directory of Open Access Journals (Sweden)

    Burtescu Emil

    2009-05-01

    Full Text Available Data warehouses were initially implemented and developed by the big firms and they were used for working out the managerial problems and for making decisions. Later on, because of the economic tendencies and of the technological progress, the data warehou

  12. 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…

  13. DSSTOX STRUCTURE-SEARCHABLE PUBLIC TOXICITY DATABASE NETWORK: CURRENT PROGRESS AND NEW INITIATIVES TO IMPROVE CHEMO-BIOINFORMATICS CAPABILITIES

    Science.gov (United States)

    The EPA DSSTox website (http://www/epa.gov/nheerl/dsstox) publishes standardized, structure-annotated toxicity databases, covering a broad range of toxicity disciplines. Each DSSTox database features documentation written in collaboration with the source authors and toxicity expe...

  14. 7 CFR 1427.11 - Warehouse receipts.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Warehouse receipts. 1427.11 Section 1427.11... Deficiency Payments § 1427.11 Warehouse receipts. (a) Producers may obtain loans on eligible cotton represented by warehouse receipts only if the warehouse receipts meet the definition of a warehouse receipt...

  15. Databases

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.

    Information on bibliographic as well as numeric/textual databases relevant to coastal geomorphology has been included in a tabular form. Databases cover a broad spectrum of related subjects like coastal environment and population aspects, coastline...

  16. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

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

  17. Flow cytometry bioinformatics.

    Directory of Open Access Journals (Sweden)

    Kieran O'Neill

    Full Text Available Flow cytometry bioinformatics is the application of bioinformatics to flow cytometry data, which involves storing, retrieving, organizing, and analyzing flow cytometry data using extensive computational resources and tools. Flow cytometry bioinformatics requires extensive use of and contributes to the development of techniques from computational statistics and machine learning. Flow cytometry and related methods allow the quantification of multiple independent biomarkers on large numbers of single cells. The rapid growth in the multidimensionality and throughput of flow cytometry data, particularly in the 2000s, has led to the creation of a variety of computational analysis methods, data standards, and public databases for the sharing of results. Computational methods exist to assist in the preprocessing of flow cytometry data, identifying cell populations within it, matching those cell populations across samples, and performing diagnosis and discovery using the results of previous steps. For preprocessing, this includes compensating for spectral overlap, transforming data onto scales conducive to visualization and analysis, assessing data for quality, and normalizing data across samples and experiments. For population identification, tools are available to aid traditional manual identification of populations in two-dimensional scatter plots (gating, to use dimensionality reduction to aid gating, and to find populations automatically in higher dimensional space in a variety of ways. It is also possible to characterize data in more comprehensive ways, such as the density-guided binary space partitioning technique known as probability binning, or by combinatorial gating. Finally, diagnosis using flow cytometry data can be aided by supervised learning techniques, and discovery of new cell types of biological importance by high-throughput statistical methods, as part of pipelines incorporating all of the aforementioned methods. Open standards, data

  18. Knowledge Warehouse Framework

    OpenAIRE

    Mir Sajjad Hussain Talpur; Hina Shafi Chandio; Sher Muhammad Chandio; Hira Sajjad Talpur

    2012-01-01

    Decision Support Systems (DSS) helps the management in making accurate and timely decisions for successful business operations. Data Warehouse (DW) is one of the solutions for decision-making process in a business organization. But it only store data for managerial purpose and has no intelligent mechanism for decision making. This raises the issue of knowledge storage in organization for high capability decision support. Problem also arises during accessing of knowledge from different sources...

  19. Health Claims Data Warehouse (HCDW)

    Data.gov (United States)

    Office of Personnel Management — The Health Claims Data Warehouse (HCDW) will receive and analyze health claims data to support management and administrative purposes. The Federal Employee Health...

  20. The Data Warehouse Lifecycle Toolkit

    CERN Document Server

    Kimball, Ralph; Thornthwaite, Warren; Mundy, Joy; Becker, Bob

    2011-01-01

    A thorough update to the industry standard for designing, developing, and deploying data warehouse and business intelligence systemsThe world of data warehousing has changed remarkably since the first edition of The Data Warehouse Lifecycle Toolkit was published in 1998. In that time, the data warehouse industry has reached full maturity and acceptance, hardware and software have made staggering advances, and the techniques promoted in the premiere edition of this book have been adopted by nearly all data warehouse vendors and practitioners. In addition, the term "business intelligence" emerge

  1. Fire detection in warehouse facilities

    CERN Document Server

    Dinaburg, Joshua

    2013-01-01

    Automatic sprinklers systems are the primary fire protection system in warehouse and storage facilities. The effectiveness of this strategy has come into question due to the challenges presented by modern warehouse facilities, including increased storage heights and areas, automated storage retrieval systems (ASRS), limitations on water supplies, and changes in firefighting strategies. The application of fire detection devices used to provide early warning and notification of incipient warehouse fire events is being considered as a component of modern warehouse fire protection.Fire Detection i

  2. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  3. Warehouses information system design and development

    Science.gov (United States)

    Darajatun, R. A.; Sukanta

    2017-12-01

    Materials/goods handling industry is fundamental for companies to ensure the smooth running of their warehouses. Efficiency and organization within every aspect of the business is essential in order to gain a competitive advantage. The purpose of this research is design and development of Kanban of inventory storage and delivery system. Application aims to facilitate inventory stock checks to be more efficient and effective. Users easily input finished goods from production department, warehouse, customer, and also suppliers. Master data designed as complete as possible to be prepared applications used in a variety of process logistic warehouse variations. The author uses Java programming language to develop the application, which is used for building Java Web applications, while the database used is MySQL. System development methodology that I use is the Waterfall methodology. Waterfall methodology has several stages of the Analysis, System Design, Implementation, Integration, Operation and Maintenance. In the process of collecting data the author uses the method of observation, interviews, and literature.

  4. TRUNCATULIX – a data warehouse for the legume community

    Directory of Open Access Journals (Sweden)

    Runte Kai J

    2009-02-01

    Full Text Available Abstract Background Databases for either sequence, annotation, or microarray experiments data are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, data from different sources develop their full capacities only when combined. The idea of a data warehouse directly adresses this problem and solves it by integrating all required data into one single database – hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula, there is currently no such single data warehouse that integrates all freely available gene sequences, the corresponding gene expression data, and annotation information. Thus, we created the data warehouse TRUNCATULIX, an integrative database of Medicago truncatula sequence and expression data. Results The TRUNCATULIX data warehouse integrates five public databases for gene sequences, and gene annotations, as well as a database for microarray expression data covering raw data, normalized datasets, and complete expression profiling experiments. It can be accessed via an AJAX-based web interface using a standard web browser. For the first time, users can now quickly search for specific genes and gene expression data in a huge database based on high-quality annotations. The results can be exported as Excel, HTML, or as csv files for further usage. Conclusion The integration of sequence, annotation, and gene expression data from several Medicago truncatula databases in TRUNCATULIX provides the legume community with access to data and data mining capability not previously available. TRUNCATULIX is freely available at http://www.cebitec.uni-bielefeld.de/truncatulix/.

  5. Model Data Warehouse dan Business Intelligence untuk Meningkatkan Penjualan pada PT. S

    Directory of Open Access Journals (Sweden)

    Rudy Rudy

    2011-06-01

    Full Text Available Today a lot of companies use information system in every business activity. Every transaction is stored electronically in the database transaction. The transactional database does not help much to assist the executives in making strategic decisions to improve the company competitiveness. The objective of this research is to analyze the operational database system and the information needed by the management to design a data warehouse model which fits the executive information needs in PT. S. The research method uses the Nine-Step Methodology data warehouse design by Ralph Kimball. The result is a data warehouse featuring business intelligence applications to display information of historical data in tables, graphs, pivot tables, and dashboards and has several points of view for the management. This research concludes that a data warehouse which combines multiple database transactions with business intelligence application can help executives to understand the reports in order to accelerate decision-making processes. 

  6. Securing Document Warehouses against Brute Force Query Attacks

    Directory of Open Access Journals (Sweden)

    Sergey Vladimirovich Zapechnikov

    2017-04-01

    Full Text Available The paper presents the scheme of data management and protocols for securing document collection against adversary users who try to abuse their access rights to find out the full content of confidential documents. The configuration of secure document retrieval system is described and a suite of protocols among the clients, warehouse server, audit server and database management server is specified. The scheme makes it infeasible for clients to establish correspondence between the documents relevant to different search queries until a moderator won’t give access to these documents. The proposed solution allows ensuring higher security level for document warehouses.

  7. Bioinformatics for cancer immunotherapy target discovery

    DEFF Research Database (Denmark)

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

    2014-01-01

    cancer immunotherapies has yet to be fulfilled. The insufficient efficacy of existing treatments can be attributed to a number of biological and technical issues. In this review, we detail the current limitations of immunotherapy target selection and design, and review computational methods to streamline...... 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...

  8. Bioinformatics and mass spectrometry for microorganism identification: proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori.

    Science.gov (United States)

    Demirev, P A; Lin, J S; Pineda, F J; Fenselaut, C

    2001-10-01

    MALDI-TOF mass spectrometry has been coupled with Internet-based proteome database search algorithms in an approach for direct microorganism identification. This approach is applied here to characterize intact H. pylori (strain 26695) Gram-negative bacteria, the most ubiquitous human pathogen. A procedure for including a specific and common posttranslational modification, N-terminal Met cleavage, in the search algorithm is described. Accounting for posttranslational modifications in putative protein biomarkers improves the identification reliability by at least an order of magnitude. The influence of other factors, such as number of detected biomarker peaks, proteome size, spectral calibration, and mass accuracy, on the microorganism identification success rate is illustrated as well.

  9. Architecture of an Open-Sourced, Extensible Data Warehouse Builder: InterBase 6 Data Warehouse Builder (IB-DWB)

    OpenAIRE

    Ling, Maurice HT; So, Chi Wai

    2003-01-01

    We report the development of an open-sourced data warehouse builder, InterBase Data Warehouse Builder (IB-DWB), based on Borland InterBase 6 Open Edition Database Server. InterBase 6 is used for its low maintenance and small footprint. IB-DWB is designed modularly and consists of 5 main components, Data Plug Platform, Discoverer Platform, Multi-Dimensional Cube Builder, and Query Supporter, bounded together by a Kernel. It is also an extensible system, made possible by the Data Plug Platform ...

  10. University Accreditation using Data Warehouse

    Science.gov (United States)

    Sinaga, A. S.; Girsang, A. S.

    2017-01-01

    The accreditation aims assuring the quality the quality of the institution education. The institution needs the comprehensive documents for giving the information accurately before reviewed by assessor. Therefore, academic documents should be stored effectively to ease fulfilling the requirement of accreditation. However, the data are generally derived from various sources, various types, not structured and dispersed. This paper proposes designing a data warehouse to integrate all various data to prepare a good academic document for accreditation in a university. The data warehouse is built using nine steps that was introduced by Kimball. This method is applied to produce a data warehouse based on the accreditation assessment focusing in academic part. The data warehouse shows that it can analyse the data to prepare the accreditation assessment documents.

  11. 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.

  12. The design and application of data warehouse during modern enterprises environment

    Science.gov (United States)

    Zhou, Lijuan; Liu, Chi; Wang, Chunying

    2006-04-01

    The interest in analyzing data has grown tremendously in recent years. To analyze data, a multitude of technologies is need, namely technologies from the fields of Data Warehouse, Data Mining, On-line Analytical Processing (OLAP). This paper proposes the system structure model of the data warehouse during modern enterprises environment according to the information demand for enterprises and the actual demand of user's, and also analyses the benefit of this kind of model in practical application, and provides the setting-up course of the data warehouse model. At the same time it has proposes the total design plans of the data warehouses of modern enterprises. The data warehouse that we build in practical application can be offered: high performance of queries; efficiency of the data; independent characteristic of logical and physical data. In addition, A Data Warehouse contains lots of materialized views over the data provided by the distributed heterogeneous databases for the purpose of efficiently implementing decision-support, OLAP queries or data mining. One of the most important decisions in designing a data warehouse is selection of right views to be materialized. In this paper, we also have designed algorithms for selecting a set of views to be materialized in a data warehouse.First, we give the algorithms for selecting materialized views. Then we use experiments do demonstrate the power of our approach. The results show the proposed algorithm delivers an optimal solution. Finally, we discuss the advantage and shortcoming of our approach and future work.

  13. 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.

  14. PEMAHAMAN TEORI DATA WAREHOUSE BAGI MAHASISWA TAHUN AWAL JENJANG STRATA SATU BIDANG ILMU KOMPUTER

    Directory of Open Access Journals (Sweden)

    Harco Leslie Hendric Spits Warnars

    2015-01-01

    Full Text Available As a Computer scientist, a computer science students should have understanding about database theory as a concept of data maintenance. Database will be needed in every single human real life computer implementation such as information systems, information technology, internet, games, artificial intelligence, robot and so on. Inevitably, the right data handling and managament will produce excellent technology implementation. Data warehouse as one of the specialization subject which is offered in computer science study program final semester, provide challenge for computer science students.A survey was conducted on 18 students of early year of computer science study program at Surya university and giving hypothesis that for those students who ever heard of a data warehouse would be interested to learn data warehouse and on other hand, students who had never heard of the data warehouse will not be interested to learn data warehouse. Therefore, it is important that delivery of the Data warehouse subject material should be understood by lecturers, so that students can well understoodwith the data warehouse.

  15. 7 CFR 735.302 - Paper warehouse receipts.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Paper warehouse receipts. 735.302 Section 735.302... AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Receipts § 735.302 Paper warehouse receipts. Paper warehouse receipts must be issued as follows: (a) On...

  16. 7 CFR 735.300 - Warehouse receipt requirements.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Warehouse receipt requirements. 735.300 Section 735..., DEPARTMENT OF AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Receipts § 735.300 Warehouse receipt requirements. (a) Warehouse receipts may be: (1) Negotiable...

  17. 7 CFR 735.303 - Electronic warehouse receipts.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Electronic warehouse receipts. 735.303 Section 735.303... AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Receipts § 735.303 Electronic warehouse receipts. (a) Warehouse operators issuing EWR under the Act may issue EWR...

  18. 7 CFR 735.107 - Warehouse charges and tariffs.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Warehouse charges and tariffs. 735.107 Section 735.107... AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Licensing § 735.107 Warehouse charges and tariffs. (a) A warehouse operator must not make any unreasonable or...

  19. 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.

  20. 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.

  1. 7 CFR 1423.10 - Exceptions for United States Warehouse Act licensed warehouses.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Exceptions for United States Warehouse Act licensed warehouses. 1423.10 Section 1423.10 Agriculture Regulations of the Department of Agriculture (Continued... CREDIT CORPORATION APPROVED WAREHOUSES § 1423.10 Exceptions for United States Warehouse Act licensed...

  2. Structuring warehouse management : Exploring the fit between warehouse characteristics and warehouse planning and control structure, and its effect on warehouse performance

    NARCIS (Netherlands)

    N. Faber (Nynke)

    2015-01-01

    markdownabstractThis dissertation studies the management processes that plan, control, and optimize warehouse operations. The inventory in warehouses decouples supply from demand. As such, economies of scale can be achieved in production, purchasing, and transport. As warehouses become more and more

  3. Stochastic Modelling and Analysis of Warehouse Operations

    NARCIS (Netherlands)

    Y. Gong (Yeming)

    2009-01-01

    textabstractThis thesis has studied stochastic models and analysis of warehouse operations. After an overview of stochastic research in warehouse operations, we explore the following topics. Firstly, we search optimal batch sizes in a parallel-aisle warehouse with online order arrivals. We employ a

  4. Cooperation between Multiple Newsvendors with Warehouses

    NARCIS (Netherlands)

    Ozen, U.; Fransoo, J.; Norde, H.W.; Slikker, M.

    2004-01-01

    This study considers a supply chain that consists of n retailers, each of them facing a newsvendor problem, m warehouses and a supplier.The retailers are supplied with a single product via some warehouses.In these warehouses, the ordered amounts of goods of these retailers become available after

  5. Determining key performance indicators for warehouse performance measurement – a case study in construction materials warehouse

    Directory of Open Access Journals (Sweden)

    Kusrini Elisa

    2018-01-01

    Full Text Available Warehouse performance measurement is needed to improve performance of logistics system. In order to improve warehouse performance, it is necessary to identify Key Performance Indicator (KPI. Different warehouses have different KPI, therefore this research aims to identify the most important KPI of warehouse so that warehouse manager can determine corrective actions in their warehouse efficiently and effectively. In this research, 25 KPI of warehouse are identified in five warehouse activities based on Frazelle model. The most important KPI are then determined in each warehouse activity using Analytical Hierarchy Process (AHP. Warehouse performance are measured and final score is determined using SNORM. Improvement steps are proposed base on benchmarking among warehouses. Warehouse performance measurement is conducted in 5 construction’s material warehouses located in Yogyakarta, Indonesia. From this study, it is found that most important KPI for receiving is productivity (receive per man-hour, KPI for put away is cycle time (put away cycle time, KPI for storage is utilization (% location and cube occupied, KPI for order picking is cycle time (order picking cycle time and KPI for shipping is productivity (order prepared for shipment per man-hour. Improving warehouse performance could be done by comparing warehouse performance with the best performance among peer group.

  6. Electronic warehouse receipts registry as a step from paper to electronic warehouse receipts

    Directory of Open Access Journals (Sweden)

    Kovačević Vlado

    2016-01-01

    Full Text Available The aim of this paper is to determine the economic viability of the electronic warehouse receipt registry introduction, as a step toward electronic warehouse receipts. Both forms of warehouse receipt paper and electronic exist in practice, but paper warehouse receipts are more widespread. In this paper, the dematerialization process is analyzed in two steps. The first step is the dematerialization of warehouse receipt registry, with warehouse receipts still in paper form. The second step is the introduction of electronic warehouse receipts themselves. Dematerialization of warehouse receipts is more complex than that for financial securities, because of the individual characteristics of each warehouse receipt. As a consequence, electronic warehouse receipts are in place for only to a handful of commodities, namely cotton and a few grains. Nevertheless, the movement towards the electronic warehouse receipt, which began several decades ago with financial securities, is now taking hold in the agricultural sector. In this paper is analyzed Serbian electronic registry, since the Serbia is first country in EU with electronic warehouse receipts registry donated by FAO. Performed analysis shows the considerable impact of electronic warehouse receipts registry establishment on enhancing the security of the system of public warehouses, and on advancing the trade with warehouse receipt.

  7. 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:…

  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. 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. A Framework for Designing a Healthcare Outcome Data Warehouse

    Science.gov (United States)

    Parmanto, Bambang; Scotch, Matthew; Ahmad, Sjarif

    2005-01-01

    Many healthcare processes involve a series of patient visits or a series of outcomes. The modeling of outcomes associated with these types of healthcare processes is different from and not as well understood as the modeling of standard industry environments. For this reason, the typical multidimensional data warehouse designs that are frequently seen in other industries are often not a good match for data obtained from healthcare processes. Dimensional modeling is a data warehouse design technique that uses a data structure similar to the easily understood entity-relationship (ER) model but is sophisticated in that it supports high-performance data access. In the context of rehabilitation services, we implemented a slight variation of the dimensional modeling technique to make a data warehouse more appropriate for healthcare. One of the key aspects of designing a healthcare data warehouse is finding the right grain (scope) for different levels of analysis. We propose three levels of grain that enable the analysis of healthcare outcomes from highly summarized reports on episodes of care to fine-grained studies of progress from one treatment visit to the next. These grains allow the database to support multiple levels of analysis, which is imperative for healthcare decision making. PMID:18066371

  11. A framework for designing a healthcare outcome data warehouse.

    Science.gov (United States)

    Parmanto, Bambang; Scotch, Matthew; Ahmad, Sjarif

    2005-09-06

    Many healthcare processes involve a series of patient visits or a series of outcomes. The modeling of outcomes associated with these types of healthcare processes is different from and not as well understood as the modeling of standard industry environments. For this reason, the typical multidimensional data warehouse designs that are frequently seen in other industries are often not a good match for data obtained from healthcare processes. Dimensional modeling is a data warehouse design technique that uses a data structure similar to the easily understood entity-relationship (ER) model but is sophisticated in that it supports high-performance data access. In the context of rehabilitation services, we implemented a slight variation of the dimensional modeling technique to make a data warehouse more appropriate for healthcare. One of the key aspects of designing a healthcare data warehouse is finding the right grain (scope) for different levels of analysis. We propose three levels of grain that enable the analysis of healthcare outcomes from highly summarized reports on episodes of care to fine-grained studies of progress from one treatment visit to the next. These grains allow the database to support multiple levels of analysis, which is imperative for healthcare decision making.

  12. Toward a fully de-identified biomedical information warehouse.

    Science.gov (United States)

    Liu, Jianhua; Erdal, Selnur; Silvey, Scott A; Ding, Jing; Riedel, John D; Marsh, Clay B; Kamal, Jyoti

    2009-11-14

    The Information Warehouse at the Ohio State University Medical Center is a comprehensive repository of business, clinical, and research data from various source systems. Data collected here is a valuable resource that facilitates both translational research and personalized healthcare. The use of such data in research is governed by federal privacy regulations with oversight by the Institutional Review Board. In 2006, the Information Warehouse was recognized by the OSU IRB as an "Honest Broker" of clinical data, providing investigators with de-identified or limited datasets under stipulations contained in a signed data use agreement. In order to streamline this process even further, the Information Warehouse is developing a de-identified data warehouse that is suitable for direct user access through a controlled query tool that is aimed to support both research and education activities. In this paper we report our findings on performance evaluation of different de-identification schemes that may be used to ensure regulatory compliance while also facilitating practical database updating and querying. We also discuss how date-shifting in the de-identification process can impact other data elements such as diagnosis and procedure codes and consider a possible solution to those problems.

  13. Perancangan Data Warehouse Nilai Mahasiswa Dengan Kimball Nine-Step Methodology

    Directory of Open Access Journals (Sweden)

    Ganda Wijaya

    2017-04-01

    Abstract Student grades has many components that can be analyzed to support decision making. Based on this, the authors conducted a study of student grades. The study was conducted on a database that is in the Bureau of Academic and Student Affairs Administration Bina Sarana Informatika (BAAK BSI. The focus of this research is "How to model a data warehouse that can meet the management needs of the data value of students as supporters of evaluation, planning and decision making?". Data warehouse grades students need to be made in order to obtain the information, reports, and can perform multi-dimensional analysis, which in turn can assist management in making policy. Development of the system is done by using System Development Life Cycle (SDLC with Waterfall approach. While the design of the data warehouse using a nine-step methodology kimball. Results obtained in the form of a star schema and data warehouse value. Data warehouses can provide a summary of information that is fast, accurate and continuous so as to assist management in making policies for the future. In general, the benefits of this research are as additional reference in building a data warehouse using a nine-step methodology kimball.   Keywords: Data Warehouse, Kimball Nine-Step Methodology.

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

    African Journals Online (AJOL)

    SERVER

    2008-03-04

    Mar 4, 2008 ... Data Warehouse is shared by the researchers across the globe. Biological databases. The rapid development of genome technologies, espe- cially automatic sequencing techniques, has produced a huge amount of data consisting essentially of nucleotide and protein sequences. For instance, the number ...

  15. Selecting materialized views in a data warehouse

    Science.gov (United States)

    Zhou, Lijuan; Liu, Chi; Liu, Daxin

    2003-01-01

    A Data Warehouse contains lots of materialized views over the data provided by the distributed heterogeneous databases for the purpose of efficiently implementing decision-support or OLAP queries. It is important to select the right view to materialize that answer a given set of queries. In this paper, we have addressed and designed algorithm to select a set of views to materialize in order to answer the most queries under the constraint of a given space. The algorithm presented in this paper aim at making out a minimum set of views, by which we can directly respond to as many as possible user"s query requests. We use experiments to demonstrate our approach. The results show that our algorithm works better. We implemented our algorithms and a performance study of the algorithm shows that the proposed algorithm gives a less complexity and higher speeds and feasible expandability.

  16. Energy Finance Data Warehouse Manual

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sangkeun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Chinthavali, Supriya [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Shankar, Mallikarjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Zeng, Claire [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hendrickson, Stephen [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-11-30

    The Office of Energy Policy and Systems Analysis s finance team (EPSA-50) requires a suite of automated applications that can extract specific data from a flexible data warehouse (where datasets characterizing energy-related finance, economics and markets are maintained and integrated), perform relevant operations and creatively visualize them to provide a better understanding of what policy options affect various operators/sectors of the electricity system. In addition, the underlying data warehouse should be structured in the most effective and efficient way so that it can become increasingly valuable over time. This report describes the Energy Finance Data Warehouse (EFDW) framework that has been developed to accomplish the defined requirement above. We also specifically dive into the Sankey generator use-case scenario to explain the components of the EFDW framework and their roles. An excel-based data warehouse was used in the creation of the energy finance Sankey diagram and other detailed data finance visualizations to support energy policy analysis. The framework also captures the methodology, calculations and estimations analysts used for the calculation as well as relevant sources so newer analysts can build on work done previously.

  17. 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.

  18. Pemanfaatan Data Warehouse pada Institusi Pemerintahan

    Directory of Open Access Journals (Sweden)

    Rudy Rudy

    2012-06-01

    Full Text Available Data warehouse has a very important role in assisting of decision making, where the data warehouse became the core. Data in the data warehouse provide valuable information for its users. By using data warehouse, governance institutions can conduct data analyzes in order to build new strategies to make benefits for all stakeholders. This paper discusses about the design of data warehouse in Balai Besar Riset Sosial Ekonomi dan Kelautan. Data warehouse design using dimensional model approach introduced by Kimball. The information required by management at Balai Besar Riset Sosial Ekonimi dan Kelautan are divided into three groups: income, consumption and commerce. With the data warehouse organizations can easily perform analyses and generate reports, which can be viewed from various scopes, including time, region, fishermen and fisheries.

  19. 7 CFR 735.108 - Inspections and examinations of warehouses.

    Science.gov (United States)

    2010-01-01

    ... Warehouse Licensing § 735.108 Inspections and examinations of warehouses. (a) Warehouse operators must permit any agent of the Department to enter and inspect or examine, on any business day during the usual hours of business, any licensed warehouse, the offices of the warehouse operator, the books, records...

  20. 27 CFR 26.211 - Warehouse receipts covering distilled spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Warehouse receipts... and Recordkeeping § 26.211 Warehouse receipts covering distilled spirits. The sale of warehouse..., warehouse receipts for distilled spirits stored in warehouses, or elsewhere, must register and keep records...

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

    Science.gov (United States)

    Schneider, Maria V; Walter, Peter; Blatter, Marie-Claude; Watson, James; Brazas, Michelle D; Rother, Kristian; Budd, Aidan; Via, Allegra; van Gelder, Celia W G; Jacob, Joachim; Fernandes, Pedro; Nyrönen, Tommi H; De Las Rivas, Javier; Blicher, Thomas; Jimenez, Rafael C; Loveland, Jane; McDowall, Jennifer; Jones, Phil; Vaughan, Brendan W; Lopez, Rodrigo; Attwood, Teresa K; Brooksbank, Catherine

    2012-05-01

    Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database 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 it, respectively, to similar initiatives and collections.

  2. 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.

  3. [Peranesthesic Anaphylactic Shocks: Contribution of a Clinical Data Warehouse].

    Science.gov (United States)

    Osmont, Marie-Noëlle; Campillo-Gimenez, Boris; Metayer, Lucie; Jantzem, Hélène; Rochefort-Morel, Cécile; Cuggia, Marc; Polard, Elisabeth

    2015-10-16

    To evaluate the performance of the collection of cases of anaphylactic shock during anesthesia in the Regional Pharmacovigilance Center of Rennes and the contribution of a query in the biomedical data warehouse of the French University Hospital of Rennes in 2009. Different sources were evaluated: the French pharmacovigilance database (including spontaneous reports and reports from a query in the database of the programme de médicalisation des systèmes d'information [PMSI]), records of patients seen in allergo-anesthesia (source considered as comprehensive as possible) and a query in the data warehouse. Analysis of allergo-anesthesia records detected all cases identified by other methods, as well as two other cases (nine cases in total). The query in the data warehouse enabled detection of seven cases out of the nine. Querying full-text reports and structured data extracted from the hospital information system improves the detection of anaphylaxis during anesthesia and facilitates access to data. © 2015 Société Française de Pharmacologie et de Thérapeutique.

  4. Selection of Structures with Grid Optimization, in Multiagent Data Warehouse

    Science.gov (United States)

    Gorawski, Marcin; Bańkowski, Sławomir; Gorawski, Michał

    The query optimization problem in data base and data warehouse management systems is quite similar. Changes to Joins sequences, projections and selections, usage of indexes, and aggregations are all decided during the analysis of an execution schedule. The main goal of these changes is to decrease the query response time. The optimization operation is often dedicated to a single node. This paper proposes optimization to grid or cluster data warehouses / databases. Tests were conducted in a multi-agent environment, and the optimization focused not only on a single node but on the whole system as well. A new idea is proposed here with multi-criteria optimization that is based on user-given parameters. Depending on query time, result admissible errors, and the level of system usage, task results were obtained along with grid optimization.

  5. Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it

    Directory of Open Access Journals (Sweden)

    Swainston Neil

    2006-12-01

    Full Text Available Abstract Background The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. Results This paper proposes a model-driven approach for the partial generation of user interfaces for searching and browsing bioinformatics data repositories. Inspired by the Model Driven Architecture (MDA of the Object Management Group (OMG, we have developed a system that generates interfaces designed for use with bioinformatics resources. This approach helps laboratory domain experts decrease the amount of time they have to spend dealing with the repetitive aspects of user interface development. As a result, the amount of time they can spend on gathering requirements and helping develop specialised features increases. The resulting system is known as Pierre, and has been validated through its application to use cases in the life sciences, including the PEDRoDB proteomics database and the e-Fungi data warehouse. Conclusion MDAs focus on generating software from models that describe aspects of service capabilities, and can be applied to support rapid development of repository

  6. ¿Why Data warehouse & Business Intelligence at Universidad Simon Bolivar?

    Directory of Open Access Journals (Sweden)

    Kamagate Azoumana

    2013-01-01

    Full Text Available Abstract The data warehouse is supposed to provide storage, functionality and responsiveness to queries beyond the capabilities of today’s transaction databases. Also Data warehouse is built to improve the data access performance of databases.   Resumen Los almacenes de datos se supone que proporcionan almacenamiento, funcionalidad y capacidad de repuesta a las consultas y análisis más eficiente que las bases de datos transaccionales. También el almacén de datos se construiye para mejorar el rendimiento de acceso a los datos.

  7. Teaching bioinformatics to engineers.

    Science.gov (United States)

    Mihalas, George I; Tudor, Anca; Paralescu, Sorin; Andor, Minodora; Stoicu-Tivadar, Lacramioara

    2014-01-01

    The paper refers to our methodology and experience in establishing the content of the course in bioinformatics introduced to the school of "Information Systems in Healthcare" (SIIS), master level. The syllabi of both lectures and laboratory works are presented and discussed.

  8. Optimizing healthcare research data warehouse design through past COSTAR query analysis.

    Science.gov (United States)

    Murphy, S N; Morgan, M M; Barnett, G O; Chueh, H C

    1999-01-01

    Over the past two years we have reviewed and implemented the specifications for a large relational database (a data warehouse) to find research cohorts from data similar to that contained within the clinical COSTAR database at the Massachusetts General Hospital. A review of 16 years of COSTAR research queries was conducted to determine the most common search strategies. These search strategies are relevant to the general research community, because they use the Medical Query Language (MQL) developed for the COSTAR M database which is extremely flexible (much more so than SQL) and allows searches by coded fields, text reports, and laboratory values in a completely ad hoc fashion. By reviewing these search strategies, we were able to obtain user specifications for a research oriented healthcare data warehouse that could support 90% of the queries. The data warehouse was implemented in a relational database using the star schema, allowing for highly optimized analytical processing. This allowed queries that performed slowly in the M database to be performed very rapidly in the relational database. It also allowed the data warehouse to scale effectively.

  9. 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

  10. Análisis de rendimiento académico estudiantil usando data warehouse y redes neuronales Analysis of students' academic performance using data warehouse and neural networks

    Directory of Open Access Journals (Sweden)

    Carolina Zambrano Matamala

    2011-12-01

    Full Text Available Cada día las organizaciones tienen más información porque sus sistemas producen una gran cantidad de operaciones diarias que se almacenan en bases de datos transaccionales. Con el fin de analizar esta información histórica, una alternativa interesante es implementar un Data Warehouse. Por otro lado, los Data Warehouse no son capaces de realizar un análisis predictivo por sí mismos, pero las técnicas de inteligencia de máquinas se pueden utilizar para clasificar, agrupar y predecir en base a información histórica con el fin de mejorar la calidad del análisis. En este trabajo se describe una arquitectura de Data Warehouse con el fin de realizar un análisis del desempeño académico de los estudiantes. El Data Warehouse es utilizado como entrada de una arquitectura de red neuronal con tal de analizar la información histórica y de tendencia en el tiempo. Los resultados muestran la viabilidad de utilizar un Data Warehouse para el análisis de rendimiento académico y la posibilidad de predecir el número de asignaturas aprobadas por los estudiantes usando solamente su propia información histórica.Every day organizations have more information because their systems produce a large amount of daily operations which are stored in transactional databases. In order to analyze this historical information, an interesting alternative is to implement a Data Warehouse. In the other hand, Data Warehouses are not able to perform predictive analysis for themselves, but machine learning techniques can be used to classify, grouping and predict historical information in order to improve the quality of analysis. This paper depicts architecture of a Data Warehouse useful to perform an analysis of students' academic performance. The Data Warehouse is used as input of a Neural Network in order to analyze historical information and forecast. The results show the viability of using Data Warehouse for academic performance analysis and the feasibility of

  11. Data warehouse for assessing animal health, welfare, risk management and -communication.

    Science.gov (United States)

    Nielsen, Annette Cleveland

    2011-01-01

    The objective of this paper is to give an overview of existing databases in Denmark and describe some of the most important of these in relation to establishment of the Danish Veterinary and Food Administrations' veterinary data warehouse. The purpose of the data warehouse and possible use of the data are described. Finally, sharing of data and validity of data is discussed. There are databases in other countries describing animal husbandry and veterinary antimicrobial consumption, but Denmark will be the first country relating all data concerning animal husbandry, -health and -welfare in Danish production animals to each other in a data warehouse. Moreover, creating access to these data for researchers and authorities will hopefully result in easier and more substantial risk based control, risk management and risk communication by the authorities and access to data for researchers for epidemiological studies in animal health and welfare.

  12. Information Architecture: The Data Warehouse Foundation.

    Science.gov (United States)

    Thomas, Charles R.

    1997-01-01

    Colleges and universities are initiating data warehouse projects to provide integrated information for planning and reporting purposes. A survey of 40 institutions with active data warehouse projects reveals the kinds of tools, contents, data cycles, and access currently used. Essential elements of an integrated information architecture are…

  13. Enhancing Warehouse Performance by Efficient Order Picking

    NARCIS (Netherlands)

    M. Yu (Mengfei)

    2008-01-01

    textabstractThis thesis studies order picking in warehouses. Order picking, the process of retrieval products from their storage locations to fill customer orders, is regarded as the most critical operation in a warehouse. Using stochastic modelling, we develop a model to estimate order picking

  14. Layout and Routing Methods for Warehouses

    NARCIS (Netherlands)

    K.J. Roodbergen (Kees-Jan)

    2001-01-01

    textabstractLayout and Routing Methods for Warehouses discusses aspects of order picking in warehouses. Order picking is the process by which products are retrieved from storage to meet customer demand. Various new routing methods are introduced to determine efficient sequences in which products

  15. AUTOMATIC IDENTIFICATION OF ITEMS IN WAREHOUSE MANAGEMENT

    OpenAIRE

    Vladimír Modrák; Peter Knuth

    2010-01-01

    Automatic identification of items saves time and is beneficial in various areas, including warehouse management. Identification can be done by many technologies, but RFID technology seems to be one of the smartest solutions. This article deals with testing and possible use of RFID technology in warehouse management. All results and measurement outcomes are documented in form of graphs followed by comprehensive analysis.

  16. Integrating Data Warehouses with Web Data

    DEFF Research Database (Denmark)

    Perez, Juan Manuel; Berlanga, Rafael; Aramburu, Maria Jose

    This paper surveys the most relevant research on combining Data Warehouse (DW) and Web data. It studies the XML technologies that are currently being used to integrate, store, query and retrieve web data, and their application to data warehouses. The paper addresses the problem of integrating het...

  17. Data Warehouse on the Web for Accelerator Fabrication And Maintenance

    International Nuclear Information System (INIS)

    Chan, A.; Crane, G.; Macgregor, I.; Meyer, S.

    2011-01-01

    A data warehouse grew out of the needs for a view of accelerator information from a lab-wide or project-wide standpoint (often needing off-site data access for the multi-lab PEP-II collaborators). A World Wide Web interface is used to link legacy database systems of the various labs and departments related to the PEP-II Accelerator. In this paper, we describe how links are made via the 'Formal Device Name' field(s) in the disparate databases. We also describe the functionality of a data warehouse in an accelerator environment. One can pick devices from the PEP-II Component List and find the actual components filling the functional slots, any calibration measurements, fabrication history, associated cables and modules, and operational maintenance records for the components. Information on inventory, drawings, publications, and purchasing history are also part of the PEP-II Database. A strategy of relying on a small team, and of linking existing databases rather than rebuilding systems is outlined.

  18. RFID system in warehouse management

    OpenAIRE

    Stipančič, Vedran

    2014-01-01

    The goal of the thesis was to create an RFID system that enables traceability of products, tagged with RFID stickers or tags and overview of data on desktop or mobile devices. In the implementation of the RFID system, two applications were developed, called RFID Portal and SCM Portal. RFID Portal is a desktop application that operates an RFID door, which detects products, that arrive at a warehouse and leave it and temperatures in which they were kept. All the collected data is sent to the we...

  19. PERANCANGAN DATA WAREHOUSE UNTUK MENDUKUNG PERENCANAAN PEMASARAN PERGURUAN TINGGI

    Directory of Open Access Journals (Sweden)

    agung prasetyo

    2017-02-01

    Full Text Available Salah satu indikasi perguruan tinggi yang besar adalah dilihat dari jumlah mahasiswa di perguruan tinggi tersebut. Karenanya, mahasiswa baru merupakan salah satu sumber daya yang menentukan berjalannya sebuah perguruan tinggi. Setiap tahunnya STMIK AMIKOM Purwokerto selalu melakukan penerimaan calon mahasiswa. Data mahasiswa baru tersebut sangat berguna bagi bagian pemasaran sebagai informasi untuk evaluasi kegiatan pemasaran berikutnya. Dengan dibangunnya data warehouse dan aplikasi OLAP dengan menggunakan aplikasi Pentaho Data Integration/Kettle sebagai perangkat ETL dan Pentaho Workbench yang merupakan Online Analytical Processing (OLAP sebagai pengolah database, manajemen di STMIK AMIKOM Purwokerto bisa mengambil beberapa informasi misalnya; banyak jumlah pendaftar per-periode/gelombang, per/asal sekolahnya, per/asal sumber informasi yang diperoleh calon mahasiswa baru, serta tren minat terhadap jurusan yang dipilih oleh calon mahasiswa baru. Data warehouse mampu menganalisis data transaksi, mampu memberikan laporan yang dinamis dan mampu memberikan informasi dalam berbagai dimensi tentang penerimaan mahasiswa baru di STMIK AMIKOM Purwokerto.Kata Kunci: Data Warehouse, OLAP, Pentaho, Penerimaan Calon Mahasiswa.

  20. 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

  1. 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.

  2. 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.

  3. Study and application of data mining and data warehouse in CIMS

    Science.gov (United States)

    Zhou, Lijuan; Liu, Chi; Liu, Daxin

    2003-03-01

    The interest in analyzing data has grown tremendously in recent years. To analyze data, a multitude of technologies is need, namely technologies from the fields of Data Warehouse, Data Mining, On-line Analytical Processing (OLAP). This paper gives a new architecture of data warehouse in CIMS according to CRGC-CIMS application engineering. The data source of this architecture comes from database of CRGC-CIMS system. The data is put in global data set by extracting, filtrating and integrating, and then the data is translated to data warehouse according information request. We have addressed two advantages of the new model in CRGC-CIMS application. In addition, a Data Warehouse contains lots of materialized views over the data provided by the distributed heterogeneous databases for the purpose of efficiently implementing decision-support, OLAP queries or data mining. It is important to select the right view to materialize that answer a given set of queries. In this paper, we also have designed algorithms for selecting a set of views to be materialized in a data warehouse in order to answer the most queries under the constraint of given space. First, we give a cost model for selecting materialized views. Then we give the algorithms that adopt gradually recursive method from bottom to top. We give description and realization of algorithms. Finally, we discuss the advantage and shortcoming of our approach and future work.

  4. Bioinformatic landscapes for plant transcription factor system research.

    Science.gov (United States)

    Wang, Yijun; Lu, Wenjie; Deng, Dexiang

    2016-02-01

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

  5. Pay-as-you-go data integration for bio-informatics

    NARCIS (Netherlands)

    Wanders, B.

    2012-01-01

    Scientific research in bio-informatics is often data-driven and supported by numerous biological databases. A biological database contains factual information collected from scientific experiments and computational analyses about areas including genomics, proteomics, metabolomics, microarray gene

  6. 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.

  7. Optimal time policy for deteriorating items of two-warehouse ...

    Indian Academy of Sciences (India)

    We consider the problem of a two-warehouse inventory system under the effect of stock dependent demand. There are two warehouses to store the goods in which the first is rented warehouse and the second is own warehouse that deteriorates with two different rates. The aim of this study is to determine the optimal order ...

  8. 19 CFR 19.13 - Requirements for establishment of warehouse.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Requirements for establishment of warehouse. 19.13...; DEPARTMENT OF THE TREASURY CUSTOMS WAREHOUSES, CONTAINER STATIONS AND CONTROL OF MERCHANDISE THEREIN Manufacturing Warehouses § 19.13 Requirements for establishment of warehouse. (a) Buildings or parts of...

  9. 27 CFR 28.285 - Receipt in manufacturing bonded warehouse.

    Science.gov (United States)

    2010-04-01

    ... bonded warehouse. 28.285 Section 28.285 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX... Export Receipt in Manufacturing Bonded Warehouse § 28.285 Receipt in manufacturing bonded warehouse. On... amended by T.D. TTB-8, 69 FR 3834, Jan. 27, 2004] Receipt in Customs Bonded Warehouse ...

  10. 19 CFR 19.17 - Application to establish warehouse; bond.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Application to establish warehouse; bond. 19.17...; DEPARTMENT OF THE TREASURY CUSTOMS WAREHOUSES, CONTAINER STATIONS AND CONTROL OF MERCHANDISE THEREIN Smelting and Refining Warehouses § 19.17 Application to establish warehouse; bond. (a) Application. Application...

  11. 19 CFR 144.27 - Withdrawal from warehouse by transferee.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Withdrawal from warehouse by transferee. 144.27...; DEPARTMENT OF THE TREASURY (CONTINUED) WAREHOUSE AND REWAREHOUSE ENTRIES AND WITHDRAWALS Transfer of Right To Withdraw Merchandise from Warehouse § 144.27 Withdrawal from warehouse by transferee. At any time within...

  12. 27 CFR 24.108 - Bonded wine warehouse application.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Bonded wine warehouse... wine warehouse application. A warehouse company or other person desiring to establish a bonded wine warehouse on bonded wine premises for storing wine or allied products for credit purposes shall file an...

  13. 27 CFR 44.111 - Change in export warehouse premises.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2010-04-01 2010-04-01 false Change in export warehouse... Qualification of Export Warehouse Proprietors Changes in Location and Premises § 44.111 Change in export warehouse premises. Where an export warehouse is to be changed to an extent which will make inaccurate the...

  14. 27 CFR 26.45 - Warehouse receipts covering distilled spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Warehouse receipts... Recordkeeping § 26.45 Warehouse receipts covering distilled spirits. The sale of warehouse receipts for... distilled spirits into the United States from Puerto Rico who sells, or offers for sale, warehouse receipts...

  15. 19 CFR 144.34 - Transfer to another warehouse.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Transfer to another warehouse. 144.34 Section 144... THE TREASURY (CONTINUED) WAREHOUSE AND REWAREHOUSE ENTRIES AND WITHDRAWALS Withdrawals from Warehouse § 144.34 Transfer to another warehouse. (a) At the same port. With the concurrence of the proprietors of...

  16. 19 CFR 144.14 - Removal to warehouse.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Removal to warehouse. 144.14 Section 144.14... TREASURY (CONTINUED) WAREHOUSE AND REWAREHOUSE ENTRIES AND WITHDRAWALS Requirements and Procedures for Warehouse Entry § 144.14 Removal to warehouse. When the entry summary, Customs Form 7501, and the bond on...

  17. [Establishment of data warehouse of needling and moxibustion literature based on data mining].

    Science.gov (United States)

    Wang, Jian-Ling; Li, Ren-Ling; Jia, Chun-Sheng

    2012-02-01

    In order to explore the efficacy specificity and valuable rules of clinical application of needling and moxibustion methods in a large quantity of information from literature, a data warehouse needs being established. On the basis of the original databases of red-hot needle therapy and hydro-acupuncture therapy, and the newly-established databases of acupoint catgut embedding therapy, acupoint application therapy, etc., and in accordance with the characteristics of different types of needling-moxibustion literature information, databases on different subjects were established first. These subject databases constitute a general "literature data warehouse on needling moxibustion methods" composing of multi-subjects and multiple dimensions so as to discover useful regularities about clinical treatment and trials collected in the literature by using data mining techniques. In the present paper, the authors introduce the design of the data warehouse, determination of subjects, establishment of subject relations, application of the administration platform, and application of data. This data warehouse will provide a standard data representation mode, enlarge data attributes and create extensive data links among literature information in the network, and may bring us with considerable convenience and profits in clinical application decision making and scientific research about needling-moxibustion techniques.

  18. Warehouse location and freight attraction in the greater El Paso region.

    Science.gov (United States)

    2013-12-01

    This project analyzes the current and future warehouse and distribution center locations along the El Paso-Juarez regions in the U.S.-Mexico border. This research seeks has developed a comprehensive database to aid in decision support process for ide...

  19. Event-Entity-Relationship Modeling in Data Warehouse Environments

    DEFF Research Database (Denmark)

    Bækgaard, Lars

    We use the event-entity-relationship model (EVER) to illustrate the use of entity-based modeling languages for conceptual schema design in data warehouse environments. EVER is a general-purpose information modeling language that supports the specification of both general schema structures and multi......-dimensional schemes that are customized to serve specific information needs. EVER is based on an event concept that is very well suited for multi-dimensional modeling because measurement data often represent events in multi-dimensional databases...

  20. Efficient data management tools for the heterogeneous big data warehouse

    Science.gov (United States)

    Alekseev, A. A.; Osipova, V. V.; Ivanov, M. A.; Klimentov, A.; Grigorieva, N. V.; Nalamwar, H. S.

    2016-09-01

    The traditional RDBMS has been consistent for the normalized data structures. RDBMS served well for decades, but the technology is not optimal for data processing and analysis in data intensive fields like social networks, oil-gas industry, experiments at the Large Hadron Collider, etc. Several challenges have been raised recently on the scalability of data warehouse like workload against the transactional schema, in particular for the analysis of archived data or the aggregation of data for summary and accounting purposes. The paper evaluates new database technologies like HBase, Cassandra, and MongoDB commonly referred as NoSQL databases for handling messy, varied and large amount of data. The evaluation depends upon the performance, throughput and scalability of the above technologies for several scientific and industrial use-cases. This paper outlines the technologies and architectures needed for processing Big Data, as well as the description of the back-end application that implements data migration from RDBMS to NoSQL data warehouse, NoSQL database organization and how it could be useful for further data analytics.

  1. Web-enabled Data Warehouse and Data Webhouse

    Directory of Open Access Journals (Sweden)

    Cerasela PIRVU

    2008-01-01

    Full Text Available In this paper, our objectives are to understanding what data warehouse means examine the reasons for doing so, appreciate the implications of the convergence of Web technologies and those of the data warehouse and examine the steps for building a Web-enabled data warehouse. The web revolution has propelled the data warehouse out onto the main stage, because in many situations the data warehouse must be the engine that controls or analysis the web experience. In order to step up to this new responsibility, the data warehouse must adjust. The nature of the data warehouse needs to be somewhat different. As a result, our data warehouses are becoming data webhouses. The data warehouse is becoming the infrastructure that supports customer relationship management (CRM. And the data warehouse is being asked to make the customer clickstream available for analysis. This rebirth of data warehousing architecture is called the data webhouse.

  2. Evaluating a healthcare data warehouse for cancer diseases

    OpenAIRE

    Sheta, Dr. Osama E.; Eldeen, Ahmed Nour

    2013-01-01

    This paper presents the evaluation of the architecture of healthcare data warehouse specific to cancer diseases. This data warehouse containing relevant cancer medical information and patient data. The data warehouse provides the source for all current and historical health data to help executive manager and doctors to improve the decision making process for cancer patients. The evaluation model based on Bill Inmon's definition of data warehouse is proposed to evaluate the Cancer data warehouse.

  3. Subcritical calculation of the nuclear material warehouse

    International Nuclear Information System (INIS)

    Garcia M, T.; Mazon R, R.

    2009-01-01

    In this work the subcritical calculation of the nuclear material warehouse of the Reactor TRIGA Mark III labyrinth in the Mexico Nuclear Center is presented. During the adaptation of the nuclear warehouse (vault I), the fuel was temporarily changed to the warehouse (vault II) and it was also carried out the subcritical calculation for this temporary arrangement. The code used for the calculation of the effective multiplication factor, it was the Monte Carlo N-Particle Extended code known as MCNPX, developed by the National Laboratory of Los Alamos, for the particles transport. (Author)

  4. Building a Data Warehouse step by step

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Data warehouses have been developed to answer the increasing demands of quality information required by the top managers and economic analysts of organizations. Their importance in now a day business area is unanimous recognized, being the foundation for developing business intelligence systems. Data warehouses offer support for decision-making process, allowing complex analyses which cannot be properly achieved from operational systems. This paper presents the ways in which a data warehouse may be developed and the stages of building it.

  5. Revolutionary Database Technology for Data Intensive Research

    NARCIS (Netherlands)

    Kersten, M.; Manegold, S.

    2012-01-01

    The ability to explore huge digital resources assembled in data warehouses, databases and files, at unprecedented speed, is becoming the driver of progress in science. However, existing database management systems (DBMS) are far from capable of meeting the scientists' requirements. The Database

  6. INNOVATIVE DEVELOPMENT OF WAREHOUSE TECHNOLOGY

    Directory of Open Access Journals (Sweden)

    Judit OLÁH

    2017-12-01

    Full Text Available The smooth operation of stocking and the warehouse play a very important role in all manufacturing companies; therefore ongoing monitoring and application of new techniques is essential to increase efficiency. The aim of our research is twofold: the utilization of the pallet shuttle racking system, and the introduction of a development opportunity by the merging of storage and order picking operations in the pallet shuttle system. It can be concluded that it is beneficial for the company to purchase two mobile cars in order to increase the utilization of the pallet shuttle racking system from 60% to 72% and that of the storage from 74% to 76%. We established that after the merging of the storage and order picking activities within the pallet shuttle system, the forklift driver can also complete the selection activities immediately after storage. By merging the two operations and saving time the number of forklift drivers can be reduced from 4 to 3 per shift.

  7. Bioinformatics Approaches for Human Gut Microbiome Research

    Directory of Open Access Journals (Sweden)

    Zhijun Zheng

    2016-07-01

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

  8. Perancangan Model Data Warehouse dan Perangkat Analitik untuk Memaksimalkan Proses Pemasaran Hotel: Studi Kasus pada Hotel Abc

    Directory of Open Access Journals (Sweden)

    Eka Miranda

    2013-06-01

    Full Text Available The increasing competition in hotel business forces every hotel to be equiped with analysis tools that can maximize its marketing performance. This paper discusses the development of a data warehouse model and analytic tools to enhance the company's competitive advantage through the utilization of a variety of data, information and knowledge held by the company as a raw material in the decision making process. A study is done at ABC Hotel which uses a database to save the transactional record. However, the database cannot be directly used to support analysis and decision making process. Based on this issue, the company needs a data warehouse model and analytic tools that can be used to store large amounts of data and also potentially to gain a new perspective of data distribution which allows to provide reporting and answers of ad hoc users questions and assist managers in making decisions. Further data warehouse model and analytic tools can be used to help manager to formulate planning and marketing strategies. Data are collected through interviews and literature study, followed by data analysis to analyze business processes, to identify the problems and the information to support analysis process. Furthermore, data warehouse is designed using analysis of records related to the activities in hotel's marketing area and data warehouse model. The result of this paper is data warehouse model and analytic tools to analyze the external and transactional data and to support decision making process in marketing area.

  9. System and method for integrating and accessing multiple data sources within a data warehouse architecture

    Science.gov (United States)

    Musick, Charles R [Castro Valley, CA; Critchlow, Terence [Livermore, CA; Ganesh, Madhaven [San Jose, CA; Slezak, Tom [Livermore, CA; Fidelis, Krzysztof [Brentwood, CA

    2006-12-19

    A system and method is disclosed for integrating and accessing multiple data sources within a data warehouse architecture. The metadata formed by the present method provide a way to declaratively present domain specific knowledge, obtained by analyzing data sources, in a consistent and useable way. Four types of information are represented by the metadata: abstract concepts, databases, transformations and mappings. A mediator generator automatically generates data management computer code based on the metadata. The resulting code defines a translation library and a mediator class. The translation library provides a data representation for domain specific knowledge represented in a data warehouse, including "get" and "set" methods for attributes that call transformation methods and derive a value of an attribute if it is missing. The mediator class defines methods that take "distinguished" high-level objects as input and traverse their data structures and enter information into the data warehouse.

  10. Protecting privacy in a clinical data warehouse.

    Science.gov (United States)

    Kong, Guilan; Xiao, Zhichun

    2015-06-01

    Peking University has several prestigious teaching hospitals in China. To make secondary use of massive medical data for research purposes, construction of a clinical data warehouse is imperative in Peking University. However, a big concern for clinical data warehouse construction is how to protect patient privacy. In this project, we propose to use a combination of symmetric block ciphers, asymmetric ciphers, and cryptographic hashing algorithms to protect patient privacy information. The novelty of our privacy protection approach lies in message-level data encryption, the key caching system, and the cryptographic key management system. The proposed privacy protection approach is scalable to clinical data warehouse construction with any size of medical data. With the composite privacy protection approach, the clinical data warehouse can be secure enough to keep the confidential data from leaking to the outside world. © The Author(s) 2014.

  11. Data Warehouse Architecture for Army Installations

    National Research Council Canada - National Science Library

    Reddy, Prameela

    1999-01-01

    .... A data warehouse is a single store of information to answer complex queries from management using cross-functional data to perform advanced data analysis methods and to compare with historical data...

  12. Konsolidasi Data Warehouse untuk Aplikasi Business Intelligence

    Directory of Open Access Journals (Sweden)

    Rudy Rudy

    2012-12-01

    Full Text Available As the business competition is getting strong, corporate leaders need complete data that as a basis for determining future business strategies. Similarly with management of company "A", a pharmaceutical company which has three distribution companies. Each distribution company already has a data warehouse to generate reports for each of them. For business operational and corporate strategies, chairman PT "A" requires an integrated report, so analysis of data owned by the three distribution companies can be done in a full reportto answer the problems faced by the managemet. Thus, data warehouse consilidation can be used as a solution for company "A". Methodology starts with analysis of information needs to be displayed on the application ofbusiness intelligence, data warehouse consolidation, ETL (extract, transform and load, data warehousing, OLAP and Dashboard. Using data warehouse consolidation, information access by management of company "A" can be done in a single presentation, which can display data comparison between the three distribution companies.

  13. Designing a Data Warehouse for Cyber Crimes

    Directory of Open Access Journals (Sweden)

    Il-Yeol Song

    2006-09-01

    Full Text Available One of the greatest challenges facing modern society is the rising tide of cyber crimes. These crimes, since they rarely fit the model of conventional crimes, are difficult to investigate, hard to analyze, and difficult to prosecute. Collecting data in a unified framework is a mandatory step that will assist the investigator in sorting through the mountains of data. In this paper, we explore designing a dimensional model for a data warehouse that can be used in analyzing cyber crime data. We also present some interesting queries and the types of cyber crime analyses that can be performed based on the data warehouse. We discuss several ways of utilizing the data warehouse using OLAP and data mining technologies. We finally discuss legal issues and data population issues for the data warehouse.

  14. 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.

  15. The Implementation of Data Warehouse and OLAP for Rehabilitation Outcome Evaluation: ReDWinE System

    Science.gov (United States)

    Guo, Fei-Ran; Parmanto, Bambang; Irrgang, James J.; Wang, Jiunjie; Fang, Huaijin

    2000-01-01

    We created a data warehouse and OLAP system on the web for outcome evaluation of rehabilitation services. Thirteen outcome indicators were use in this research. Efficiency of therapists and clinics, expected utility of treatments and graphic patterns were generated for data exploration, data mining and decision support. Users can retrieve plenty of graphs and statistical tables without knowing database structure or attributes. Our experiences showed that multi-dimensional database and OLAP could serve as a decision support system.

  16. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

    International Nuclear Information System (INIS)

    Taylor, Ronald C.

    2010-01-01

    Bioinformatics researchers are increasingly confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.

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

    Science.gov (United States)

    Li, Lang

    2015-10-01

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

  18. 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...

  19. Bioinformatics meets parasitology.

    Science.gov (United States)

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

    2012-05-01

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

  20. 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…

  1. 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…

  2. Modeling of regional warehouse network generation

    Directory of Open Access Journals (Sweden)

    Popov Pavel Vladimirovich

    2016-08-01

    Full Text Available One of the factors that has a significant impact on the socio-economic development of the Russian Federation’s regions is the logistics infrastructure. It provides integrated transportation and distribution service of material flows. One of the main elements of logistics infrastructure is a storage infrastructure, which includes distribution center, distribution-and-sortout and sortout warehouses. It is the most expedient to place distribution center in the vicinity of the regional center. One of the tasks of the distribution network creation within the regions of the Russian Federation is to determine the location, capacity and number of stores. When determining regional network location of general purpose warehouses methodological approaches to solving the problems of location of production and non-production can be used which depend on various economic factors. The mathematical models for solving relevant problems are the deployment models. However, the existing models focus on the dimensionless power storage. The purpose of the given work is to develop a model to determine the optimal location of general-purpose warehouses on the Russian Federation area. At the first stage of the work, the authors assess the main economic indicators influencing the choice of the location of general purpose warehouses. An algorithm for solving the first stage, based on ABC, discriminant and cluster analysis were proposed by the authors in earlier papers. At the second stage the specific locations of general purpose warehouses and their power is chosen to provide the cost minimization for the construction and subsequent maintenance of warehouses and transportation heterogeneous products. In order to solve this problem the authors developed a mathematical model that takes into account the possibility of delivery in heterogeneous goods from suppliers and manufacturers in the distribution and storage sorting with specified set of capacities. The model allows

  3. 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.

  4. Bioinformatics on the cloud computing platform Azure.

    Directory of Open Access Journals (Sweden)

    Hugh P Shanahan

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

  5. 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.

  6. PERANCANGAN SISTEM METADATA UNTUK DATA WAREHOUSE DENGAN STUDI KASUS REVENUE TRACKING PADA PT. TELKOM DIVRE V JAWA TIMUR

    Directory of Open Access Journals (Sweden)

    Yudhi Purwananto

    2004-07-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Data warehouse merupakan media penyimpanan data dalam perusahaan yang diambil dari berbagai sistem dan dapat digunakan untuk berbagai keperluan seperti analisis dan pelaporan. Di PT Telkom Divre V Jawa Timur telah dibangun sebuah data warehouse yang disebut dengan Regional Database. Di Regional Database memerlukan sebuah komponen penting dalam data warehouse yaitu metadata. Definisi metadata secara sederhana adalah "data tentang data". Dalam penelitian ini dirancang sistem metadata dengan studi kasus Revenue Tracking sebagai komponen analisis dan pelaporan pada Regional Database. Metadata sangat perlu digunakan dalam pengelolaan dan memberikan informasi tentang data warehouse. Proses - proses di dalam data warehouse serta komponen - komponen yang berkaitan dengan data warehouse harus saling terintegrasi untuk mewujudkan karakteristik data warehouse yang subject-oriented, integrated, time-variant, dan non-volatile. Karena itu metadata juga harus memiliki kemampuan mempertukarkan informasi (exchange antar komponen dalam data warehouse tersebut. Web service digunakan sebagai mekanisme pertukaran ini. Web service menggunakan teknologi XML dan protokol HTTP dalam berkomunikasi. Dengan web service, setiap komponen

  7. Impact of Omni channel in a central warehouse: An analysis of warehouse activities for an electronic retailer

    OpenAIRE

    Boldt, Elin; Patel, Gita

    2015-01-01

    Purpose: The purpose of this study is to analyze the impact Omni channel has on the ware-house activities in a central warehouse for electronic retailers. In order to fulfill the purpose the following research questions are analyzed and answered; “What are the challenges in the warehouse activities in a central warehouse for an electronic retailer when Omni channel is utilized?” and “How can the challenges in the warehouse activities be managed in a central warehouse for an electronic retaile...

  8. Data warehouse based decision support system in nuclear power plants

    International Nuclear Information System (INIS)

    Nadinic, B.

    2004-01-01

    Safety is an important element in business decision making processes in nuclear power plants. Information about component reliability, structures and systems, data recorded during the nuclear power plant's operation and outage periods, as well as experiences from other power plants are located in different database systems throughout the power plant. It would be possible to create a decision support system which would collect data, transform it into a standardized form and store it in a single location in a format more suitable for analyses and knowledge discovery. This single location where the data would be stored would be a data warehouse. Such data warehouse based decision support system could help make decision making processes more efficient by providing more information about business processes and predicting possible consequences of different decisions. Two main functionalities in this decision support system would be an OLAP (On Line Analytical Processing) and a data mining system. An OLAP system would enable the users to perform fast, simple and efficient multidimensional analysis of existing data and identify trends. Data mining techniques and algorithms would help discover new, previously unknown information from the data as well as hidden dependencies between various parameters. Data mining would also enable analysts to create relevant prediction models that could predict behaviour of different systems during operation and inspection results during outages. The basic characteristics and theoretical foundations of such decision support system are described and the reasons for choosing a data warehouse as the underlying structure are explained. The article analyzes obvious business benefits of such system as well as potential uses of OLAP and data mining technologies. Possible implementation methodologies and problems that may arise, especially in the field of data integration, are discussed and analyzed.(author)

  9. Establishment of the Integrated Plant Data Warehouse

    International Nuclear Information System (INIS)

    Oota, Yoshimi; Yoshinaga, Toshiaki

    1999-01-01

    This paper presents 'The Establishment of the Integrated Plant Data Warehouse and Verification Tests on Inter-corporate Electronic Commerce based on the Data Warehouse (PDWH)', one of the 'Shared Infrastructure for the Electronic Commerce Consolidation Project', promoted by the Ministry of International Trade and Industry (MITI) through the Information-Technology Promotion Agency (IPA), Japan. A study group called Japan Plant EC (PlantEC) was organized to perform relevant activities. One of the main activities of plantEC involves the construction of the Integrated (including manufacturers, engineering companies, plant construction companies, and machinery and parts manufacturers, etc.) Data Warehouse which is an essential part of the infrastructure necessary for a system to share information on industrial life cycle ranging from planning/designing to operation/maintenance. Another activity is the utilization of this warehouse for the purpose of conducting verification tests to prove its usefulness. Through these verification tests, PlantEC will endeavor to establish a warehouse with standardized data which can be used for the infrastructure of EC in the process plant industry. (author)

  10. 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…

  11. 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...

  12. Tractor pulling on data warehouses

    NARCIS (Netherlands)

    Kersten, M.L.; Kemper, A.; Markl, V.; Nica, A.; Poess, M.; Sattler, K.

    2011-01-01

    Robustness of database systems under stress is hard to quantify, because there are many factors involved, most notably the user expectation to perform a job within certain bounds of the user requirements. Nevertheless, robustness of database system is very important to end users. In this paper we

  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. 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.

  15. European experience of signing contract storage in warehouse

    OpenAIRE

    Демчук, Антон Михайлович; Demchuk, Anton M.

    2015-01-01

    The article is devoted to the development of relations stored on the warehouse of origin from England to its development in Ukraine. This article analyzes the experience of warehousing in Europe and the legislative provision storage in Ukrainian law. We analyze the concluding a separate contract storage at the warehouse simultaneously with the transfer of warehouse receipts. The necessity of referring to the warehouse receipts securities. Analyzed the following types of ware...

  16. How to test bioinformatics software?

    Science.gov (United States)

    Kamali, Amir Hossein; Giannoulatou, Eleni; Chen, Tsong Yueh; Charleston, Michael A; McEwan, Alistair L; Ho, Joshua W K

    2015-09-01

    Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Bioinformatics programs developed for computational simulation and large-scale data analysis are widely used in almost all areas of biophysics. The appropriate choice of algorithms and correct implementation of these algorithms are critical for obtaining reliable computational results. Nonetheless, it is often very difficult to systematically test these programs as it is often hard to verify the correctness of the output, and to effectively generate failure-revealing test cases. Software testing is an important process of verification and validation of scientific software, but very few studies have directly dealt with the issues of bioinformatics software testing. In this work, we review important concepts and state-of-the-art methods in the field of software testing. We also discuss recent reports on adapting and implementing software testing methodologies in the bioinformatics field, with specific examples drawn from systems biology and genomic medicine.

  17. Harvesting Information from a Library Data Warehouse

    Directory of Open Access Journals (Sweden)

    Siew-Phek T. Su

    2017-09-01

    Full Text Available Data warehousing technology has been defined by John Ladley as "a set of methods, techniques, and tools that are leveraged together and used to produce a vehicle that delivers data to end users on an integrated platform." (1 This concept h s been applied increasingly by industries worldwide to develop data warehouses for decision support and knowledge discovery. In the academic sector, several universities have developed data warehouses containing the universities' financial, payroll, personnel, budget, and student data. (2 These data warehouses across all industries and academia have met with varying degrees of success. Data warehousing technology and its related issues have been widely discussed and published. (3 Little has been done, however, on the application of this cutting edge technology in the library environment using library data.

  18. 27 CFR 24.141 - Bonded wine warehouse.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Bonded wine warehouse. 24..., DEPARTMENT OF THE TREASURY LIQUORS WINE Establishment and Operations Permanent Discontinuance of Operations § 24.141 Bonded wine warehouse. Where all operations at a bonded wine warehouse are to be permanently...

  19. What Academia Can Gain from Building a Data Warehouse.

    Science.gov (United States)

    Wierschem, David; McMillen, Jeremy; McBroom, Randy

    2003-01-01

    Describes how, when used effectively, data warehouses can be a significant component of strategic decision making on campus. Discusses what a data warehouse is and what its informational contents may include, environmental drivers and obstacles, and strategies to justify developing a data warehouse for an academic institution. (EV)

  20. Optimization of the warehouse system in the selected production plant

    OpenAIRE

    KOVÁŘOVÁ, Zuzana

    2017-01-01

    The aim of the diploma thesis was optimization of the warehouse system according to suitability for use in assortment in a selected production company focusing on material and information flows, decay processes, warehouse technology, logistic costs and relevant logistics indicators. The partial objective was to determine the critical factors in terms of management and operation in the warehouse of the selected manufacturing enterprise.

  1. Using a TSP heuristic for routing order pickers in warehouses

    NARCIS (Netherlands)

    Theys, Christophe; Bräysy, Olli; Dullaert, Wout; Raa, Birger

    2010-01-01

    In this paper, we deal with the sequencing and routing problem of order pickers in conventional multi-parallel-aisle warehouse systems. For this NP-hard Steiner travelling salesman problem (TSP), exact algorithms only exist for warehouses with at most three cross aisles, while for other warehouse

  2. Nigerian Concept Of Bonded Warehouses And Dry Ports | Ndikom ...

    African Journals Online (AJOL)

    The bonded warehouse in Nigeria is a strategic expansion of ordinary warehouses that are usually developed in the ports and related cities, strictly meant for safe-keeping of cargoes for owners before final take-over by consignees after payment of some customs duties. A bonded warehouse and ICDs are seen as ...

  3. Contextual snowflake modelling for pattern warehouse logical design

    Indian Academy of Sciences (India)

    Pattern warehouse provides the infrastructure for knowledge representation and mining by allowing the patterns to be stored permanently. The goal of this paper is to discuss the pattern warehouse design and related quality issues. In the present work, we focus on conceptual and logical design of pattern warehouse, ...

  4. 29 CFR 779.113 - Warehouse and stock room employees.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Warehouse and stock room employees. 779.113 Section 779.113 Labor Regulations Relating to Labor (Continued) WAGE AND HOUR DIVISION, DEPARTMENT OF LABOR STATEMENTS....113 Warehouse and stock room employees. Warehouse and stock room employees of retail businesses who...

  5. 19 CFR 143.16 - Substitution of warehouse entry.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Substitution of warehouse entry. 143.16 Section 143.16 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT... warehouse entry. The importer may substitute an entry for warehouse at any time within 1 year from the date...

  6. Zero energy buildings in the logistics warehouse systems

    Science.gov (United States)

    Zajac, Pawel; Kwasniowski, Stanislaw

    2017-11-01

    The article discusses the evaluation of possible reductions of energy consumption in warehouse buildings and the analysis of construction and functioning of modern storage warehouses. For a warehouse the following are presented: operation evaluation measures and indexes, an energy balance, ideas for improvements in terms of energy conservation in particular functioning zones.

  7. 27 CFR 27.31 - Warehouse receipts covering distilled spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Warehouse receipts... BEER Dealer Registration and Recordkeeping § 27.31 Warehouse receipts covering distilled spirits. The sale of warehouse receipts for distilled spirits is equivalent to the sale of distilled spirits...

  8. 76 FR 28801 - Agency Information Collection Activities: Bonded Warehouse Regulations

    Science.gov (United States)

    2011-05-18

    ... Activities: Bonded Warehouse Regulations AGENCY: U.S. Customs and Border Protection, Department of Homeland... (OMB) for review and approval in accordance with the Paperwork Reduction Act: Bonded Warehouse.... Title: Bonded Warehouse Regulations. OMB Number: 1651-0041. Form Number: None. Abstract: Owners or...

  9. 76 FR 12364 - Agency Information Collection Activities: Bonded Warehouse Regulations

    Science.gov (United States)

    2011-03-07

    ... Activities: Bonded Warehouse Regulations AGENCY: U.S. Customs and Border Protection (CBP), Department of... requirement concerning the Bonded Warehouse Regulations. This request for comment is being made pursuant to...: Title: Bonded Warehouse Regulations. OMB Number: 1651-0041. Form Number: None. Abstract: Owners or...

  10. 27 CFR 31.47 - Warehouse receipts covering spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Warehouse receipts... Part Certain Organizations, Agencies, and Persons § 31.47 Warehouse receipts covering spirits. The sale of warehouse receipts for distilled spirits is equivalent to the sale of distilled spirits...

  11. 27 CFR 28.244 - Shipment to manufacturing bonded warehouse.

    Science.gov (United States)

    2010-04-01

    ... bonded warehouse. 28.244 Section 28.244 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX... Export Consignment § 28.244 Shipment to manufacturing bonded warehouse. Distilled spirits and wines withdrawn for shipment to a manufacturing bonded warehouse shall be consigned to the proprietor of such...

  12. 19 CFR 146.64 - Entry for warehouse.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Entry for warehouse. 146.64 Section 146.64 Customs... (CONTINUED) FOREIGN TRADE ZONES Transfer of Merchandise From a Zone § 146.64 Entry for warehouse. (a) Foreign... status may not be entered for warehouse from a zone. Merchandise in nonprivileged foreign status...

  13. Revolutionary Database Technology for Data Intensive Research

    NARCIS (Netherlands)

    M.L. Kersten (Martin); S. Manegold (Stefan)

    2012-01-01

    textabstractThe ability to explore huge digital resources assembled in data warehouses, databases and files, at unprecedented speed, is becoming the driver of progress in science. However, existing database management systems (DBMS) are far from capable of meeting the scientists’ requirements.

  14. Genome Exploitation and Bioinformatics Tools

    Science.gov (United States)

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

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

  15. IR and OLAP in XML document warehouses

    DEFF Research Database (Denmark)

    Perez, Juan Manuel; Pedersen, Torben Bach; Berlanga, Rafael

    2005-01-01

    In this paper we propose to combine IR and OLAP (On-Line Analytical Processing) technologies to exploit a warehouse of text-rich XML documents. In the system we plan to develop, a multidimensional implementation of a relevance modeling document model will be used for interactively querying...... the warehouse by allowing navigation in the structure of documents and in a concept hierarchy of query terms. The facts described in the relevant documents will be ranked and analyzed in a novel OLAP cube model able to represent and manage facts with relevance indexes....

  16. Application of XML in real-time data warehouse

    Science.gov (United States)

    Zhao, Yanhong; Wang, Beizhan; Liu, Lizhao; Ye, Su

    2009-07-01

    At present, XML is one of the most widely-used technologies of data-describing and data-exchanging, and the needs for real-time data make real-time data warehouse a popular area in the research of data warehouse. What effects can we have if we apply XML technology to the research of real-time data warehouse? XML technology solves many technologic problems which are impossible to be addressed in traditional real-time data warehouse, and realize the integration of OLAP (On-line Analytical Processing) and OLTP (Online transaction processing) environment. Then real-time data warehouse can truly be called "real time".

  17. Modelling of Data Warehouse on Food Distribution Center and Reserves in the Ministry of Agriculture

    Directory of Open Access Journals (Sweden)

    Edi Purnomo Putra

    2015-09-01

    Full Text Available The purpose of this study is to perform database’s planning that supports Prototype Modeling Data Warehouse in the Ministry of Agriculture, especially in the Distribution Center and Reserves in the field of distribution, reserve and price. With the prototype of Data Warehouse, the process of data analysis anddecision-making process by the top management will be easier and more accurate. Research’s method used was data collection and design method. Data warehouse’s design method was done by using Kimball’s nine stepsmethodology. Database design was done by using the ERD (Entity Relationship Diagram and activity diagram. The data used for the analysis was obtained from an interview with the head of Distribution, Reserve and Food Price. The results obtained through the analysis incorporated into the Data Warehouse Prototype have been designed to support decision-making. To conclude, Prototype Data Warehouse facilitates the analysis of data, the searching of history data and decision-making by the top management.

  18. Emerging strengths in Asia Pacific bioinformatics

    OpenAIRE

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

    2008-01-01

    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,...

  19. Automated Data Aggregation for Time-Series Analysis: Study Case on Anaesthesia Data Warehouse.

    Science.gov (United States)

    Lamer, Antoine; Jeanne, Mathieu; Ficheur, Grégoire; Marcilly, Romaric

    2016-01-01

    Data stored in operational databases are not reusable directly. Aggregation modules are necessary to facilitate secondary use. They decrease volume of data while increasing the number of available information. In this paper, we present four automated engines of aggregation, integrated into an anaesthesia data warehouse. Four instances of clinical questions illustrate the use of those engines for various improvements of quality of care: duration of procedure, drug administration, assessment of hypotension and its related treatment.

  20. MouseMine: a new data warehouse for MGI.

    Science.gov (United States)

    Motenko, H; Neuhauser, S B; O'Keefe, M; Richardson, J E

    2015-08-01

    MouseMine (www.mousemine.org) is a new data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Based on the InterMine software framework, MouseMine supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. Through MouseMine, users can access a significant portion of MGI data in new and useful ways. Importantly, MouseMine is also a member of a growing community of online data resources based on InterMine, including those established by other model organism databases. Adopting common interfaces and collaborating on data representation standards are critical to fostering cross-species data analysis. This paper presents a general introduction to MouseMine, presents examples of its use, and discusses the potential for further integration into the MGI interface.

  1. Information Support of Processes in Warehouse Logistics

    Directory of Open Access Journals (Sweden)

    Gordei Kirill

    2013-11-01

    Full Text Available In the conditions of globalization and the world economic communications, the role of information support of business processes increases in various branches and fields of activity. There is not an exception for the warehouse activity. Such information support is realized in warehouse logistic systems. In relation to territorial administratively education, the warehouse logistic system gets a format of difficult social and economic structure which controls the economic streams covering the intermediary, trade and transport organizations and the enterprises of other branches and spheres. Spatial movement of inventory items makes new demands to participants of merchandising. Warehousing (in the meaning – storage – is one of the operations entering into logistic activity, on the organization of a material stream, as a requirement. Therefore, warehousing as "management of spatial movement of stocks" – is justified. Warehousing, in such understanding, tries to get rid of the perception as to containing stocks – a business expensive. This aspiration finds reflection in the logistic systems working by the principle: "just in time", "economical production" and others. Therefore, the role of warehouses as places of storage is transformed to understanding of warehousing as an innovative logistic system.

  2. Temporal and Evolving Data Warehouse Design

    Directory of Open Access Journals (Sweden)

    Sidra Faisal

    2017-01-01

    Full Text Available The data model of the classical data warehouse (formally, dimensional model does not offer comprehensive support for temporal data management. The underlying reason is that it requires consideration of several temporal aspects, which involve various time stamps. Also, transactional systems, which serves as a data source for data warehouse, have the tendency to change themselves due to changing business requirements. The classical dimensional model is deficient in handling changes to transaction sources. This has led to the development of various schemes, including evolution of data and evolution of data model and versioning of dimensional model. These models have their own strengths and limitations, but none fully satisfies the above-stated broad range of aspects, making it difficult to compare the proposed schemes with one another. This paper analyses the schemes that satisfy such challenging aspects faced by a data warehouse and proposes taxonomy for characterizing the existing models to temporal data management in data warehouse. The paper also discusses some open challenges.

  3. IR and OLAP in XML document warehouses

    DEFF Research Database (Denmark)

    Perez, Juan Manuel; Pedersen, Torben Bach; Berlanga, Rafael

    2005-01-01

    In this paper we propose to combine IR and OLAP (On-Line Analytical Processing) technologies to exploit a warehouse of text-rich XML documents. In the system we plan to develop, a multidimensional implementation of a relevance modeling document model will be used for interactively querying...

  4. Models for warehouse management: Classification and examples

    NARCIS (Netherlands)

    van den Berg, J.P.; van den Berg, J.P.; Zijm, Willem H.M.

    1999-01-01

    In this paper we discuss warehousing systems and present a classification of warehouse management problems. We start with a typology and a brief description of several types of warehousing systems. Next, we present a hierarchy of decision problems encountered in setting up warehousing systems,

  5. Warehouse receipts functioning to reduce market risk

    Directory of Open Access Journals (Sweden)

    Jovičić Daliborka

    2014-01-01

    Full Text Available Cereal production underlies the market risk to a great extent due to its elastic demand. Prices of grain have cyclic movements and significant decline in the harvest periods as a result of insufficient supply and high demand. The very specificity of agricultural production leads to the fact that agricultures are forced to sell their products at unfavorable conditions in order to resume production. The Public Warehouses System allows the agriculturers, who were previously unable to use the bank loans to finance the continuation of their production, to efficiently acquire the necessary funds, by the support of the warehouse receipts which serve as collaterals. Based on the results obtained by applying statistical methods (variance and standard deviation, as a measure of market risk under the assumption that warehouse receipts' prices will approximately follow the overall consumer price index, it can be concluded that the warehouse receipts trade will have a significant impact on risk reduction in cereal production. Positive effects can be manifested through the stabilization of prices, reduction of cyclic movements in the production of basic grains and, in the final stage, on the country's food security.

  6. WAREHOUSE PERFORMANCE MEASUREMENT - A CASE STUDY

    Directory of Open Access Journals (Sweden)

    Crisan Emil

    2009-05-01

    Full Text Available Companies could gain cost advantage using their logistics area of the business. Warehouse management is a possible source of cost improvements from logistics that companies could use during this economic crisis. The goal of this article is to expose a few

  7. Computer modeling of commercial refrigerated warehouse facilities

    International Nuclear Information System (INIS)

    Nicoulin, C.V.; Jacobs, P.C.; Tory, S.

    1997-01-01

    The use of computer models to simulate the energy performance of large commercial refrigeration systems typically found in food processing facilities is an area of engineering practice that has seen little development to date. Current techniques employed in predicting energy consumption by such systems have focused on temperature bin methods of analysis. Existing simulation tools such as DOE2 are designed to model commercial buildings and grocery store refrigeration systems. The HVAC and Refrigeration system performance models in these simulations tools model equipment common to commercial buildings and groceries, and respond to energy-efficiency measures likely to be applied to these building types. The applicability of traditional building energy simulation tools to model refrigerated warehouse performance and analyze energy-saving options is limited. The paper will present the results of modeling work undertaken to evaluate energy savings resulting from incentives offered by a California utility to its Refrigerated Warehouse Program participants. The TRNSYS general-purpose transient simulation model was used to predict facility performance and estimate program savings. Custom TRNSYS components were developed to address modeling issues specific to refrigerated warehouse systems, including warehouse loading door infiltration calculations, an evaporator model, single-state and multi-stage compressor models, evaporative condenser models, and defrost energy requirements. The main focus of the paper will be on the modeling approach. The results from the computer simulations, along with overall program impact evaluation results, will also be presented

  8. Managing dual warehouses with an incentive policy for deteriorating items

    Science.gov (United States)

    Yu, Jonas C. P.; Wang, Kung-Jeng; Lin, Yu-Siang

    2016-02-01

    Distributors in a supply chain usually limit their own warehouse in finite capacity for cost reduction and excess stock is held in a rent warehouse. In this study, we examine inventory control for deteriorating items in a two-warehouse setting. Assuming that there is an incentive offered by a rent warehouse that allows the rental fee to decrease over time, the objective of this study is to maximise the joint profit of the manufacturer and the distributor. An optimisation procedure is developed to derive the optimal joint economic lot size policy. Several criteria are identified to select the most appropriate warehouse configuration and inventory policy on the basis of storage duration of materials in a rent warehouse. Sensitivity analysis is done to examine the results of model robustness. The proposed model enables a manufacturer with a channel distributor to coordinate the use of alternative warehouses, and to maximise the joint profit of the manufacturer and the distributor.

  9. 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.

  10. 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

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

    Directory of Open Access Journals (Sweden)

    Ashokkumar A. Patel

    2007-01-01

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

  12. Developing expertise in bioinformatics for biomedical research in Africa.

    Science.gov (United States)

    Karikari, Thomas K; Quansah, Emmanuel; Mohamed, Wael M Y

    2015-09-01

    Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases) that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.

  13. Developing expertise in bioinformatics for biomedical research in Africa

    Directory of Open Access Journals (Sweden)

    Thomas K. Karikari

    2015-09-01

    Full Text Available Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.

  14. Bioinformatic training needs at a health sciences campus.

    Science.gov (United States)

    Oliver, Jeffrey C

    2017-01-01

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

  15. A Million Cancer Genome Warehouse

    Science.gov (United States)

    2012-11-20

    retraction , versioning, etc. must be coordinated between the interpretation level and the lower levels. Finally, the database layer must contain reasonably...structural-biology group led by Geoffrey Chang of the Scripps Research Institute … to retract five papers published in Science, the Journal of...and 4 PCIe slots (from x16 to x4). In 2014 we could build 192 GB per board and 10 cores per processor. Two motherboards fit in a chassis , with three

  16. Handling Imprecision in Qualitative Data Warehouse: Urban Building Sites Annoyance Analysis Use Case

    Science.gov (United States)

    Amanzougarene, F.; Chachoua, M.; Zeitouni, K.

    2013-05-01

    Data warehouse means a decision support database allowing integration, organization, historisation, and management of data from heterogeneous sources, with the aim of exploiting them for decision-making. Data warehouses are essentially based on multidimensional model. This model organizes data into facts (subjects of analysis) and dimensions (axes of analysis). In classical data warehouses, facts are composed of numerical measures and dimensions which characterize it. Dimensions are organized into hierarchical levels of detail. Based on the navigation and aggregation mechanisms offered by OLAP (On-Line Analytical Processing) tools, facts can be analyzed according to the desired level of detail. In real world applications, facts are not always numerical, and can be of qualitative nature. In addition, sometimes a human expert or learned model such as a decision tree provides a qualitative evaluation of phenomenon based on its different parameters i.e. dimensions. Conventional data warehouses are thus not adapted to qualitative reasoning and have not the ability to deal with qualitative data. In previous work, we have proposed an original approach of qualitative data warehouse modeling, which permits integrating qualitative measures. Based on computing with words methodology, we have extended classical multidimensional data model to allow the aggregation and analysis of qualitative data in OLAP environment. We have implemented this model in a Spatial Decision Support System to help managers of public spaces to reduce annoyances and improve the quality of life of the citizens. In this paper, we will focus our study on the representation and management of imprecision in annoyance analysis process. The main objective of this process consists in determining the least harmful scenario of urban building sites, particularly in dense urban environments.

  17. 7 CFR 1427.1086 - Approval of warehouse, requests for reconsideration.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Approval of warehouse, requests for reconsideration... Standards for Approval of Warehouses for Cotton and Cotton Linters § 1427.1086 Approval of warehouse, requests for reconsideration. (a) CCC will approve a warehouse if it determines that the warehouse meets...

  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. 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...

  20. The Aspergillus Mine - publishing bioinformatics

    DEFF Research Database (Denmark)

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

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

  1. 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

  2. Computational intelligence techniques in bioinformatics.

    Science.gov (United States)

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

    2013-12-01

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

  3. Bioinformatics: searching the Net.

    Science.gov (United States)

    Kastin, S; Wexler, J

    1998-04-01

    During the past 30 years, there has been an explosion in the volume of published medical information. As this volume has increased, so has the need for efficient methods for searching the data. MEDLINE, the primary medical database, is currently limited to abstracts of the medical literature. MEDLINE searches use AND/OR/NOT logical searching for keywords that have been assigned to each article and for textwords included in article abstracts. Recently, the complete text of some scientific journals, including figures and tables, has become accessible electronically. Keyword and textword searches can provide an overwhelming number of results. Search engines that use phrase searching, or searches that limit the number of words between two finds, improve the precision of search engines. The development of the Internet as a vehicle for worldwide communication, and the emergence of the World Wide Web (WWW) as a common vehicle for communication have made instantaneous access to much of the entire body of medical information an exciting possibility. There is more than one way to search the WWW for information. At the present time, two broad strategies have emerged for cataloging the WWW: directories and search engines. These allow more efficient searching of the WWW. Directories catalog WWW information by creating categories and subcategories of information and then publishing pointers to information within the category listings. Directories are analogous to yellow pages of the phone book. Search engines make no attempt to categorize information. They automatically scour the WWW looking for words and then automatically create an index of those words. When a specific search engine is used, its index is searched for a particular word. Usually, search engines are nonspecific and produce voluminous results. Use of AND/OR/NOT and "near" and "adjacent" search refinements greatly improve the results of a search. Search engines that limit their scope to specific sites, and

  4. Clinical Use of an Enterprise Data Warehouse

    Science.gov (United States)

    Evans, R. Scott; Lloyd, James F.; Pierce, Lee A.

    2012-01-01

    The enormous amount of data being collected by electronic medical records (EMR) has found additional value when integrated and stored in data warehouses. The enterprise data warehouse (EDW) allows all data from an organization with numerous inpatient and outpatient facilities to be integrated and analyzed. We have found the EDW at Intermountain Healthcare to not only be an essential tool for management and strategic decision making, but also for patient specific clinical decision support. This paper presents the structure and two case studies of a framework that has provided us the ability to create a number of decision support applications that are dependent on the integration of previous enterprise-wide data in addition to a patient’s current information in the EMR. PMID:23304288

  5. Configurable Web Warehouses construction through BPM Systems

    Directory of Open Access Journals (Sweden)

    Andrea Delgado

    2016-08-01

    Full Text Available The process of building Data Warehouses (DW is well known with well defined stages but at the same time, mostly carried out manually by IT people in conjunction with business people. Web Warehouses (WW are DW whose data sources are taken from the web. We define a flexible WW, which can be configured accordingly to different domains, through the selection of the web sources and the definition of data processing characteristics. A Business Process Management (BPM System allows modeling and executing Business Processes (BPs providing support for the automation of processes. To support the process of building flexible WW we propose a two BPs level: a configuration process to support the selection of web sources and the definition of schemas and mappings, and a feeding process which takes the defined configuration and loads the data into the WW. In this paper we present a proof of concept of both processes, with focus on the configuration process and the defined data.

  6. PEMODELAN INTEGRASI NEARLY REAL TIME DATA WAREHOUSE DENGAN SERVICE ORIENTED ARCHITECTURE UNTUK MENUNJANG SISTEM INFORMASI RETAIL

    Directory of Open Access Journals (Sweden)

    I Made Dwi Jendra Sulastra

    2015-12-01

    Full Text Available Updates the data in the data warehouse is not traditionally done every transaction. Retail information systems require the latest data and can be accessed from anywhere for business analysis needs. Therefore, in this study will be made data warehouse model that is able to produce the information near real time, and can be accessed from anywhere by end users application. Modeling design integration of nearly real time data warehouse (NRTDWH with a service oriented architecture (SOA to support the retail information system is done in two stages. In the first stage will be designed modeling NRTDWH using Change Data Capture (CDC based Transaction Log. In the second stage will be designed modeling NRTDWH integration with SOA-based web service. Tests conducted by a simulation test applications. Test applications used retail information systems, web-based web service client, desktop, and mobile. Results of this study were (1 ETL-based CDC captures changes to the source table and then store it in the database NRTDWH with the help of a scheduler; (2 Middleware web service makes 6 service based on data contained in the database NRTDWH, and each of these services accessible and implemented by the web service client.

  7. Warehouse Order-Picking Process. Review

    Directory of Open Access Journals (Sweden)

    E. V. Korobkov

    2015-01-01

    Full Text Available This article describes basic warehousing activities, namely: movement, information storage and transfer, as well as connections between typical warehouse operations (reception, transfer, assigning storage position and put-away, order-picking, hoarding and sorting, cross-docking, shipping. It presents a classification of the warehouse order-picking systems in terms of manual labor on offer as well as external (marketing channels, consumer’s demand structure, supplier’s replenishment structure and inventory level, total production demand, economic situation and internal (mechanization level, information accessibility, warehouse dimensionality, method of dispatch for shipping, zoning, batching, storage assignment method, routing method factors affecting the designing systems complexity. Basic optimization considerations are described. There is a literature review on the following sub-problems of planning and control of orderpicking processes.A layout design problem has been taken in account at two levels — external (facility layout problem and internal (aisle configuration problem. For a problem of distributing goods or stock keeping units the following methods are emphasized: random, nearest open storage position, and dedicated (COI-based, frequency-based distribution, as well as class-based and familygrouped (complimentary- and contact-based one. Batching problem can be solved by two main methods, i.e. proximity order batching (seed and saving algorithms and time-window order batching. There are two strategies for a zoning problem: progressive and synchronized, and also a special case of zoning — bucket brigades method. Hoarding/sorting problem is briefly reviewed. Order-picking routing problem will be thoroughly described in the next article of the cycle “Warehouse order-picking process”.

  8. EURASIP journal on bioinformatics & systems biology

    National Research Council Canada - National Science Library

    2006-01-01

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

  9. An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics.

    Science.gov (United States)

    Taylor, Ronald C

    2010-12-21

    Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBase project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date. Hadoop and the MapReduce programming paradigm already have a substantial base in the bioinformatics community, especially in the field of next-generation sequencing analysis, and such use is increasing. This is due to the cost-effectiveness of Hadoop-based analysis on commodity Linux clusters, and in the cloud via data upload to cloud vendors who have implemented Hadoop/HBase; and due to the effectiveness and ease-of-use of the MapReduce method in parallelization of many data analysis algorithms.

  10. Data warehouse til elbilers opladning og elpriser

    DEFF Research Database (Denmark)

    Andersen, Ove; Krogh, Benjamin Bjerre; Torp, Kristian

    Denne rapport præsenterer, hvordan GPS og CAN bus målinger fra opladning af elbilerne er renset for typiske fejl og gemt i et data warehouse. GPS og CAN bus målingerne er i data warehouset integreret med priserne fra det Nordeuropæiske el spotmarked Nord Pool Spot. Denne integration muliggør...... målinger om opladningen af elbiler er sammen med priserne fra el spotmarkedet indlæst i et data warehouse, som er fuldt ud implementeret. Den logiske data model for dette data warehouse præsenteres i detaljer. Håndteringen af GPS og CAN bus målingerne er generisk og kan udvides til nye data kilder......-en-elbil projektet. Data er renset for fejl så som uventede hop i kilometertælleren, uventede hop i State of Charge (SoC) værdien og svingende SoC værdier. For hver fejltype er fejlen beskrevet med et konkret eksempel fra rå data og antal af fejl er listet. Det beskrives yderligere, hvordan hver enkelt fejl er...

  11. Designing a Clinical Data Warehouse Architecture to Support Quality Improvement Initiatives.

    Science.gov (United States)

    Chelico, John D; Wilcox, Adam B; Vawdrey, David K; Kuperman, Gilad J

    2016-01-01

    Clinical data warehouses, initially directed towards clinical research or financial analyses, are evolving to support quality improvement efforts, and must now address the quality improvement life cycle. In addition, data that are needed for quality improvement often do not reside in a single database, requiring easier methods to query data across multiple disparate sources. We created a virtual data warehouse at NewYork Presbyterian Hospital that allowed us to bring together data from several source systems throughout the organization. We also created a framework to match the maturity of a data request in the quality improvement life cycle to proper tools needed for each request. As projects progress in the Define, Measure, Analyze, Improve, Control stages of quality improvement, there is a proper matching of resources the data needs at each step. We describe the analysis and design creating a robust model for applying clinical data warehousing to quality improvement.

  12. Bioinformatics goes to school--new avenues for teaching contemporary biology.

    Science.gov (United States)

    Wood, Louisa; Gebhardt, Philipp

    2013-01-01

    Since 2010, the European Molecular Biology Laboratory's (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students. In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers.

  13. 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

  14. Bioinformatics in the information age

    Energy Technology Data Exchange (ETDEWEB)

    Spengler, Sylvia J.

    2000-02-01

    There is a well-known story about the blind man examining the elephant: the part of the elephant examined determines his perception of the whole beast. Perhaps bioinformatics--the shotgun marriage between biology and mathematics, computer science, and engineering--is like an elephant that occupies a large chair in the scientific living room. Given the demand for and shortage of researchers with the computer skills to handle large volumes of biological data, where exactly does the bioinformatics elephant sit? There are probably many biologists who feel that a major product of this bioinformatics elephant is large piles of waste material. If you have tried to plow through Web sites and software packages in search of a specific tool for analyzing and collating large amounts of research data, you may well feel the same way. But there has been progress with major initiatives to develop more computing power, educate biologists about computers, increase funding, and set standards. For our purposes, bioinformatics is not simply a biologically inclined rehash of information theory (1) nor is it a hodgepodge of computer science techniques for building, updating, and accessing biological data. Rather bioinformatics incorporates both of these capabilities into a broad interdisciplinary science that involves both conceptual and practical tools for the understanding, generation, processing, and propagation of biological information. As such, bioinformatics is the sine qua non of 21st-century biology. Analyzing gene expression using cDNA microarrays immobilized on slides or other solid supports (gene chips) is set to revolutionize biology and medicine and, in so doing, generate vast quantities of data that have to be accurately interpreted (Fig. 1). As discussed at a meeting a few months ago (Microarray Algorithms and Statistical Analysis: Methods and Standards; Tahoe City, California; 9-12 November 1999), experiments with cDNA arrays must be subjected to quality control

  15. The impact of e-commerce on warehouse operations

    Directory of Open Access Journals (Sweden)

    Wiktor Żuchowski

    2016-03-01

    Full Text Available Background: We often encounter opinions concerning the unusual nature of warehouses used for the purposes of e-commerce, most often spread by providers of modern technological equipment and designers of such solutions. Of course, in the case of newly built facilities, it is advisable to consider innovative technologies, especially in terms of order picking. However, in many cases, the differences between "standard" warehouses, serving, for example, the vehicle spare parts market, and warehouses that are ready to handle retail orders placed electronically (defined as e-commerce are negligible. The scale of the differences between the existing "standard" warehouses and those adapted to handle e-commerce is dependent on the industry and supported of customers' structure. Methods: On the basis of experiences and on examples of enterprises two cases of the impact of a hypothetical e-commerce implementation for the warehouse organization and technology have been analysed. Results: The introduction of e-commerce into warehouses entails respective changes to previously handled orders. Warehouses serving the retail market are in principle prepared to process electronic orders. In this case, the introduction of (direct electronic sales is justified and feasible with relatively little effort. Conclusions: It cannot be said with certainty that the introduction of e-commerce in the warehouse is a revolution for its employees and managers. It depends on the markets in which the company operates, and on customers served by the warehouse prior to the introduction of e-commerce.

  16. Utility library for structural bioinformatics.

    Science.gov (United States)

    Gront, Dominik; Kolinski, Andrzej

    2008-02-15

    In this Note we present a new software library for structural bioinformatics. The library contains programs, computing sequence- and profile-based alignments and a variety of structural calculations with user-friendly handling of various data formats. The software organization is very flexible. Algorithms are written in Java language and may be used by Java programs. Moreover the modules can be accessed from Jython (Python scripting language implemented in Java) scripts. Finally, the new version of BioShell delivers several utility programs that can do typical bioinformatics task from a command-line level. Availability The software is available for download free of charge from its website: http://bioshell.chem.uw.edu.pl. This website provides also numerous examples, code snippets and API documentation.

  17. Database Resources of the BIG Data Center in 2018.

    Science.gov (United States)

    2018-01-04

    The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Database Resources of the BIG Data Center in 2018

    Science.gov (United States)

    Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

    2018-01-01

    Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

  19. Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools

    Directory of Open Access Journals (Sweden)

    Daisuke Kihara

    2006-01-01

    Full Text Available The immensely popular fields of cancer research and bioinformatics overlap in many different areas, e.g. large data repositories that allow for users to analyze data from many experiments (data handling, databases, pattern mining, microarray data analysis, and interpretation of proteomics data. There are many newly available resources in these areas that may be unfamiliar to most cancer researchers wanting to incorporate bioinformatics tools and analyses into their work, and also to bioinformaticians looking for real data to develop and test algorithms. This review reveals the interdependence of cancer research and bioinformatics, and highlight the most appropriate and useful resources available to cancer researchers. These include not only public databases, but general and specific bioinformatics tools which can be useful to the cancer researcher. The primary foci are function and structure prediction tools of protein genes. The result is a useful reference to cancer researchers and bioinformaticians studying cancer alike.

  20. 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

    Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010's top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and interpret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research. Educators have responded by incorporating bioinformatics into diverse life science curricula. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algorithms. Moreover, effectively integrating bioinformatics

  1. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows

    NARCIS (Netherlands)

    Katayama, T.; Arakawa, K.; Nakao, M.; Prins, J.C.P.

    2010-01-01

    Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However,

  2. 27 CFR 46.236 - Articles in a warehouse.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2010-04-01 2010-04-01 false Articles in a warehouse... Tubes Held for Sale on April 1, 2009 Filing Requirements § 46.236 Articles in a warehouse. (a) Articles... articles will be offered for sale. (b) Articles offered for sale at several locations must be reported on a...

  3. Multidimensi Pada Data Warehouse Dengan Menggunakan Rumus Kombinasi

    OpenAIRE

    Hendric, Spits Warnars Harco Leslie

    2006-01-01

    Multidimensional in data warehouse is a compulsion and become the most important for information delivery, without multidimensional data warehouse is incomplete. Multidimensional give the able to analyze business measurement in many different ways. Multidimensional is also synonymous with online analytical processing (OLAP).

  4. Building a data warehouse with examples in SQL server

    CERN Document Server

    Rainardi, Vincent

    2008-01-01

    ""Building a Data Warehouse: With Examples in SQL Server"" describes how to build a data warehouse completely from scratch and shows practical examples on how to do it. Author Rainardi also describes some practical issues that developers are likely to encounter in their first data warehousing project, along with solutions and advice.

  5. Design and Control of Warehouse Order Picking: a literature review

    NARCIS (Netherlands)

    M.B.M. de Koster (René); T. Le-Duc (Tho); K.J. Roodbergen (Kees-Jan)

    2006-01-01

    textabstractOrder picking has long been identified as the most labour-intensive and costly activity for almost every warehouse; the cost of order picking is estimated to be as much as 55% of the total warehouse operating expense. Any underperformance in order picking can lead to unsatisfactory

  6. Optimal time policy for deteriorating items of two-warehouse

    Indian Academy of Sciences (India)

    ... goods in which the first is rented warehouse and the second is own warehouse that deteriorates with two different rates. The aim of this study is to determine the optimal order quantity to maximize the profit of the projected model. Finally, some numerical examples and sensitivity analysis of parameters are made to validate ...

  7. 27 CFR 28.286 - Receipt in customs bonded warehouse.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Receipt in customs bonded... in Customs Bonded Warehouse § 28.286 Receipt in customs bonded warehouse. On receipt of the distilled spirits or wine and the related TTB Form 5100.11 or 5110.30 as the case may be, the customs officer in...

  8. 19 CFR 19.1 - Classes of customs warehouses.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Classes of customs warehouses. 19.1 Section 19.1 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CUSTOMS WAREHOUSES, CONTAINER STATIONS AND CONTROL OF MERCHANDISE THEREIN § 19.1 Classes of...

  9. An Improved Data Warehouse Architecture for SPGS, MAUTECH ...

    African Journals Online (AJOL)

    PROF. OLIVER OSUAGWA

    2015-06-01

    Jun 1, 2015 ... The DW Architecture provides an integrated data warehouse environment while delivering incremental solutions. The architectural design focuses on the application of a centralized data warehouse, data marts, individual marts, metadata repositories, and incremental solution architectures. As the process ...

  10. Contextual snowflake modelling for pattern warehouse logical design

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Pattern warehouse provides the infrastructure for knowledge representation and mining by allowing the patterns to be stored permanently. The goal of this paper is to discuss the pattern warehouse design and related quality issues. In the present work, we focus on conceptual and logical design of pattern ...

  11. Contextual snowflake modelling for pattern warehouse logical design

    Indian Academy of Sciences (India)

    A pattern warehouse is as attractive as data warehouse as the main repository of an organization's pattern and can .... such knowledge artifacts, generated by data mining applications (Tiwari et al 2010). So the ...... 31st International Conference on Very Large Data Bases (VLDB), (pp)1346–1349, Trondheim, Norway,. ACM.

  12. Simultaneous determination of warehouse layout and control policies

    NARCIS (Netherlands)

    Roodbergen, Kees Jan; Vis, Iris F. A.; Taylor, G. Don

    2015-01-01

    In a supply chain's order fulfilment process, it is often the warehouse that plays a central role in making the right product available to the right customer at the right time. This paper aims to improve warehouse performance by deriving an effective design method for the simultaneous determination

  13. Refrigerated Warehouse Demand Response Strategy Guide

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Doug [VaCom Technologies, San Luis Obispo, CA (United States); Castillo, Rafael [VaCom Technologies, San Luis Obispo, CA (United States); Larson, Kyle [VaCom Technologies, San Luis Obispo, CA (United States); Dobbs, Brian [VaCom Technologies, San Luis Obispo, CA (United States); Olsen, Daniel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2015-11-01

    This guide summarizes demand response measures that can be implemented in refrigerated warehouses. In an appendix, it also addresses related energy efficiency opportunities. Reducing overall grid demand during peak periods and energy consumption has benefits for facility operators, grid operators, utility companies, and society. State wide demand response potential for the refrigerated warehouse sector in California is estimated to be over 22.1 Megawatts. Two categories of demand response strategies are described in this guide: load shifting and load shedding. Load shifting can be accomplished via pre-cooling, capacity limiting, and battery charger load management. Load shedding can be achieved by lighting reduction, demand defrost and defrost termination, infiltration reduction, and shutting down miscellaneous equipment. Estimation of the costs and benefits of demand response participation yields simple payback periods of 2-4 years. To improve demand response performance, it’s suggested to install air curtains and another form of infiltration barrier, such as a rollup door, for the passageways. Further modifications to increase efficiency of the refrigeration unit are also analyzed. A larger condenser can maintain the minimum saturated condensing temperature (SCT) for more hours of the day. Lowering the SCT reduces the compressor lift, which results in an overall increase in refrigeration system capacity and energy efficiency. Another way of saving energy in refrigerated warehouses is eliminating the use of under-floor resistance heaters. A more energy efficient alternative to resistance heaters is to utilize the heat that is being rejected from the condenser through a heat exchanger. These energy efficiency measures improve efficiency either by reducing the required electric energy input for the refrigeration system, by helping to curtail the refrigeration load on the system, or by reducing both the load and required energy input.

  14. Analisis Dan Perancangan Data Warehouse Pada PT Gajah Tunggal Prakarsa

    Directory of Open Access Journals (Sweden)

    Choirul Huda

    2010-12-01

    Full Text Available The purpose of this helpful in making decisions more quickly and precisely. Research methodology includes analysis study was to analyze the data base support in helping decisions making, identifying needs and designing a data warehouse. With the support of data warehouse, company leaders can be more of current systems, library research, designing a data warehouse using star schema. The result of this research is the availability of a data warehouse that can generate information quickly and precisely, thus helping the company in making decisions. The conclusion of this research is the application of data warehouse can be a media aide related parties on PT. Gajah Tunggal initiative in decision making. 

  15. Automatic generation of warehouse mediators using an ontology engine

    Energy Technology Data Exchange (ETDEWEB)

    Critchlow, T., LLNL

    1998-04-01

    Data warehouses created for dynamic scientific environments, such as genetics, face significant challenges to their long-term feasibility One of the most significant of these is the high frequency of schema evolution resulting from both technological advances and scientific insight Failure to quickly incorporate these modifications will quickly render the warehouse obsolete, yet each evolution requires significant effort to ensure the changes are correctly propagated DataFoundry utilizes a mediated warehouse architecture with an ontology infrastructure to reduce the maintenance acquirements of a warehouse. Among the things, the ontology is used as an information source for automatically generating mediators, the methods that transfer data between the data sources and the warehouse The identification, definition and representation of the metadata required to perform this task is a primary contribution of this work.

  16. Congestion-Aware Warehouse Flow Analysis and Optimization

    KAUST Repository

    AlHalawani, Sawsan

    2015-12-18

    Generating realistic configurations of urban models is a vital part of the modeling process, especially if these models are used for evaluation and analysis. In this work, we address the problem of assigning objects to their storage locations inside a warehouse which has a great impact on the quality of operations within a warehouse. Existing storage policies aim to improve the efficiency by minimizing travel time or by classifying the items based on some features. We go beyond existing methods as we analyze warehouse layout network in an attempt to understand the factors that affect traffic within the warehouse. We use simulated annealing based sampling to assign items to their storage locations while reducing traffic congestion and enhancing the speed of order picking processes. The proposed method enables a range of applications including efficient storage assignment, warehouse reliability evaluation and traffic congestion estimation.

  17. Protection of warehouses and plants under capacity constraint

    International Nuclear Information System (INIS)

    Bricha, Naji; Nourelfath, Mustapha

    2015-01-01

    While warehouses may be subjected to less protection effort than plants, their unavailability may have substantial impact on the supply chain performance. This paper presents a method for protection of plants and warehouses against intentional attacks in the context of the capacitated plant and warehouses location and capacity acquisition problem. A non-cooperative two-period game is developed to find the equilibrium solution and the optimal defender strategy under capacity constraints. The defender invests in the first period to minimize the expected damage and the attacker moves in the second period to maximize the expected damage. Extra-capacity of neighboring functional plants and warehouses is used after attacks, to satisfy all customers demand and to avoid the backorders. The contest success function is used to evaluate success probability of an attack of plants and warehouses. A numerical example is presented to illustrate an application of the model. The defender strategy obtained by our model is compared to the case where warehouses are subjected to less protection effort than the plants. This comparison allows us to measure how much our method is better, and illustrates the effect of direct investments in protection and indirect protection by warehouse extra-capacities to reduce the expected damage. - Highlights: • Protection of warehouses and plants against intentional attacks. • Capacitated plant and warehouse location and capacity acquisition problem. • A non-cooperative two-period game between the defender and the attacker. • A method to evaluate the utilities and determine the optimal defender strategy. • Using warehouse extra-capacities to reduce the expected damage

  18. The Data Warehouse: Keeping It Simple. MIT Shares Valuable Lessons Learned from a Successful Data Warehouse Implementation.

    Science.gov (United States)

    Thorne, Scott

    2000-01-01

    Explains why the data warehouse is important to the Massachusetts Institute of Technology community, describing its basic functions and technical design points; sharing some non-technical aspects of the school's data warehouse implementation that have proved to be important; examining the importance of proper training in a successful warehouse…

  19. Integrating Brazilian health information systems in order to support the building of data warehouses

    Directory of Open Access Journals (Sweden)

    Sergio Miranda Freire

    Full Text Available AbstractIntroductionThis paper's aim is to develop a data warehouse from the integration of the files of three Brazilian health information systems concerned with the production of ambulatory and hospital procedures for cancer care, and cancer mortality. These systems do not have a unique patient identification, which makes their integration difficult even within a single system.MethodsData from the Brazilian Public Hospital Information System (SIH-SUS, the Oncology Module for the Outpatient Information System (APAC-ONCO and the Mortality Information System (SIM for the State of Rio de Janeiro, in the period from January 2000 to December 2004 were used. Each of the systems has the monthly data production compiled in dbase files (dbf. All the files pertaining to the same system were then read into a corresponding table in a MySQL Server 5.1. The SIH-SUS and APAC-ONCO tables were linked internally and with one another through record linkage methods. The APAC-ONCO table was linked to the SIM table. Afterwards a data warehouse was built using Pentaho and the MySQL database management system.ResultsThe sensitivities and specificities of the linkage processes were above 95% and close to 100% respectively. The data warehouse provided several analytical views that are accessed through the Pentaho Schema Workbench.ConclusionThis study presented a proposal for the integration of Brazilian Health Systems to support the building of data warehouses and provide information beyond those currently available with the individual systems.

  20. Customer and household matching: resolving entity identity in data warehouses

    Science.gov (United States)

    Berndt, Donald J.; Satterfield, Ronald K.

    2000-04-01

    The data preparation and cleansing tasks necessary to ensure high quality data are among the most difficult challenges faced in data warehousing and data mining projects. The extraction of source data, transformation into new forms, and loading into a data warehouse environment are all time consuming tasks that can be supported by methodologies and tools. This paper focuses on the problem of record linkage or entity matching, tasks that can be very important in providing high quality data. Merging two or more large databases into a single integrated system is a difficult problem in many industries, especially in the wake of acquisitions. For example, managing customer lists can be challenging when duplicate entries, data entry problems, and changing information conspire to make data quality an elusive target. Common tasks with regard to customer lists include customer matching to reduce duplicate entries and household matching to group customers. These often O(n2) problems can consume significant resources, both in computing infrastructure and human oversight, and the goal of high accuracy in the final integrated database can be difficult to assure. This paper distinguishes between attribute corruption and entity corruption, discussing the various impacts on quality. A metajoin operator is proposed and used to organize past and current entity matching techniques. Finally, a logistic regression approach to implementing the metajoin operator is discussed and illustrated with an example. The metajoin can be used to determine whether two records match, don't match, or require further evaluation by human experts. Properly implemented, the metajoin operator could allow the integration of individual databases with greater accuracy and lower cost.

  1. WATCHMAN: A Data Warehouse Intelligent Cache Manager

    Science.gov (United States)

    Scheuermann, Peter; Shim, Junho; Vingralek, Radek

    1996-01-01

    Data warehouses store large volumes of data which are used frequently by decision support applications. Such applications involve complex queries. Query performance in such an environment is critical because decision support applications often require interactive query response time. Because data warehouses are updated infrequently, it becomes possible to improve query performance by caching sets retrieved by queries in addition to query execution plans. In this paper we report on the design of an intelligent cache manager for sets retrieved by queries called WATCHMAN, which is particularly well suited for data warehousing environment. Our cache manager employs two novel, complementary algorithms for cache replacement and for cache admission. WATCHMAN aims at minimizing query response time and its cache replacement policy swaps out entire retrieved sets of queries instead of individual pages. The cache replacement and admission algorithms make use of a profit metric, which considers for each retrieved set its average rate of reference, its size, and execution cost of the associated query. We report on a performance evaluation based on the TPC-D and Set Query benchmarks. These experiments show that WATCHMAN achieves a substantial performance improvement in a decision support environment when compared to a traditional LRU replacement algorithm.

  2. Storage of hazardous substances in bonded warehouses

    International Nuclear Information System (INIS)

    Villalobos Artavia, Beatriz

    2008-01-01

    A variety of special regulations exist in Costa Rica for registration and transport of hazardous substances; these set the requirements for entry into the country and the security of transport units. However, the regulations mentioned no specific rules for storing hazardous substances. Tax deposits have been the initial place where are stored the substances that enter the country.The creation of basic rules that would be regulating the storage of hazardous substances has taken place through the analysis of regulations and national and international laws governing hazardous substances. The regulatory domain that currently exists will be established with a field research in fiscal deposits in the metropolitan area. The storage and security measures that have been used by the personnel handling the substances will be identified to be putting the reality with that the hazardous substances have been handled in tax deposits. A rule base for the storage of hazardous substances in tax deposits can be made, protecting the safety of the environment in which are manipulated and avoiding a possible accident causing a mess around. The rule will have the characteristics of the storage warehouses hazardous substances, such as safety standards, labeling standards, infrastructure features, common storage and transitional measures that must possess and meet all bonded warehouses to store hazardous substances. (author) [es

  3. Bioinformatics in Africa: The Rise of Ghana?

    Directory of Open Access Journals (Sweden)

    Thomas K Karikari

    2015-09-01

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

  4. Bioinformatics in Africa: The Rise of Ghana?

    Science.gov (United States)

    Karikari, Thomas K

    2015-09-01

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

  5. Search strategies in structural bioinformatics.

    Science.gov (United States)

    Oakley, Mark T; Barthel, Daniel; Bykov, Yuri; Garibaldi, Jonathan M; Burke, Edmund K; Krasnogor, Natalio; Hirst, Jonathan D

    2008-06-01

    Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.

  6. 7 CFR 1423.11 - Delivery and shipping standards for cotton warehouses.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Delivery and shipping standards for cotton warehouses... CORPORATION APPROVED WAREHOUSES § 1423.11 Delivery and shipping standards for cotton warehouses. (a) Unless... warehouse operator will: (1) Deliver stored cotton without unnecessary delay. (2) Be considered to have...

  7. 19 CFR 19.14 - Materials for use in manufacturing warehouse.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Materials for use in manufacturing warehouse. 19...; DEPARTMENT OF THE TREASURY CUSTOMS WAREHOUSES, CONTAINER STATIONS AND CONTROL OF MERCHANDISE THEREIN Manufacturing Warehouses § 19.14 Materials for use in manufacturing warehouse. (a) Imported merchandise to be...

  8. 7 CFR 800.185 - Duties of official personnel and warehouse samplers.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Duties of official personnel and warehouse samplers... official personnel and warehouse samplers. (a) General. Official personnel and warehouse samplers shall... of § 800.161. (d) Scope of operations. Official personnel and warehouse samplers shall operate only...

  9. 7 CFR 29.9406 - Failure of warehouse to comply with opening and selling schedule.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Failure of warehouse to comply with opening and... Markets § 29.9406 Failure of warehouse to comply with opening and selling schedule. (a) Each warehouse... warehouse may exceed its scheduled sales opportunity for designated or undesignated tobacco, but the pounds...

  10. 48 CFR 47.303-12 - Ex dock, pier, or warehouse, port of importation.

    Science.gov (United States)

    2010-10-01

    ... warehouse, port of importation. 47.303-12 Section 47.303-12 Federal Acquisition Regulations System FEDERAL..., pier, or warehouse, port of importation. (a) Explanation of delivery term. Ex dock, pier, or warehouse... in the warehouse at the specified port of importation. (b) Contractor responsibilities. The...

  11. 48 CFR 52.247-40 - Ex Dock, Pier, or Warehouse, Port of Importation.

    Science.gov (United States)

    2010-10-01

    ... Warehouse, Port of Importation. 52.247-40 Section 52.247-40 Federal Acquisition Regulations System FEDERAL... Provisions and Clauses 52.247-40 Ex Dock, Pier, or Warehouse, Port of Importation. As prescribed in 47.303-12..., pier, or warehouse, port of importation: Ex Dock, Pier, or Warehouse, Port of Importation (APR 1984) (a...

  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. A Relevance-Extended Multi-dimensional Model for a Data Warehouse Contextualized with Documents

    DEFF Research Database (Denmark)

    Perez, Juan Manuel; Pedersen, Torben Bach; Berlanga, Rafael

    2005-01-01

    Current data warehouse and OLAP technologies can be applied to analyze the structured data that companies store in their databases. The circumstances that describe the context associated with these data can be found in other internal and external sources of documents. In this paper we propose...... is represented as a novel type of OLAP cube, here called R-cube. R-cubes are characterized by two special dimensions, namely: the relevance and the context dimensions. The first dimension measures the relevance of each fact in the selected analysis context, whereas the second one relates each fact...

  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

    Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response...... to the development of ‘high-throughput biology’, the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes...... to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials...

  15. 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.

  16. BIRCH: a user-oriented, locally-customizable, bioinformatics system.

    Science.gov (United States)

    Fristensky, Brian

    2007-02-09

    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. 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. 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.

  17. Warehouse order-picking process. Order-picker routing problem

    Directory of Open Access Journals (Sweden)

    E. V. Korobkov

    2015-01-01

    Full Text Available This article continues “Warehouse order-picking process” cycle and describes order-picker routing sub-problem of a warehouse order-picking process. It draws analogies between the orderpickers’ routing problem and traveling salesman’s problem, shows differences between the standard problem statement of a traveling salesman and routing problem of warehouse orderpickers, and gives the particular Steiner’s problem statement of a traveling salesman.Warehouse layout with a typical order is represented by a graph, with some its vertices corresponding to mandatory order-picker’s visits and some other ones being noncompulsory. The paper describes an optimal Ratliff-Rosenthal algorithm to solve order-picker’s routing problem for the single-block warehouses, i.e. warehouses with only two crossing aisles, defines seven equivalent classes of partial routing sub-graphs and five transitions used to have an optimal routing sub-graph of a order-picker. An extension of optimal Ratliff-Rosenthal order-picker routing algorithm for multi-block warehouses is presented and also reasons for using the routing heuristics instead of exact optimal algorithms are given. The paper offers algorithmic description of the following seven routing heuristics: S-shaped, return, midpoint, largest gap, aisle-by-aisle, composite, and combined as well as modification of combined heuristics. The comparison of orderpicker routing heuristics for one- and two-block warehouses is to be described in the next article of the “Warehouse order-picking process” cycle.

  18. E-MSD: an integrated data resource for bioinformatics.

    Science.gov (United States)

    Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

    2005-01-01

    The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

  19. Criticality calculation of the nuclear material warehouse of the ININ

    International Nuclear Information System (INIS)

    Garcia, T.; Angeles, A.; Flores C, J.

    2013-10-01

    In this work the conditions of nuclear safety were determined as much in normal conditions as in the accident event of the nuclear fuel warehouse of the reactor TRIGA Mark III of the Instituto Nacional de Investigaciones Nucleares (ININ). The warehouse contains standard fuel elements Leu - 8.5/20, a control rod with follower of standard fuel type Leu - 8.5/20, fuel elements Leu - 30/20, and the reactor fuel Sur-100. To check the subcritical state of the warehouse the effective multiplication factor (keff) was calculated. The keff calculation was carried out with the code MCNPX. (Author)

  20. CHOmine: an integrated data warehouse for CHO systems biology and modeling.

    Science.gov (United States)

    Gerstl, Matthias P; Hanscho, Michael; Ruckerbauer, David E; Zanghellini, Jürgen; Borth, Nicole

    2017-01-01

    The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. http://www.chogenome.org. © The Author(s) 2017. Published by Oxford University Press.

  1. Managing data warehouse metadata using the Web: A Web-based DBA maintenance tool suite

    Energy Technology Data Exchange (ETDEWEB)

    Yow, T. [Oak Ridge National Lab., TN (United States); Grubb, J.; Jennings, S. [Univ. of Tennessee, Knoxville, TN (United States)

    1998-12-31

    The Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC), which is associated with NASA`s Earth Observing System Data and Information System (EOSDIS), provides access to datasets used in environmental research. As a data warehouse for NASA, the ORNL DAAC archives and distributes data from NASA`s ground-based field experiments. In order to manage its large and diverse data holdings, the DAAC has mined metadata that is stored in several Sybase databases. However, the task of managing the metadata itself has become such a complicated task that the DAAC has developed a Web-based Graphical User Interface (GUI) called the DBA maintenance Tool Suite. This Web-based tool allows the DBA to maintain the DAAC`s metadata databases with the click of a mouse button. This tool greatly reduces the complexities of database maintenance and facilitates the task of data delivery to the DAAC`s user community.

  2. Fundamentals of bioinformatics and computational biology methods and exercises in matlab

    CERN Document Server

    Singh, Gautam B

    2015-01-01

    This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolbox™. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence compar...

  3. Warehouse Optimization Model Based on Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Guofeng Qin

    2013-01-01

    Full Text Available This paper takes Bao Steel logistics automated warehouse system as an example. The premise is to maintain the focus of the shelf below half of the height of the shelf. As a result, the cost time of getting or putting goods on the shelf is reduced, and the distance of the same kind of goods is also reduced. Construct a multiobjective optimization model, using genetic algorithm to optimize problem. At last, we get a local optimal solution. Before optimization, the average cost time of getting or putting goods is 4.52996 s, and the average distance of the same kinds of goods is 2.35318 m. After optimization, the average cost time is 4.28859 s, and the average distance is 1.97366 m. After analysis, we can draw the conclusion that this model can improve the efficiency of cargo storage.

  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. 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. 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…

  7. 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…

  8. 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.

  9. 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.

  10. 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.

  11. Bioinformatics clouds for big data manipulation

    Science.gov (United States)

    2012-01-01

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

  12. 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.

  13. 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.

  14. 31 CFR 560.408 - Importation into and release from a bonded warehouse or foreign trade zone.

    Science.gov (United States)

    2010-07-01

    ... bonded warehouse or foreign trade zone. 560.408 Section 560.408 Money and Finance: Treasury Regulations... warehouse or foreign trade zone. The prohibitions in § 560.201 apply to importation into a bonded warehouse... bonded warehouse or a foreign trade zone of Iranian-origin goods imported into a bonded warehouse or a...

  15. A Multidimensional Data Warehouse for Community Health Centers

    Science.gov (United States)

    Kunjan, Kislaya; Toscos, Tammy; Turkcan, Ayten; Doebbeling, Brad N.

    2015-01-01

    Community health centers (CHCs) play a pivotal role in healthcare delivery to vulnerable populations, but have not yet benefited from a data warehouse that can support improvements in clinical and financial outcomes across the practice. We have developed a multidimensional clinic data warehouse (CDW) by working with 7 CHCs across the state of Indiana and integrating their operational, financial and electronic patient records to support ongoing delivery of care. We describe in detail the rationale for the project, the data architecture employed, the content of the data warehouse, along with a description of the challenges experienced and strategies used in the development of this repository that may help other researchers, managers and leaders in health informatics. The resulting multidimensional data warehouse is highly practical and is designed to provide a foundation for wide-ranging healthcare data analytics over time and across the community health research enterprise. PMID:26958297

  16. A Multidimensional Data Warehouse for Community Health Centers.

    Science.gov (United States)

    Kunjan, Kislaya; Toscos, Tammy; Turkcan, Ayten; Doebbeling, Brad N

    2015-01-01

    Community health centers (CHCs) play a pivotal role in healthcare delivery to vulnerable populations, but have not yet benefited from a data warehouse that can support improvements in clinical and financial outcomes across the practice. We have developed a multidimensional clinic data warehouse (CDW) by working with 7 CHCs across the state of Indiana and integrating their operational, financial and electronic patient records to support ongoing delivery of care. We describe in detail the rationale for the project, the data architecture employed, the content of the data warehouse, along with a description of the challenges experienced and strategies used in the development of this repository that may help other researchers, managers and leaders in health informatics. The resulting multidimensional data warehouse is highly practical and is designed to provide a foundation for wide-ranging healthcare data analytics over time and across the community health research enterprise.

  17. Statewide Transportation Engineering Warehouse for Archived Regional Data (STEWARD).

    Science.gov (United States)

    2009-12-01

    This report documents Phase III of the development and operation of a prototype for the Statewide Transportation : Engineering Warehouse for Archived Regional Data (STEWARD). It reflects the progress on the development and : operation of STEWARD sinc...

  18. Data Warehouse Maintenance Under Concurrent Schema and Data Updates

    National Research Council Canada - National Science Library

    Zhang, Xin

    1998-01-01

    .... Recently, proposed view maintenance algorithms tackle the problem of (concurrent) data updates happening at different autonomous ISs, whereas the EVE system addresses the maintenance of a data warehouse after schema changes of ISs...

  19. Implemetasi Data Warehouse pada Bagian Pemasaran Perguruan Tinggi

    Directory of Open Access Journals (Sweden)

    Eka Miranda

    2012-06-01

    Full Text Available Transactional data are widely owned by higher education institutes, but the utilization of the data to support decision making has not functioned maximally. Therefore, higher education institutes need analysis tools to maximize decision making processes. Based on the issue, then data warehouse design was created to: (1 store large-amount data; (2 potentially gain new perspectives of distributed data; (3 provide reports and answers to users’ ad hoc questions; (4 perform data analysis of external conditions and transactional data from the marketing activities of universities, since marketing is one supporting field as well as the cutting edge of higher education institutes. The methods used to design and implement data warehouse are analysis of records related to the marketing activities of higher education institutes and data warehouse design. This study results in a data warehouse design and its implementation to analyze the external data and transactional data from the marketing activities of universities to support decision making.

  20. Minimizing Warehouse Space with a Dedicated Storage Policy

    Directory of Open Access Journals (Sweden)

    Andrea Fumi

    2013-07-01

    inevitably be supported by warehouse management system software. On the contrary, the proposed methodology relies upon a dedicated storage policy, which is easily implementable by companies of all sizes without the need for investing in expensive IT tools.

  1. Outpatient health care statistics data warehouse--implementation.

    Science.gov (United States)

    Zilli, D

    1999-01-01

    Data warehouse implementation is assumed to be a very knowledge-demanding, expensive and long-lasting process. As such it requires senior management sponsorship, involvement of experts, a big budget and probably years of development time. Presented Outpatient Health Care Statistics Data Warehouse implementation research provides ample evidence against the infallibility of the above statements. New, inexpensive, but powerful technology, which provides outstanding platform for On-Line Analytical Processing (OLAP), has emerged recently. Presumably, it will be the basis for the estimated future growth of data warehouse market, both in the medical and in other business fields. Methods and tools for building, maintaining and exploiting data warehouses are also briefly discussed in the paper.

  2. Operational management system for warehouse logistics of metal trading companies

    Directory of Open Access Journals (Sweden)

    Khayrullin Rustam Zinnatullovich

    2014-07-01

    Full Text Available Logistics is an effective tool in business management. Metal trading business is a part of metal promotion chain from producer to consumer. It's designed to serve as a link connecting the interests of steel producers and end users. We should account for the specifics warehousing trading. The specificity of warehouse metal trading consists primarily in the fact that the purchase is made in large lots, and the sale - in medium and small parties. Loading and unloading of cars and trucks is produced by overhead cranes. Some part of the purchased goods are shipped in relatively large lots without presales preparation. Another part of the goods undergoes presale preparation. Indoor and outdoor warehouses are used with the address storage system. In the process of prolonged storage the metal rusts. Some part of the goods is subjected to final completion (cutting, welding, coloration in service centers and small factories, usually located at the warehouse. The quantity of simultaneously shipped cars, and the quantity of the loader workers brigade can reach few dozens. So it is necessary to control the loading workers, to coordinate and monitor the performance of loading and unloading operations, to make the daily analysis of their work, to evaluate the warehouse operations as a whole. There is a need to manage and control movement of cars and trucks on the warehouse territory to reduce storage and transport costs and improve customer service. ERP-systems and WMS-systems, which are widely used, do not cover fully the functions and processes of the warehouse trading, and do not effectively manage all logistics processes. In this paper the specialized software is proposed. The software is intended for operational logistics management in warehouse metal products trading. The basic functions and processes of metal warehouse trading are described. The effectiveness indices for logistics processes and key effective indicators of warehouse trading are proposed

  3. The impact of e-commerce on warehouse operations

    OpenAIRE

    Wiktor Żuchowski

    2016-01-01

    Background: We often encounter opinions concerning the unusual nature of warehouses used for the purposes of e-commerce, most often spread by providers of modern technological equipment and designers of such solutions. Of course, in the case of newly built facilities, it is advisable to consider innovative technologies, especially in terms of order picking. However, in many cases, the differences between "standard" warehouses, serving, for example, the vehicle spare parts market, an...

  4. A Performance Evaluation of Online Warehouse Update Algorithms

    Science.gov (United States)

    1998-01-01

    able to present a fully consistent ver- sion of the warehouse to the queries while the warehouse is being updated. Multiversioning has been used...LST97]). Special- ized multiversion access structures have also been proposed ([LS89, LS90, dBS96, BC97, VV97, MOPW98]) In the context of OLTP systems...collection processes. 2.1 Multiversioning MVNL supports multiple versions by using Time Travel ([Sto87]). Each row has two extra at- tributes, Tmin

  5. A study on building data warehouse of hospital information system.

    Science.gov (United States)

    Li, Ping; Wu, Tao; Chen, Mu; Zhou, Bin; Xu, Wei-guo

    2011-08-01

    Existing hospital information systems with simple statistical functions cannot meet current management needs. It is well known that hospital resources are distributed with private property rights among hospitals, such as in the case of the regional coordination of medical services. In this study, to integrate and make full use of medical data effectively, we propose a data warehouse modeling method for the hospital information system. The method can also be employed for a distributed-hospital medical service system. To ensure that hospital information supports the diverse needs of health care, the framework of the hospital information system has three layers: datacenter layer, system-function layer, and user-interface layer. This paper discusses the role of a data warehouse management system in handling hospital information from the establishment of the data theme to the design of a data model to the establishment of a data warehouse. Online analytical processing tools assist user-friendly multidimensional analysis from a number of different angles to extract the required data and information. Use of the data warehouse improves online analytical processing and mitigates deficiencies in the decision support system. The hospital information system based on a data warehouse effectively employs statistical analysis and data mining technology to handle massive quantities of historical data, and summarizes from clinical and hospital information for decision making. This paper proposes the use of a data warehouse for a hospital information system, specifically a data warehouse for the theme of hospital information to determine latitude, modeling and so on. The processing of patient information is given as an example that demonstrates the usefulness of this method in the case of hospital information management. Data warehouse technology is an evolving technology, and more and more decision support information extracted by data mining and with decision-making technology is

  6. DEVS Models of Palletized Ground Stacking in Storeyed Grain Warehouse

    Directory of Open Access Journals (Sweden)

    Hou Shu-Yi

    2016-01-01

    Full Text Available Processed grain stored in storeyed warehouse is generally stacked on the ground without pallets. However, in order to improve the storing way, we developed a new stacking method, palletized ground stacking. Simulation should be used to present this new storing way. DEVS provides a formalized way to describe the system model. In this paper, DEVS models of palletized ground stacking in storeyed grain warehouse are given and a simulation model is developed by AutoMod.

  7. WU-Blast2 server at the European Bioinformatics Institute

    Science.gov (United States)

    Lopez, Rodrigo; Silventoinen, Ville; Robinson, Stephen; Kibria, Asif; Gish, Warren

    2003-01-01

    Since 1995, the WU-BLAST programs (http://blast.wustl.edu) have provided a fast, flexible and reliable method for similarity searching of biological sequence databases. The software is in use at many locales and web sites. The European Bioinformatics Institute's WU-Blast2 (http://www.ebi.ac.uk/blast2/) server has been providing free access to these search services since 1997 and today supports many features that both enhance the usability and expand on the scope of the software. PMID:12824421

  8. Design and Applications of a Multimodality Image Data Warehouse Framework

    Science.gov (United States)

    Wong, Stephen T.C.; Hoo, Kent Soo; Knowlton, Robert C.; Laxer, Kenneth D.; Cao, Xinhau; Hawkins, Randall A.; Dillon, William P.; Arenson, Ronald L.

    2002-01-01

    A comprehensive data warehouse framework is needed, which encompasses imaging and non-imaging information in supporting disease management and research. The authors propose such a framework, describe general design principles and system architecture, and illustrate a multimodality neuroimaging data warehouse system implemented for clinical epilepsy research. The data warehouse system is built on top of a picture archiving and communication system (PACS) environment and applies an iterative object-oriented analysis and design (OOAD) approach and recognized data interface and design standards. The implementation is based on a Java CORBA (Common Object Request Broker Architecture) and Web-based architecture that separates the graphical user interface presentation, data warehouse business services, data staging area, and backend source systems into distinct software layers. To illustrate the practicality of the data warehouse system, the authors describe two distinct biomedical applications—namely, clinical diagnostic workup of multimodality neuroimaging cases and research data analysis and decision threshold on seizure foci lateralization. The image data warehouse framework can be modified and generalized for new application domains. PMID:11971885

  9. An efficiency improvement in warehouse operation using simulation analysis

    Science.gov (United States)

    Samattapapong, N.

    2017-11-01

    In general, industry requires an efficient system for warehouse operation. There are many important factors that must be considered when designing an efficient warehouse system. The most important is an effective warehouse operation system that can help transfer raw material, reduce costs and support transportation. By all these factors, researchers are interested in studying about work systems and warehouse distribution. We start by collecting the important data for storage, such as the information on products, information on size and location, information on data collection and information on production, and all this information to build simulation model in Flexsim® simulation software. The result for simulation analysis found that the conveyor belt was a bottleneck in the warehouse operation. Therefore, many scenarios to improve that problem were generated and testing through simulation analysis process. The result showed that an average queuing time was reduced from 89.8% to 48.7% and the ability in transporting the product increased from 10.2% to 50.9%. Thus, it can be stated that this is the best method for increasing efficiency in the warehouse operation.

  10. Decision method for optimal selection of warehouse material handling strategies by production companies

    Science.gov (United States)

    Dobos, P.; Tamás, P.; Illés, B.

    2016-11-01

    Adequate establishment and operation of warehouse logistics determines the companies’ competitiveness significantly because it effects greatly the quality and the selling price of the goods that the production companies produce. In order to implement and manage an adequate warehouse system, adequate warehouse position, stock management model, warehouse technology, motivated work force committed to process improvement and material handling strategy are necessary. In practical life, companies have paid small attantion to select the warehouse strategy properly. Although it has a major influence on the production in the case of material warehouse and on smooth costumer service in the case of finished goods warehouse because this can happen with a huge loss in material handling. Due to the dynamically changing production structure, frequent reorganization of warehouse activities is needed, on what the majority of the companies react basically with no reactions. This work presents a simulation test system frames for eligible warehouse material handling strategy selection and also the decision method for selection.

  11. Computational Biology and Bioinformatics in Nigeria

    Science.gov (United States)

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

    2014-01-01

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

  12. Computational biology and bioinformatics in Nigeria.

    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.

  13. 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.

  14. 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.

  15. Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

    Science.gov (United States)

    Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

    2012-01-01

    With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

  16. Surfing the data tsunami, a bioinformatic dissection of the proangiogenic monocyte

    NARCIS (Netherlands)

    van der Pouw Kraan, T. C. T. M.; van der Laan, A. M.; Piek, J. J.; Horrevoets, A. J. G.

    2012-01-01

    In this review we compare expression studies on monocyte subsets as an example to show the integrated possibilities of molecular databases and bioinformatic analysis tools. Monocytes have been recognized as cells with great plasticity and differentiation potential that play a pivotal role in

  17. Why Choose This One? Factors in Scientists' Selection of Bioinformatics Tools

    Science.gov (United States)

    Bartlett, Joan C.; Ishimura, Yusuke; Kloda, Lorie A.

    2011-01-01

    Purpose: The objective was to identify and understand the factors involved in scientists' selection of preferred bioinformatics tools, such as databases of gene or protein sequence information (e.g., GenBank) or programs that manipulate and analyse biological data (e.g., BLAST). Methods: Eight scientists maintained research diaries for a two-week…

  18. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

    DEFF Research Database (Denmark)

    Boomsma, Wouter Krogh; Nielsen, Sofie Vincents; Lindorff-Larsen, Kresten

    2016-01-01

    conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology...

  19. A Complementary Bioinformatics Approach to Identify Potential Plant Cell Wall Glycosyltransferase-Encoding Genes

    DEFF Research Database (Denmark)

    Egelund, Jack; Skjøt, Michael; Geshi, Naomi

    2004-01-01

    . Although much is known with regard to composition and fine structures of the plant CW, only a handful of CW biosynthetic GT genes-all classified in the CAZy system-have been characterized. In an effort to identify CW GTs that have not yet been classified in the CAZy database, a simple bioinformatics...

  20. Bioinformatics Analyst | Center for Cancer Research

    Science.gov (United States)

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

  1. Coronavirus Genomics and Bioinformatics Analysis

    Directory of Open Access Journals (Sweden)

    Kwok-Yung Yuen

    2010-08-01

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

  2. Study on resources and environmental data integration towards data warehouse construction covering trans-boundary area of China, Russia and Mongolia

    International Nuclear Information System (INIS)

    Wang, J; Song, J; Gao, M; Zhu, L

    2014-01-01

    The trans-boundary area between Northern China, Mongolia and eastern Siberia of Russia is a continuous geographical area located in north eastern Asia. Many common issues in this region need to be addressed based on a uniform resources and environmental data warehouse. Based on the practice of joint scientific expedition, the paper presented a data integration solution including 3 steps, i.e., data collection standards and specifications making, data reorganization and process, data warehouse design and development. A series of data collection standards and specifications were drawn up firstly covering more than 10 domains. According to the uniform standard, 20 resources and environmental survey databases in regional scale, and 11 in-situ observation databases were reorganized and integrated. North East Asia Resources and Environmental Data Warehouse was designed, which included 4 layers, i.e., resources layer, core business logic layer, internet interoperation layer, and web portal layer. The data warehouse prototype was developed and deployed initially. All the integrated data in this area can be accessed online

  3. Study on resources and environmental data integration towards data warehouse construction covering trans-boundary area of China, Russia and Mongolia

    Science.gov (United States)

    Wang, J.; Song, J.; Gao, M.; Zhu, L.

    2014-02-01

    The trans-boundary area between Northern China, Mongolia and eastern Siberia of Russia is a continuous geographical area located in north eastern Asia. Many common issues in this region need to be addressed based on a uniform resources and environmental data warehouse. Based on the practice of joint scientific expedition, the paper presented a data integration solution including 3 steps, i.e., data collection standards and specifications making, data reorganization and process, data warehouse design and development. A series of data collection standards and specifications were drawn up firstly covering more than 10 domains. According to the uniform standard, 20 resources and environmental survey databases in regional scale, and 11 in-situ observation databases were reorganized and integrated. North East Asia Resources and Environmental Data Warehouse was designed, which included 4 layers, i.e., resources layer, core business logic layer, internet interoperation layer, and web portal layer. The data warehouse prototype was developed and deployed initially. All the integrated data in this area can be accessed online.

  4. Multifractal Detrended Cross-Correlation Analysis for Large-Scale Warehouse-Out Behaviors

    Science.gov (United States)

    Yao, Can-Zhong; Lin, Ji-Nan; Zheng, Xu-Zhou

    2015-09-01

    Based on cross-correlation algorithm, we analyze the correlation property of warehouse-out quantity of different warehouses, respectively, and different products of each warehouse. Our study identifies that significant cross-correlation relationship for warehouse-out quantity exists among different warehouses and different products of a warehouse. Further, we take multifractal detrended cross-correlation analysis for warehouse-out quantity among different warehouses and different products of a warehouse. The results show that for the warehouse-out behaviors of total amount, different warehouses and different products of a warehouse significantly follow multifractal property. Specifically for each warehouse, the coupling relationships of rebar and wire rod reveal long-term memory characteristics, no matter for large fluctuation or small one. The cross-correlation effect on long-range memory property among warehouses probably has less to do with product types,and the long-term memory of YZ warehouse is greater than others especially in total amount and wire rod product. Finally, we shuffle and surrogate data to explore the source of multifractal cross-correlation property in logistics system. Taking the total amount of warehouse-out quantity as example, we confirm that the fat-tail distribution of warehouse-out quantity sequences is the main factor for multifractal cross-correlation. Through comparing the performance of the multifractal detrended cross-correlation analysis (MF-DCCA), centered multifractal detrending moving average cross-correlation analysis (MF-X-DMA) algorithms, the forward and backward MF-X-DMA algorithms, we find that the forward and backward MF-X-DMA algorithms exhibit a better performance than the other ones.

  5. Multidimensional Databases and Data Warehousing

    CERN Document Server

    Jensen, Christian

    2010-01-01

    The present book's subject is multidimensional data models and data modeling concepts as they are applied in real data warehouses. The book aims to present the most important concepts within this subject in a precise and understandable manner. The book's coverage of fundamental concepts includes data cubes and their elements, such as dimensions, facts, and measures and their representation in a relational setting; it includes architecture-related concepts; and it includes the querying of multidimensional databases.The book also covers advanced multidimensional concepts that are considered to b

  6. Report from the first Workshop on Extremely Large Databases

    Directory of Open Access Journals (Sweden)

    J Becla

    2008-02-01

    Full Text Available Industrial and scientific datasets have been growing enormously in size and complexity in recent years. The largest transactional databases and data warehouses can no longer be hosted cost-effectively in off-the-shelf commercial database management systems. There are other forums for discussing databases and data warehouses, but they typically deal with problems occurring at smaller scales and do not always focus on practical solutions or influencing DBMS vendors. Given the relatively small (but highly influential and growing number of users with these databases and the relatively small number of opportunities to exchange practical information related to DBMSes at extremely large scale, a workshop on extremely large databases was organized. This paper is the final report of the discussions and activities at the workshop.

  7. Application of data mining techniques in healthcare database ...

    African Journals Online (AJOL)

    Healthcare system have several and vast databases. Valuable information can be extracted from these data stores through the application of data mining techniques. Data mining is a powerful tool that will help healthcare system to focus on the data warehouse important information as it extracts hidden predictive ...

  8. Creating a Data Warehouse using SQL Server

    DEFF Research Database (Denmark)

    Sørensen, Jens Otto; Alnor, Karl

    1999-01-01

    In this paper we construct a Star Join Schema and show how this schema can be created using the basic tools delivered with SQL Server 7.0. Major objectives are to keep the operational database unchanged so that data loading can be done with out disturbing the business logic of the operational...... database....

  9. The Data Warehouse in Service Oriented Architectures and Network Centric Warfare

    National Research Council Canada - National Science Library

    Lenahan, Jack

    2005-01-01

    ... at all policy and command levels to support superior decision making? Analyzing the anticipated massive amount of GIG data will almost certainly require data warehouses and federated data warehouses...

  10. Perbaikan Tata Kelola Warehouse PT Mustika Ratu Semarang dengan Konsep 5s + Pengaplikasian Rak Barang

    OpenAIRE

    Prasetyo, Mochammad Sidiq Saifuddin; Sriyanto, Sriyanto

    2016-01-01

    REDESIGN OF PT MUSTIKA RATU SEMARANG'S WAREHOUSE USING 5S CONCEPT AND GOODS RACK – The goal of this research if to identify and analyze the problem of warehouse management in PT Mustika Ratu Semarang, calculate the needs of warehouse volume to store the goods, calculate the rack dimension include the amount of the needs, and arrange the effective and efficient layout. The primary data came from interview and observation, while the secondary data came from PT Mustika Ratu Semarang's warehouse ...

  11. Radio frequency identification (RFID) technologies for locating warehouse resources: A conceptual framework

    OpenAIRE

    Hassan, M; Ali, M; Aktas, E

    2012-01-01

    Copyright @ 2012 Information Technology Society In the supply chain, a warehouse is a crucial component for linking all chain parties. It is necessary to track the real time resource location and status to support warehouse operations effectively. Therefore, RFID technology has been adopted to facilitate the collection and sharing of data in a warehouse environment. However, an essential decision should be made on the type of RFID tags the warehouse managers should adopt, because it is ver...

  12. The Analytic Information Warehouse (AIW): a Platform for Analytics using Electronic Health Record Data

    Science.gov (United States)

    Post, Andrew R.; Kurc, Tahsin; Cholleti, Sharath; Gao, Jingjing; Lin, Xia; Bornstein, William; Cantrell, Dedra; Levine, David; Hohmann, Sam; Saltz, Joel H.

    2013-01-01

    Objective To create an analytics platform for specifying and detecting clinical phenotypes and other derived variables in electronic health record (EHR) data for quality improvement investigations. Materials and Methods We have developed an architecture for an Analytic Information Warehouse (AIW). It supports transforming data represented in different physical schemas into a common data model, specifying derived variables in terms of the common model to enable their reuse, computing derived variables while enforcing invariants and ensuring correctness and consistency of data transformations, long-term curation of derived data, and export of derived data into standard analysis tools. It includes software that implements these features and a computing environment that enables secure high-performance access to and processing of large datasets extracted from EHRs. Results We have implemented and deployed the architecture in production locally. The software is available as open source. We have used it as part of hospital operations in a project to reduce rates of hospital readmission within 30 days. The project examined the association of over 100 derived variables representing disease and co-morbidity phenotypes with readmissions in five years of data from our institution’s clinical data warehouse and the UHC Clinical Database (CDB). The CDB contains administrative data from over 200 hospitals that are in academic medical centers or affiliated with such centers. Discussion and Conclusion A widely available platform for managing and detecting phenotypes in EHR data could accelerate the use of such data in quality improvement and comparative effectiveness studies. PMID:23402960

  13. The Analytic Information Warehouse (AIW): a platform for analytics using electronic health record data.

    Science.gov (United States)

    Post, Andrew R; Kurc, Tahsin; Cholleti, Sharath; Gao, Jingjing; Lin, Xia; Bornstein, William; Cantrell, Dedra; Levine, David; Hohmann, Sam; Saltz, Joel H

    2013-06-01

    To create an analytics platform for specifying and detecting clinical phenotypes and other derived variables in electronic health record (EHR) data for quality improvement investigations. We have developed an architecture for an Analytic Information Warehouse (AIW). It supports transforming data represented in different physical schemas into a common data model, specifying derived variables in terms of the common model to enable their reuse, computing derived variables while enforcing invariants and ensuring correctness and consistency of data transformations, long-term curation of derived data, and export of derived data into standard analysis tools. It includes software that implements these features and a computing environment that enables secure high-performance access to and processing of large datasets extracted from EHRs. We have implemented and deployed the architecture in production locally. The software is available as open source. We have used it as part of hospital operations in a project to reduce rates of hospital readmission within 30days. The project examined the association of over 100 derived variables representing disease and co-morbidity phenotypes with readmissions in 5years of data from our institution's clinical data warehouse and the UHC Clinical Database (CDB). The CDB contains administrative data from over 200 hospitals that are in academic medical centers or affiliated with such centers. A widely available platform for managing and detecting phenotypes in EHR data could accelerate the use of such data in quality improvement and comparative effectiveness studies. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. Development of a Clinical Data Warehouse for Hospital Infection Control

    Science.gov (United States)

    Wisniewski, Mary F.; Kieszkowski, Piotr; Zagorski, Brandon M.; Trick, William E.; Sommers, Michael; Weinstein, Robert A.

    2003-01-01

    Existing data stored in a hospital's transactional servers have enormous potential to improve performance measurement and health care quality. Accessing, organizing, and using these data to support research and quality improvement projects are evolving challenges for hospital systems. The authors report development of a clinical data warehouse that they created by importing data from the information systems of three affiliated public hospitals. They describe their methodology; difficulties encountered; responses from administrators, computer specialists, and clinicians; and the steps taken to capture and store patient-level data. The authors provide examples of their use of the clinical data warehouse to monitor antimicrobial resistance, to measure antimicrobial use, to detect hospital-acquired bloodstream infections, to measure the cost of infections, and to detect antimicrobial prescribing errors. In addition, they estimate the amount of time and money saved and the increased precision achieved through the practical application of the data warehouse. PMID:12807807

  15. Development of global data warehouse for beam diagnostics at SSRF

    International Nuclear Information System (INIS)

    Lai Longwei; Leng Yongbin; Yan Yingbing; Chen Zhichu

    2015-01-01

    The beam diagnostic system is adequate during the daily operation and machine study at the Shanghai Synchrotron Radiation Facility (SSRF). Without the effective event detecting mechanism, it is difficult to dump and analyze abnormal phenomena such as the global orbital disturbance, the malfunction of the BPM and the noise of the DCCT. The global beam diagnostic data warehouse was built in order to monitor the status of the accelerator and the beam instruments. The data warehouse was designed as a Soft IOC hosted on an independent server. Once abnormal phenomena happen it will be triggered and will store the relevant data for further analysis. The results show that the data warehouse can detect abnormal phenomena of the machine and the beam diagnostic system effectively, and can be used for calculating confidential indicators of the beam instruments. It provides an efficient tool for the improvement of the beam diagnostic system and accelerator. (authors)

  16. Development of a public health reporting data warehouse: lessons learned.

    Science.gov (United States)

    Rizi, Seyed Ali Mussavi; Roudsari, Abdul

    2013-01-01

    Data warehouse projects are perceived to be risky and prone to failure due to many organizational and technical challenges. However, often iterative and lengthy processes of implementation of data warehouses at an enterprise level provide an opportunity for formative evaluation of these solutions. This paper describes lessons learned from successful development and implementation of the first phase of an enterprise data warehouse to support public health surveillance at British Columbia Centre for Disease Control. Iterative and prototyping approach to development, overcoming technical challenges of extraction and integration of data from large scale clinical and ancillary systems, a novel approach to record linkage, flexible and reusable modeling of clinical data, and securing senior management support at the right time were the main factors that contributed to the success of the data warehousing project.

  17. Development of a clinical data warehouse for hospital infection control.

    Science.gov (United States)

    Wisniewski, Mary F; Kieszkowski, Piotr; Zagorski, Brandon M; Trick, William E; Sommers, Michael; Weinstein, Robert A

    2003-01-01

    Existing data stored in a hospital's transactional servers have enormous potential to improve performance measurement and health care quality. Accessing, organizing, and using these data to support research and quality improvement projects are evolving challenges for hospital systems. The authors report development of a clinical data warehouse that they created by importing data from the information systems of three affiliated public hospitals. They describe their methodology; difficulties encountered; responses from administrators, computer specialists, and clinicians; and the steps taken to capture and store patient-level data. The authors provide examples of their use of the clinical data warehouse to monitor antimicrobial resistance, to measure antimicrobial use, to detect hospital-acquired bloodstream infections, to measure the cost of infections, and to detect antimicrobial prescribing errors. In addition, they estimate the amount of time and money saved and the increased precision achieved through the practical application of the data warehouse.

  18. Lagrange multiplier for perishable inventory model considering warehouse capacity planning

    Science.gov (United States)

    Amran, Tiena Gustina; Fatima, Zenny

    2017-06-01

    This paper presented Lagrange Muktiplier approach for solving perishable raw material inventory planning considering warehouse capacity. A food company faced an issue of managing perishable raw materials and marinades which have limited shelf life. Another constraint to be considered was the capacity of the warehouse. Therefore, an inventory model considering shelf life and raw material warehouse capacity are needed in order to minimize the company's inventory cost. The inventory model implemented in this study was the adapted economic order quantity (EOQ) model which is optimized using Lagrange multiplier. The model and solution approach were applied to solve a case industry in a food manufacturer. The result showed that the total inventory cost decreased 2.42% after applying the proposed approach.

  19. A simulated annealing approach for redesigning a warehouse network problem

    Science.gov (United States)

    Khairuddin, Rozieana; Marlizawati Zainuddin, Zaitul; Jiun, Gan Jia

    2017-09-01

    Now a day, several companies consider downsizing their distribution networks in ways that involve consolidation or phase-out of some of their current warehousing facilities due to the increasing competition, mounting cost pressure and taking advantage on the economies of scale. Consequently, the changes on economic situation after a certain period of time require an adjustment on the network model in order to get the optimal cost under the current economic conditions. This paper aimed to develop a mixed-integer linear programming model for a two-echelon warehouse network redesign problem with capacitated plant and uncapacitated warehouses. The main contribution of this study is considering capacity constraint for existing warehouses. A Simulated Annealing algorithm is proposed to tackle with the proposed model. The numerical solution showed the model and method of solution proposed was practical.

  20. WORKPLACE EXPOSURES AND PROTECTIVE PRACTICES OF HISPANIC WAREHOUSE WORKERS

    Science.gov (United States)

    Livaudais, Jennifer C.; Thompson, Beti; Islas, Ilda; Ibarra, Genoveva; Anderson, Jennifer; Coronado, Gloria D.

    2009-01-01

    Background This study was undertaken to assess workplace hazards and protective practices among Hispanic men and women working post-harvest in asparagus, apple and pear packaging warehouses. Methods Three focus groups were conducted in July 2003 with 25 workers (20 women, 5 men) recruited from communities in the Yakima Valley, Washington. Focus group content informed the design of an in-person structured interview administered to 50 additional warehouse workers from August-November 2006. Results Focus group participants reported difficult working conditions, exposure to chemicals, adverse health effects and use of work and home protective practices to minimize exposures for themselves and their families. Structured interview participants reported few workplace exposures to chemicals although many reported engaging in workplace and home protective practices. Discussion Findings from this research can direct initial efforts to determine if and how interventions for warehouse workers may be designed to protect against hazardous workplace exposures. PMID:18543104

  1. 78 FR 77662 - Notice of Availability (NOA) for General Purpose Warehouse and Information Technology Center...

    Science.gov (United States)

    2013-12-24

    ... (NOA) for General Purpose Warehouse and Information Technology Center Construction (GPW/IT)--Tracy Site.... ACTION: Notice of Availability (NOA) for General Purpose Warehouse and Information Technology Center... FR 65300) announcing the publication of the General Purpose Warehouse and Information Technology...

  2. 7 CFR 1421.106 - Warehouse-stored marketing assistance loan collateral.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Warehouse-stored marketing assistance loan collateral... Marketing Assistance Loans § 1421.106 Warehouse-stored marketing assistance loan collateral. (a) A commodity may be pledged as collateral for a warehouse-stored marketing assistance loan in the quantity...

  3. Expanding Post-Harvest Finance Through Warehouse Receipts and Related Instruments

    OpenAIRE

    Baldwin, Marisa; Bryla, Erin; Langenbucher, Anja

    2006-01-01

    Warehouse receipt financing and similar types of collateralized lending provide an alternative to traditional lending requirements of banks and other financiers and could provide opportunities to expand this lending in emerging economies for agricultural trade. The main contents include: what is warehouse receipt financing; what is the value of warehouse receipt financing; other collater...

  4. 31 CFR 575.412 - Release of Iraqi goods from bonded warehouse or foreign trade zone.

    Science.gov (United States)

    2010-07-01

    ... warehouse or foreign trade zone. 575.412 Section 575.412 Money and Finance: Treasury Regulations Relating to... SANCTIONS REGULATIONS Interpretations § 575.412 Release of Iraqi goods from bonded warehouse or foreign trade zone. Section 575.204 does not prohibit the release from a bonded warehouse or a foreign trade...

  5. 27 CFR 44.201 - Return to manufacturer or customs warehouse proprietor.

    Science.gov (United States)

    2010-04-01

    ... customs warehouse proprietor. 44.201 Section 44.201 Alcohol, Tobacco Products and Firearms ALCOHOL AND... Shipments of Tobacco Products and Cigarette Papers and Tubes by Manufacturers and Export Warehouse Proprietors Notice of Removal of Shipment § 44.201 Return to manufacturer or customs warehouse proprietor...

  6. 77 FR 6814 - Agency Information Collection Activities: Bonded Warehouse Proprietor's Submission

    Science.gov (United States)

    2012-02-09

    ... Activities: Bonded Warehouse Proprietor's Submission AGENCY: U.S. Customs and Border Protection (CBP... requirement concerning the Bonded Warehouse Proprietor's Submission (CBP Form 300). This request for comment... collection: Title: Bonded Warehouse Proprietor's Submission. OMB Number: 1651-0033. Form Number: CBP Form 300...

  7. 19 CFR 191.155 - Merchandise withdrawn from warehouse for exportation.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Merchandise withdrawn from warehouse for... Custody § 191.155 Merchandise withdrawn from warehouse for exportation. The regulations in part 18 of this... from warehouse for exportation without payment of duty shall be followed to the extent applicable. ...

  8. 77 FR 26024 - Agency Information Collection Activities: Bonded Warehouse Proprietor's Submission

    Science.gov (United States)

    2012-05-02

    ... Activities: Bonded Warehouse Proprietor's Submission AGENCY: U.S. Customs and Border Protection, Department... Budget (OMB) for review and approval in accordance with the Paperwork Reduction Act: Bonded Warehouse..., or other technological techniques or other forms of information. Title: Bonded Warehouse Proprietor's...

  9. 19 CFR 125.32 - Merchandise delivered to a bonded store or bonded warehouse.

    Science.gov (United States)

    2010-04-01

    ... warehouse. 125.32 Section 125.32 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND... Merchandise delivered to a bonded store or bonded warehouse. When merchandise is carried, carted or lightered to and received in a bonded store or bonded warehouse, the proprietor or his representative shall...

  10. 19 CFR 159.52 - Warehouse entry not liquidated until final withdrawal.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Warehouse entry not liquidated until final withdrawal. 159.52 Section 159.52 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND... Warehouse entry not liquidated until final withdrawal. Liquidation of a warehouse or rewarehouse entry shall...

  11. 27 CFR 44.190 - Return of shipment to a manufacturer or customs warehouse proprietor.

    Science.gov (United States)

    2010-04-01

    ... manufacturer or customs warehouse proprietor. 44.190 Section 44.190 Alcohol, Tobacco Products and Firearms... of Shipments of Tobacco Products and Cigarette Papers and Tubes by Manufacturers and Export Warehouse Proprietors Consignment of Shipment § 44.190 Return of shipment to a manufacturer or customs warehouse...

  12. 27 CFR 31.61 - Single sale of liquors or warehouse receipts.

    Science.gov (United States)

    2010-04-01

    ... warehouse receipts. 31.61 Section 31.61 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND... Persons Who Are Not Dealers in Liquors Or Beer § 31.61 Single sale of liquors or warehouse receipts. A single sale of distilled spirits, wines, or beer, or a single sale of one or more warehouse receipts for...

  13. 27 CFR 44.210 - Return of shipment to factory or export warehouse.

    Science.gov (United States)

    2010-04-01

    ... factory or export warehouse. 44.210 Section 44.210 Alcohol, Tobacco Products and Firearms ALCOHOL AND... Shipments of Tobacco Products and Cigarette Papers and Tubes by Manufacturers and Export Warehouse Proprietors Miscellaneous Provisions § 44.210 Return of shipment to factory or export warehouse. A...

  14. 77 FR 20353 - United States Warehouse Act; Export Food Aid Commodities Licensing Agreement

    Science.gov (United States)

    2012-04-04

    ... States Warehouse Act; Export Food Aid Commodities Licensing Agreement AGENCY: Farm Service Agency, USDA...) under the United States Warehouse Act (USWA). Agricultural products that may be stored under an EFAC..., beans, and lentils. USWA licensing is a voluntary program. Warehouse operators that apply for USWA...

  15. 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...

  16. Study of the Vertical Distribution of Air Temperature in Warehouses

    Directory of Open Access Journals (Sweden)

    César Porras-Amores

    2014-02-01

    Full Text Available Warehouses are usually large, plain industrial buildings commonly used for storage of goods. Vertical distribution of air temperature is an important aspect for indoor environment design, which must be taken into account by architects and engineers in the early stages of warehouse design. The aim of this work is to analyze the vertical temperature gradients existing in warehouses, quantifying their value and analyzing their evolution along the year. To do so, the study outlines the monitoring of several warehouses with different building typology and height located in different areas of Spain for a complete annual cycle. The results obtained when applying a simple linear regression analysis to 175,200 vertical temperature profiles show that there is a strong influence of the outdoor temperature over the stratification of the indoor air. During warm months, the ceiling and the upper strata get warmer, whereas the cold air accumulates in the lower levels, increasing the stratification of indoor air (maximum values between 0.3 °C/m and 0.7 °C/m. During cold months, the ceiling gets cold due to its contact with the outdoor air, therefore, the colder, heavier air moves down to the lower strata, registering insignificant vertical temperature differences. Air conditioning of the warehouse, besides controlling the temperature, limits the influence of the outdoor environment on the stratification of temperatures. The results of the study may be of great use for warehouses for products sensitive to temperature, which may suffer a different evolution, conservation or maturation when the temperature differences are maintained for a long time.

  17. Demand Response Opportunities in Industrial Refrigerated Warehouses in California

    Energy Technology Data Exchange (ETDEWEB)

    Goli, Sasank; McKane, Aimee; Olsen, Daniel

    2011-06-14

    Industrial refrigerated warehouses that implemented energy efficiency measures and have centralized control systems can be excellent candidates for Automated Demand Response (Auto-DR) due to equipment synergies, and receptivity of facility managers to strategies that control energy costs without disrupting facility operations. Auto-DR utilizes OpenADR protocol for continuous and open communication signals over internet, allowing facilities to automate their Demand Response (DR). Refrigerated warehouses were selected for research because: They have significant power demand especially during utility peak periods; most processes are not sensitive to short-term (2-4 hours) lower power and DR activities are often not disruptive to facility operations; the number of processes is limited and well understood; and past experience with some DR strategies successful in commercial buildings may apply to refrigerated warehouses. This paper presents an overview of the potential for load sheds and shifts from baseline electricity use in response to DR events, along with physical configurations and operating characteristics of refrigerated warehouses. Analysis of data from two case studies and nine facilities in Pacific Gas and Electric territory, confirmed the DR abilities inherent to refrigerated warehouses but showed significant variation across facilities. Further, while load from California's refrigerated warehouses in 2008 was 360 MW with estimated DR potential of 45-90 MW, actual achieved was much less due to low participation. Efforts to overcome barriers to increased participation may include, improved marketing and recruitment of potential DR sites, better alignment and emphasis on financial benefits of participation, and use of Auto-DR to increase consistency of participation.

  18. A database for coconut crop improvement.

    Science.gov (United States)

    Rajagopal, Velamoor; Manimekalai, Ramaswamy; Devakumar, Krishnamurthy; Rajesh; Karun, Anitha; Niral, Vittal; Gopal, Murali; Aziz, Shamina; Gunasekaran, Marimuthu; Kumar, Mundappurathe Ramesh; Chandrasekar, Arumugam

    2005-12-08

    Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA. http://www.bioinfcpcri.org.

  19. The network control system of high-bay warehouse

    Directory of Open Access Journals (Sweden)

    Malaka Julian

    2017-01-01

    Full Text Available Presentation of developing a method of automation of the storage process using electric drives with frequency converters, logic control and communication in industrial networks was the main purpose of this article. A connection structure was proposed to exchange information between devices that are part of a high-storage warehouse. It was assumed that modern communication protocols are used to synchronize the drives and to create a central control and information center in the PLC. The results of theoretical considerations were applied in practice by performing a laboratory model of a high storage warehouse with a developed automatic control system. Benefits of the proposed solutions was shown in the conclusions.

  20. Reliability in Warehouse-Scale Computing: Why Low Latency Matters

    DEFF Research Database (Denmark)

    Nannarelli, Alberto

    2015-01-01

    , the limiting factor of these warehouse-scale data centers is the power dissipation. Power is dissipated not only in the computation itself, but also in heat removal (fans, air conditioning, etc.) to keep the temperature of the devices within the operating ranges. The need to keep the temperature low within......Warehouse sized buildings are nowadays hosting several types of large computing systems: from supercomputers to large clusters of servers to provide the infrastructure to the cloud. Although the main target, especially for high-performance computing, is still to achieve high throughput...

  1. A study of multidimensional modeling approaches for data warehouse

    Science.gov (United States)

    Yusof, Sharmila Mat; Sidi, Fatimah; Ibrahim, Hamidah; Affendey, Lilly Suriani

    2016-08-01

    Data warehouse system is used to support the process of organizational decision making. Hence, the system must extract and integrate information from heterogeneous data sources in order to uncover relevant knowledge suitable for decision making process. However, the development of data warehouse is a difficult and complex process especially in its conceptual design (multidimensional modeling). Thus, there have been various approaches proposed to overcome the difficulty. This study surveys and compares the approaches of multidimensional modeling and highlights the issues, trend and solution proposed to date. The contribution is on the state of the art of the multidimensional modeling design.

  2. Occupational lifting by nursing aides and warehouse workers.

    Science.gov (United States)

    Ljungberg, A S; Kilbom, A; Hägg, G M

    1989-01-01

    Nursing aides (18 women and six men) at one traditional and one modern geriatric ward, and warehouse workers (16 men) at two different types of warehouse departments were studied during occupational work. The vertical load during manual handling was measured using strain gauges built into wooden shoes. The warehouse workers performed four times as many lifts as the nursing aides and transferred five times as great a mass per unit time. Less than 25% of the lifts were carried out with the load evenly distributed on both feet during both the upward lift and lowering. In the warehouses the lifts were short, while the nursing aides were exposed both to lifts of longer duration and to carrying, as well as a greater frequency of unexpected, sudden and high peak load. The heart rate and oxygen uptake values recorded were relatively low, and both groups utilized approximately 25% of their maximum aerobic power. According to official occupational injury statistics, both warehouse workers and nursing aides belong to risk groups with a high frequency of reported back injuries. However, more injuries are reported by nursing aides than by warehouse workers. Greater muscle strength in male workers may partly explain this difference. Qualitative differences in the design of the lifting work, with more lifts of long duration in awkward work postures, more carrying, more exertion of horizontal forces and a greater frequency of unexpected rapid lifts in the nursing aides may also contribute to the differences in risk of injury between these occupational groups. Considerable differences were found between the two hospital wards as regards lifting frequency, force, duration and the proportion of lifts with an even distribution of load on both feet during upward lift. The lifting work was approximately 50% less in the modern ward, which has easily maneuvered electric overhead hoists, spacious premises and better work organization than in the traditional ward, even though the patient

  3. Mastering data warehouse design relational and dimensional techniques

    CERN Document Server

    Imhoff, Claudia; Geiger, Jonathan G

    2003-01-01

    A cutting-edge response to Ralph Kimball''s challenge to the data warehouse community that answers some tough questions about the effectiveness of the relational approach to data warehousingWritten by one of the best-known exponents of the Bill Inmon approach to data warehousingAddresses head-on the tough issues raised by Kimball and explains how to choose the best modeling technique for solving common data warehouse design problemsWeighs the pros and cons of relational vs. dimensional modeling techniquesFocuses on tough modeling problems, including creating and maintaining keys and modeling c

  4. Bioinformatics in microbial biotechnology – a mini review

    Directory of Open Access Journals (Sweden)

    Bansal Arvind K

    2005-06-01

    Full Text Available Abstract The revolutionary growth in the computation speed and memory storage capability has fueled a new era in the analysis of biological data. Hundreds of microbial genomes and many eukaryotic genomes including a cleaner draft of human genome have been sequenced raising the expectation of better control of microorganisms. The goals are as lofty as the development of rational drugs and antimicrobial agents, development of new enhanced bacterial strains for bioremediation and pollution control, development of better and easy to administer vaccines, the development of protein biomarkers for various bacterial diseases, and better understanding of host-bacteria interaction to prevent bacterial infections. In the last decade the development of many new bioinformatics techniques and integrated databases has facilitated the realization of these goals. Current research in bioinformatics can be classified into: (i genomics – sequencing and comparative study of genomes to identify gene and genome functionality, (ii proteomics – identification and characterization of protein related properties and reconstruction of metabolic and regulatory pathways, (iii cell visualization and simulation to study and model cell behavior, and (iv application to the development of drugs and anti-microbial agents. In this article, we will focus on the techniques and their limitations in genomics and proteomics. Bioinformatics research can be classified under three major approaches: (1 analysis based upon the available experimental wet-lab data, (2 the use of mathematical modeling to derive new information, and (3 an integrated approach that integrates search techniques with mathematical modeling. The major impact of bioinformatics research has been to automate the genome sequencing, automated development of integrated genomics and proteomics databases, automated genome comparisons to identify the genome function, automated derivation of metabolic pathways, gene

  5. Engaging Students in a Bioinformatics Activity to Introduce Gene Structure and Function

    Directory of Open Access Journals (Sweden)

    Barbara J. May

    2013-02-01

    Full Text Available Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools.  This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools.  Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the putative function of this gene with the use of additional online databases.

  6. Databases and QSAR for Cancer Research

    Directory of Open Access Journals (Sweden)

    Adeel Malik

    2006-01-01

    Full Text Available In this review, we take a survey of bioinformatics databases and quantitative structure-activity relationship studies reported in published literature. Databases from the most general to special cancer-related ones have been included. Most commonly used methods of structure-based analysis of molecules have been reviewed, along with some case studies where they have been used in cancer research. This article is expected to be of use for general bioinformatics researchers interested in cancer and will also provide an update to those who have been actively pursuing this field of research.

  7. Planning bioinformatics workflows using an expert system.

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T

    2017-04-15

    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. 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. https://github.com/jefftc/changlab. jeffrey.t.chang@uth.tmc.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  8. 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

  9. Embedded Systems Programming: Accessing Databases from Esterel

    Directory of Open Access Journals (Sweden)

    White David

    2008-01-01

    Full Text Available Abstract A current limitation in embedded controller design and programming is the lack of database support in development tools such as Esterel Studio. This article proposes a way of integrating databases and Esterel by providing two application programming interfaces (APIs which enable the use of relational databases inside Esterel programs. As databases and Esterel programs are often executed on different machines, result sets returned as responses to database queries may be processed either locally and according to Esterel's synchrony hypothesis, or remotely along several of Esterel's execution cycles. These different scenarios are reflected in the design and usage rules of the two APIs presented in this article, which rely on Esterel's facilities for extending the language by external data types, external functions, and procedures, as well as tasks. The APIs' utility is demonstrated by means of a case study modelling an automated warehouse storage system, which is constructed using Lego Mindstorms robotics kits. The robot's controller is programmed in Esterel in a way that takes dynamic ordering information and the warehouse's floor layout into account, both of which are stored in a MySQL database.

  10. Sustainable Transport Data Collection and Application: China Urban Transport Database

    OpenAIRE

    Tian Jiang; Zhongyi Wu; Yu Song; Xianglong Liu; Haode Liu; Haozhi Zhang

    2013-01-01

    Transport policy making process of national and local governments should be supported by a comprehensive database to ensure a sustainable and healthy development of urban transport. China Urban Transport Database (CUTD) has been built to play such a role. This paper is to make an introduction of CUTD framework including user management, data warehouse, and application modules. Considering the urban transport development features of Chinese cities, sustainable urban transport development indic...

  11. What is bioinformatics? A proposed definition and overview of the field.

    Science.gov (United States)

    Luscombe, N M; Greenbaum, D; Gerstein, M

    2001-01-01

    The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems. Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (e.g. expression data). Additional information includes the text of scientific papers and "relationship data" from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a wide range of computational techniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches integrating a variety of computational methods and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.

  12. 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

  13. Expiration of Historical Databases

    DEFF Research Database (Denmark)

    Toman, David

    2001-01-01

    We present a technique for automatic expiration of data in a historical data warehouse that preserves answers to a known and fixed set of first-order queries. In addition, we show that for queries with output size bounded by a function of the active data domain size (the number of values that have...... ever appeared in the warehouse), the size of the portion of the data warehouse history needed to answer the queries is also bounded by a function of the active data do-main size and therefore does not depend on the age of the warehouse (the length of the history)....

  14. Semantic integration of medication data into the EHOP Clinical Data Warehouse.

    Science.gov (United States)

    Delamarre, Denis; Bouzille, Guillaume; Dalleau, Kevin; Courtel, Denis; Cuggia, Marc

    2015-01-01

    Reusing medication data is crucial for many medical research domains. Semantic integration of such data in clinical data warehouse (CDW) is quite challenging. Our objective was to develop a reliable and scalable method for integrating prescription data into EHOP (a French CDW). PN13/PHAST was used as the semantic interoperability standard during the ETL process, and to store the prescriptions as documents in the CDW. Theriaque was used as a drug knowledge database (DKDB), to annotate the prescription dataset with the finest granularity, and to provide semantic capabilities to the EHOP query workbench. the system was evaluated on a clinical data set. Depending on the use case, the precision ranged from 52% to 100%, Recall was always 100%. interoperability standards and DKDB, document approach, and the finest granularity approach are the key factors for successful drug data integration in CDW.

  15. Selection of Forklift Unit for Warehouse Operation by Applying Multi-Criteria Analysis

    Directory of Open Access Journals (Sweden)

    Predrag Atanasković

    2013-07-01

    Full Text Available This paper presents research related to the choice of the criteria that can be used to perform an optimal selection of the forklift unit for warehouse operation. The analysis has been done with the aim of exploring the requirements and defining relevant criteria that are important when investment decision is made for forklift procurement, and based on the conducted research by applying multi-criteria analysis, to determine the appropriate parameters and their relative weights that form the input data and database for selection of the optimal handling unit. This paper presents an example of choosing the optimal forklift based on the selected criteria for the purpose of making the relevant investment decision.

  16. Risk control for staff planning in e-commerce warehouses

    NARCIS (Netherlands)

    Wruck, S.; Vis, I.F.A.; Boter, J.

    2017-01-01

    Internet sale supply chains often need to fulfil quickly small orders for many customers. The resulting high demand and planning uncertainties pose new challenges for e-commerce warehouse operations. Here, we develop a decision support tool to assist managers in selecting appropriate risk policies

  17. Risk control for staff planning in e-commerce warehouses

    NARCIS (Netherlands)

    Wruck, Susanne; Vis, Iris F A; Boter, Jaap

    2016-01-01

    Internet sale supply chains often need to fulfil quickly small orders for many customers. The resulting high demand and planning uncertainties pose new challenges for e-commerce warehouse operations. Here, we develop a decision support tool to assist managers in selecting appropriate risk policies

  18. Contextual snowflake modelling for pattern warehouse logical design

    Indian Academy of Sciences (India)

    presented the architecture of PWMS where patterns are managed in type tier and pattern tier layers. In this paper ... terns management techniques, languages or design methodologies for pattern warehouse. The concept of making the ... Several important specific implementation issues still need to be investigated. The work ...

  19. A novel approach for intelligent distribution of data warehouses

    Directory of Open Access Journals (Sweden)

    Abhay Kumar Agarwal

    2016-07-01

    Full Text Available With the continuous growth in the amount of data, data storage systems have come a long way from flat files systems to RDBMS, Data Warehousing (DW and Distributed Data Warehousing systems. This paper proposes a new distributed data warehouse model. The model is built on a novel approach, for the intelligent distribution of data warehouse. Overall the model is named as Intelligent and Distributed Data Warehouse (IDDW. The proposed model has N-levels and is based on top-down hierarchical design approach of building distributed data warehouse. The building process of IDDW starts with the identification of various locations where DW may be built. Initially, a single location is considered at top-most level of IDDW where DW is built. Thereafter, DW at any other location of any level may be built. A method, to transfer concerned data from any upper level DW to concerned lower level DW, is also presented in the paper. The paper also presents IDDW modeling, its architecture based on modeling, the internal organization of IDDW via which all the operations within IDDW are performed.

  20. How Can My State Benefit from an Educational Data Warehouse?

    Science.gov (United States)

    Bergner, Terry; Smith, Nancy J.

    2007-01-01

    Imagine if, at the start of the school year, a teacher could have detailed information about the academic history of every student in her or his classroom. This is possible if the teacher can log on to a Web site that provides access to an educational data warehouse. The teacher would see not only several years of state assessment results, but…

  1. Developing and Marketing a Client/Server-Based Data Warehouse.

    Science.gov (United States)

    Singleton, Michele; And Others

    1993-01-01

    To provide better access to information, the University of Arizona information technology center has designed a data warehouse accessible from the desktop computer. A team approach has proved successful in introducing and demonstrating a prototype to the campus community. (Author/MSE)

  2. Warehouse Management System a jeho implementace

    OpenAIRE

    Kovařík, Šimon

    2014-01-01

    This bachelor thesis deals with Warehouse management system and its implementation in certain company. The first theoretical part of this thesis describes WMS in general and its software solutions. The practical part analyzes particular solution KARAT WMS in company Novum, spol. s.r.o. and compares it with theoretical findings from first part.

  3. Data-driven warehouse optimization : Deploying skills of order pickers

    NARCIS (Netherlands)

    M. Matusiak (Marek); M.B.M. de Koster (René); J. Saarinen (Jari)

    2015-01-01

    textabstractBatching orders and routing order pickers is a commonly studied problem in many picker-to-parts warehouses. The impact of individual differences in picking skills on performance has received little attention. In this paper, we show that taking into account differences in the skills of

  4. An Improved Data Warehouse Architecture for SPGS, MAUTECH ...

    African Journals Online (AJOL)

    PROF. OLIVER OSUAGWA

    2015-06-01

    Jun 1, 2015 ... An Improved Data Warehouse Architecture for SPGS, MAUTECH, Yola,. Nigeria. Ibrahim Inuwa. 1 and E.J. Garba. 2. 1Department of Information Technology, Modibbo Adama University of Technology, Yola. Adamawa State Nigeria. ibrahiminuwa1985@gmail.com. +2348065273810. 2 Department of ...

  5. Annotation and retrieval in protein interaction databases

    Science.gov (United States)

    Cannataro, Mario; Hiram Guzzi, Pietro; Veltri, Pierangelo

    2014-06-01

    Biological databases have been developed with a special focus on the efficient retrieval of single records or the efficient computation of specialized bioinformatics algorithms against the overall database, such as in sequence alignment. The continuos production of biological knowledge spread on several biological databases and ontologies, such as Gene Ontology, and the availability of efficient techniques to handle such knowledge, such as annotation and semantic similarity measures, enable the development on novel bioinformatics applications that explicitly use and integrate such knowledge. After introducing the annotation process and the main semantic similarity measures, this paper shows how annotations and semantic similarity can be exploited to improve the extraction and analysis of biologically relevant data from protein interaction databases. As case studies, the paper presents two novel software tools, OntoPIN and CytoSeVis, both based on the use of Gene Ontology annotations, for the advanced querying of protein interaction databases and for the enhanced visualization of protein interaction networks.

  6. The Androgen Receptor Gene Mutations Database.

    Science.gov (United States)

    Gottlieb, B; Lehvaslaiho, H; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

    1998-01-01

    The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 272 to 309 in the past year. We have expanded the database: (i) by giving each entry an accession number; (ii) by adding information on the length of polymorphic polyglutamine (polyGln) and polyglycine (polyGly) tracts in exon 1; (iii) by adding information on large gene deletions; (iv) by providing a direct link with a completely searchable database (courtesy EMBL-European Bioinformatics Institute). The addition of the exon 1 polymorphisms is discussed in light of their possible relevance as markers for predisposition to prostate or breast cancer. The database is also available on the internet (http://www.mcgill. ca/androgendb/ ), from EMBL-European Bioinformatics Institute (ftp. ebi.ac.uk/pub/databases/androgen ), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca).

  7. Quality assessment of digital annotated ECG data from clinical trials by the FDA ECG Warehouse.

    Science.gov (United States)

    Sarapa, Nenad

    2007-09-01

    The FDA mandates that digital electrocardiograms (ECGs) from 'thorough' QTc trials be submitted into the ECG Warehouse in Health Level 7 extended markup language format with annotated onset and offset points of waveforms. The FDA did not disclose the exact Warehouse metrics and minimal acceptable quality standards. The author describes the Warehouse scoring algorithms and metrics used by FDA, points out ways to improve FDA review and suggests Warehouse benefits for pharmaceutical sponsors. The Warehouse ranks individual ECGs according to their score for each quality metric and produces histogram distributions with Warehouse-specific thresholds that identify ECGs of questionable quality. Automatic Warehouse algorithms assess the quality of QT annotation and duration of manual QT measurement by the central ECG laboratory.

  8. Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics

    DEFF Research Database (Denmark)

    Kouskoumvekaki, Irene; Shublaq, Nour; Brunak, Søren

    2014-01-01

    As both the amount of generated biological data and the processing compute power increase, computational experimentation is no longer the exclusivity of bioinformaticians, but it is moving across all biomedical domains. For bioinformatics to realize its translational potential, domain experts need...... access to user-friendly solutions to navigate, integrate and extract information out of biological databases, as well as to combine tools and data resources in bioinformatics workflows. In this review, we present services that assist biomedical scientists in incorporating bioinformatics tools...... into their research.We review recent applications of Cytoscape, BioGPS and DAVID for data visualization, integration and functional enrichment. Moreover, we illustrate the use of Taverna, Kepler, GenePattern, and Galaxy as open-access workbenches for bioinformatics workflows. Finally, we mention services...

  9. Multidimensional Databases and Data Warehousing

    DEFF Research Database (Denmark)

    Jensen, Christian S.; Pedersen, Torben Bach; Thomsen, Christian

    The present book's subject is multidimensional data models and data modeling concepts as they are applied in real data warehouses. The book aims to present the most important concepts within this subject in a precise and understandable manner. The book's coverage of fundamental concepts includes...... data cubes and their elements, such as dimensions, facts, and measures and their representation in a relational setting; it includes architecture-related concepts; and it includes the querying of multidimensional databases. The book also covers advanced multidimensional concepts that are considered...... techniques that are particularly important to multidimensional databases, including materialized views, bitmap indices, join indices, and star join processing. The book ends with a chapter that presents the literature on which the book is based and offers further readings for those readers who wish to engage...

  10. A bioinformatics approach to marker development

    NARCIS (Netherlands)

    Tang, J.

    2008-01-01

    The thesis focuses on two bioinformatics research topics: the development of tools for an efficient and reliable identification of single nucleotides polymorphisms (SNPs) and polymorphic simple sequence repeats (SSRs) from expressed sequence tags (ESTs) (Chapter 2, 3 and 4), and the subsequent

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

    Indian Academy of Sciences (India)

    An integrative bioinformatics pipeline for the genomewide identification of novel porcine microRNA genes. Wei Fang, Na Zhou, Dengyun Li, Zhigang Chen, Pengfei Jiang and Deli Zhang. J. Genet. 92,587 593. Figure 1. Primary sequence of the predicted SSc-mir-2053 precursor and locations of some terms in the secondary ...

  12. Novel bioinformatic developments for exome sequencing

    NARCIS (Netherlands)

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

    2016-01-01

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

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

    Indian Academy of Sciences (India)

    2013-12-06

    Dec 6, 2013 ... The majority of miRNAs in pig (Sus scrofa), an impor- tant domestic animal, remain unknown. From this perspec- tive, we attempted the genomewide identification of novel porcine miRNAs. Here, we propose a novel integrative bioinformatics pipeline to identify conservative and non- conservative novel ...

  14. 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 ...

  15. 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.

  16. 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...

  17. "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).…

  18. 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...

  19. 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…

  20. Bioinformatics applications in proteomics data analysis

    NARCIS (Netherlands)

    Peng, M.

    2015-01-01

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

  1. 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

  2. Agile parallel bioinformatics workflow management using Pwrake.

    Science.gov (United States)

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

    2011-09-08

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

  3. Agile parallel bioinformatics workflow management using Pwrake

    Science.gov (United States)

    2011-01-01

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

  4. 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.

  5. Quantum Bio-Informatics IV

    Science.gov (United States)

    Accardi, Luigi; Freudenberg, Wolfgang; Ohya, Masanori

    2011-01-01

    The QP-DYN algorithms / L. Accardi, M. Regoli and M. Ohya -- Study of transcriptional regulatory network based on Cis module database / S. Akasaka ... [et al.] -- On Lie group-Lie algebra correspondences of unitary groups in finite von Neumann algebras / H. Ando, I. Ojima and Y. Matsuzawa -- On a general form of time operators of a Hamiltonian with purely discrete spectrum / A. Arai -- Quantum uncertainty and decision-making in game theory / M. Asano ... [et al.] -- New types of quantum entropies and additive information capacities / V. P. Belavkin -- Non-Markovian dynamics of quantum systems / D. Chruscinski and A. Kossakowski -- Self-collapses of quantum systems and brain activities / K.-H. Fichtner ... [et al.] -- Statistical analysis of random number generators / L. Accardi and M. Gabler -- Entangled effects of two consecutive pairs in residues and its use in alignment / T. Ham, K. Sato and M. Ohya -- The passage from digital to analogue in white noise analysis and applications / T. Hida -- Remarks on the degree of entanglement / D. Chruscinski ... [et al.] -- A completely discrete particle model derived from a stochastic partial differential equation by point systems / K.-H. Fichtner, K. Inoue and M. Ohya -- On quantum algorithm for exptime problem / S. Iriyama and M. Ohya -- On sufficient algebraic conditions for identification of quantum states / A. Jamiolkowski -- Concurrence and its estimations by entanglement witnesses / J. Jurkowski -- Classical wave model of quantum-like processing in brain / A. Khrennikov -- Entanglement mapping vs. quantum conditional probability operator / D. Chruscinski ... [et al.] -- Constructing multipartite entanglement witnesses / M. Michalski -- On Kadison-Schwarz property of quantum quadratic operators on M[symbol](C) / F. Mukhamedov and A. Abduganiev -- On phase transitions in quantum Markov chains on Cayley Tree / L. Accardi, F. Mukhamedov and M. Saburov -- Space(-time) emergence as symmetry breaking effect / I. Ojima

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

    Science.gov (United States)

    Hiew, Hong Liang; Bellgard, Matthew

    2007-11-01

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

  7. Data warehouse governance programs in healthcare settings: a literature review and a call to action.

    Science.gov (United States)

    Elliott, Thomas E; Holmes, John H; Davidson, Arthur J; La Chance, Pierre-Andre; Nelson, Andrew F; Steiner, John F

    2013-01-01

    Given the extensive data stored in healthcare data warehouses, data warehouse governance policies are needed to ensure data integrity and privacy. This review examines the current state of the data warehouse governance literature as it applies to healthcare data warehouses, identifies knowledge gaps, provides recommendations, and suggests approaches for further research. A comprehensive literature search using five data bases, journal article title-search, and citation searches was conducted between 1997 and 2012. Data warehouse governance documents from two healthcare systems in the USA were also reviewed. A modified version of nine components from the Data Governance Institute Framework for data warehouse governance guided the qualitative analysis. Fifteen articles were retrieved. Only three were related to healthcare settings, each of which addressed only one of the nine framework components. Of the remaining 12 articles, 10 addressed between one and seven framework components and the remainder addressed none. Each of the two data warehouse governance plans obtained from healthcare systems in the USA addressed a subset of the framework components, and between them they covered all nine. While published data warehouse governance policies are rare, the 15 articles and two healthcare organizational documents reviewed in this study may provide guidance to creating such policies. Additional research is needed in this area to ensure that data warehouse governance polices are feasible and effective. The gap between the development of data warehouses in healthcare settings and formal governance policies is substantial, as evidenced by the sparse literature in this domain.

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

    African Journals Online (AJOL)

    The aim of this review is to discuss the importance of bioinformatics and emphasize the need to acquire bioinformatics training and skills so as to maximize its potentials for improved delivery of animal health. In this review, bioinformatics is introduced, challenges to effective animal disease diagnosis, prevention and control, ...

  9. 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…

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

    Science.gov (United States)

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

    2016-12-22

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

  11. The eBioKit, a stand-alone educational platform for bioinformatics.

    Science.gov (United States)

    Hernández-de-Diego, Rafael; de Villiers, Etienne P; Klingström, Tomas; Gourlé, Hadrien; Conesa, Ana; Bongcam-Rudloff, Erik

    2017-09-01

    Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.

  12. 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...... changes. These methods have been developed further and applied for computational screens of genomic sequence. Furthermore, a number of additional directions have emerged. These include methods to search for RNA 3D structure, RNA-RNA interactions, and design of interfering RNAs (RNAi) as well as methods...... 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....

  13. Routing Optimization of Intelligent Vehicle in Automated Warehouse

    Directory of Open Access Journals (Sweden)

    Yan-cong Zhou

    2014-01-01

    Full Text Available Routing optimization is a key technology in the intelligent warehouse logistics. In order to get an optimal route for warehouse intelligent vehicle, routing optimization in complex global dynamic environment is studied. A new evolutionary ant colony algorithm based on RFID and knowledge-refinement is proposed. The new algorithm gets environmental information timely through the RFID technology and updates the environment map at the same time. It adopts elite ant kept, fallback, and pheromones limitation adjustment strategy. The current optimal route in population space is optimized based on experiential knowledge. The experimental results show that the new algorithm has higher convergence speed and can jump out the U-type or V-type obstacle traps easily. It can also find the global optimal route or approximate optimal one with higher probability in the complex dynamic environment. The new algorithm is proved feasible and effective by simulation results.

  14. Capturing Complex Multidimensional Data in Location-Based Data Warehouses

    DEFF Research Database (Denmark)

    Timko, Igor; Pedersen, Torben Bach

    2004-01-01

    Motivated by the increasing need to handle complex multidimensional data inlocation-based data warehouses, this paper proposes apowerful data model that is able to capture the complexities of such data. The model provides a foundation for handling complex transportationinfrastructures and the att...... and the attached static and dynamic content,and performing queries on this data. The model is motivated with a comprehensive real-world case study, basedon our collaboration with a leading Danish vendor of location-based services.......Motivated by the increasing need to handle complex multidimensional data inlocation-based data warehouses, this paper proposes apowerful data model that is able to capture the complexities of such data. The model provides a foundation for handling complex transportationinfrastructures...

  15. Saccharomyces genome database informs human biology

    OpenAIRE

    Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Hellerstedt, Sage T; Engel, Stacia R; Karra, Kalpana; Weng, Shuai; Sheppard, Travis K; Binkley, Gail; Simison, Matt; Miyasato, Stuart R; Cherry, J Michael

    2017-01-01

    Abstract The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and...

  16. VLSI Microsystem for Rapid Bioinformatic Pattern Recognition

    Science.gov (United States)

    Fang, Wai-Chi; Lue, Jaw-Chyng

    2009-01-01

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

  17. 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

  18. 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

  19. 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

  20. ballaxy: web services for structural bioinformatics.

    Science.gov (United States)

    Hildebrandt, Anna Katharina; Stöckel, Daniel; Fischer, Nina M; de la Garza, Luis; Krüger, Jens; Nickels, Stefan; Röttig, Marc; Schärfe, Charlotta; Schumann, Marcel; Thiel, Philipp; Lenhof, Hans-Peter; Kohlbacher, Oliver; Hildebrandt, Andreas

    2015-01-01

    Web-based workflow systems have gained considerable momentum in sequence-oriented bioinformatics. In structural bioinformatics, however, such systems are still relatively rare; while commercial stand-alone workflow applications are common in the pharmaceutical industry, academic researchers often still rely on command-line scripting to glue individual tools together. In this work, we address the problem of building a web-based system for workflows in structural bioinformatics. For the underlying molecular modelling engine, we opted for the BALL framework because of its extensive and well-tested functionality in the field of structural bioinformatics. The large number of molecular data structures and algorithms implemented in BALL allows for elegant and sophisticated development of new approaches in the field. We hence connected the versatile BALL library and its visualization and editing front end BALLView with the Galaxy workflow framework. The result, which we call ballaxy, enables the user to simply and intuitively create sophisticated pipelines for applications in structure-based computational biology, integrated into a standard tool for molecular modelling.  ballaxy consists of three parts: some minor modifications to the Galaxy system, a collection of tools and an integration into the BALL framework and the BALLView application for molecular modelling. Modifications to Galaxy will be submitted to the Galaxy project, and the BALL and BALLView integrations will be integrated in the next major BALL release. After acceptance of the modifications into the Galaxy project, we will publish all ballaxy tools via the Galaxy toolshed. In the meantime, all three components are available from http://www.ball-project.org/ballaxy. Also, docker images for ballaxy are available at https://registry.hub.docker.com/u/anhi/ballaxy/dockerfile/. ballaxy is licensed under the terms of the GPL. © The Author 2014. Published by Oxford University Press. All rights reserved. For

  1. THE DEVELOPMENT OF THE APPLICATION OF A DATA WAREHOUSE AT PT JKL

    Directory of Open Access Journals (Sweden)

    Choirul Huda

    2012-05-01

    Full Text Available One rapidly evolving technology today is information technology, which can help decision-making in an organization or a company. The data warehouse is one form of information technology that supports those needs, as one of the right solutions for companies in decision-making. The objective of this research is the development of a data warehouse at PT JKL in order to support executives in analyzing the organization and support the decision-making process. Methodology of this research is conducting interview with related units, literature study and document examination. This research also used the Nine Step Methodology developed by Kimball to design the data warehouse. The results obtained is an application that can summarize the data warehouse, integrating and presenting historical data in multidimensional. The conclusion from this research is the data warehouse can help companies to analyze data in a flexible, fast, and effective data access.Keywords: Data Warehouse; Inventory; Contract Approval; Inventory; Dashboard

  2. Application genetic algorithms for load management in refrigerated warehouses with wind power penetration

    DEFF Research Database (Denmark)

    Zong, Yi; Cronin, Tom; Gehrke, Oliver

    2009-01-01

    Wind energy is produced at random times, whereas the energy consumption pattern shows distinct demand peaks during day-time and low levels during the night. The use of a refrigerated warehouse as a giant battery for wind energy is a new possibility that is being studied for wind energy integration...... as well as a way to store electricity produced during night-time by wind turbines. The controller for load management in a refrigerated warehouse with wind power penetration by GA-based is introduced in this paper. The objective function is to minimize the energy consumption for operating the refrigerated...... warehouse. It can be seen that the GA-based control strategy achieves feasible results for operating the temperature in refrigerated warehouse. Balancing the wind power production with refrigerated warehouse load management promises to be a clean and cost effective method. For refrigerated warehouse owners...

  3. Feasibility study for the project of a radioactive waste warehouse design and implementation in Madagascar- INSTN

    International Nuclear Information System (INIS)

    RALAIVELO, M.A.L

    2007-01-01

    The objective of this work is to design a standardized warehouse making possible to manage and store the radioactive waste of the INSTN (Madagascar-INSTN). For that, the principles and fundamental rules of management of radioactive waste are considered according to their nature: pre-treatment, treatment and conditioning. Then, the different types of waste storage are treated: surface storage, semi deep storage and deep storage. This last part was devoted to prepare a comparative study quality/price between the two types of warehouses: surface waste warehouse and semi deep waste warehouse. It is noted that the semi deep warehouse is much more efficient with regard to radiation. However the protection use of such warehouse is not practical due to the fact that is completely buried. [fr

  4. Warehouse multipoint temperature and humidity monitoring system design based on Kingview

    Science.gov (United States)

    Ou, Yanghui; Wang, Xifu; Liu, Jingyun

    2017-04-01

    Storage is the key link of modern logistics. Warehouse environment monitoring is an important part of storage safety management. To meet the storage requirements of different materials, guarantee their quality in the greatest extent, which has great significance. In the warehouse environment monitoring, the most important parameters are air temperature and relative humidity. In this paper, a design of warehouse multipoint temperature and humidity monitoring system based on King view, which realizes the multipoint temperature and humidity data real-time acquisition, monitoring and storage in warehouse by using temperature and humidity sensor. Also, this paper will take the bulk grain warehouse as an example and based on the data collected in real-time monitoring, giving the corresponding expert advice that combined with the corresponding algorithm, providing theoretical guidance to control the temperature and humidity in grain warehouse.

  5. 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

  6. 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.

  7. The ATLAS Distributed Data Management System & Databases

    CERN Document Server

    Garonne, V; The ATLAS collaboration; Barisits, M; Beermann, T; Vigne, R; Serfon, C

    2013-01-01

    The ATLAS Distributed Data Management (DDM) System is responsible for the global management of petabytes of high energy physics data. The current system, DQ2, has a critical dependency on Relational Database Management Systems (RDBMS), like Oracle. RDBMS are well-suited to enforcing data integrity in online transaction processing applications, however, concerns have been raised about the scalability of its data warehouse-like workload. In particular, analysis of archived data or aggregation of transactional data for summary purposes is problematic. Therefore, we have evaluated new approaches to handle vast amounts of data. We have investigated a class of database technologies commonly referred to as NoSQL databases. This includes distributed filesystems, like HDFS, that support parallel execution of computational tasks on distributed data, as well as schema-less approaches via key-value stores, like HBase. In this talk we will describe our use cases in ATLAS, share our experiences with various databases used ...

  8. Data Warehouse Design from HL7 Clinical Document Architecture Schema.

    Science.gov (United States)

    Pecoraro, Fabrizio; Luzi, Daniela; Ricci, Fabrizio L

    2015-01-01

    This paper proposes a semi-automatic approach to extract clinical information structured in a HL7 Clinical Document Architecture (CDA) and transform it in a data warehouse dimensional model schema. It is based on a conceptual framework published in a previous work that maps the dimensional model primitives with CDA elements. Its feasibility is demonstrated providing a case study based on the analysis of vital signs gathered during laboratory tests.

  9. Warehouse Redesign Process: A case study at Enics Sweden AB

    OpenAIRE

    Daraei, Maryam

    2013-01-01

    Nowadays warehousing became one of the most important and critical part in supply chain systems due to the fact that it consumes a considerable part of logistic cost. Designing phase of warehousing system is the most important part in warehousing since most of the strategic and tactical decisions should be taken in this phase. Majority of academic papers are primarily analysis oriented and does not give a systematic method and techniques as a basis for warehouse redesign. So there is a need t...

  10. Bioinformatics training: a review of challenges, actions and support requirements.

    Science.gov (United States)

    Schneider, Maria Victoria; Watson, James; Attwood, Teresa; Rother, Kristian; Budd, Aidan; McDowall, Jennifer; Via, Allegra; Fernandes, Pedro; Nyronen, Tommy; Blicher, Thomas; Jones, Phil; Blatter, Marie-Claude; De Las Rivas, Javier; Judge, David Phillip; van der Gool, Wouter; Brooksbank, Cath

    2010-11-01

    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 Trainer Networking Session held under the auspices of the EU-funded SLING Integrating Activity, which took place in November 2009.

  11. 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...

  12. DFVF: database of fungal virulence factors

    Science.gov (United States)

    Lu, Tao; Yao, Bo; Zhang, Chi

    2012-01-01

    Fungal pathogens cause various diseases for plant and animal hosts. Despite the extensive impact of fungi on human health and life, the threats posed by emerging fungal pathogens are poorly understood. Specifically, there exist few fungal virulence gene databases, which prevent effective bioinformatics studies on fungal pathogens. Therefore, we constructed a comprehensive online database of known fungal virulence factors, which collected 2058 pathogenic genes produced by 228 fungal strains from 85 genera. This database creates a pivotal platform capable of stimulating and facilitating further bench studies on fungal pathogens. Database URL: http://sysbio.unl.edu/DFVF/ PMID:23092926

  13. PENGEMBANGAN DATA WAREHOUSE DAN ON-LINE ANALYTICAL PROCESSING (OLAP UNTUK PENEMUAN INFORMASI DAN ANALISIS DATA (Studi Kasus : Sistem Informasi Penerimaan Mahasiswa Baru STMIK AMIKOM PURWOKERTO

    Directory of Open Access Journals (Sweden)

    Giat Karyono

    2011-08-01

    databases (OLTP SIPMB process of creating a data warehouse is done on different machines by performing replicate of the database used SIPMB. For the needs of the application is made data analysis OLAP PMB. These applications could present multidimensional data in grid view. Analysis of these data may include analysis of specialization in new student enrollment based on the period of new admissions, enrollment surge, home school, home province and district, Pengembangan Data Warehouse dan On-line Analytical Processing (OLAP Untuk Penemuan Informasi Dan Analisis DataJurnal Telematika Vol. 4 No.2 Agustus 2011 14registration information, day, month, or year. So that the results of data analysis can be the management in determining the appropriate marketing strategies to increase the number of freshmen applicants either currently running or for admission in the coming year.

  14. toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research.

    Science.gov (United States)

    Rhee, David B; Croken, Matthew McKnight; Shieh, Kevin R; Sullivan, Julie; Micklem, Gos; Kim, Kami; Golden, Aaron

    2015-01-01

    Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that must monitor for changes in the host environment and respond accordingly; however, it is still not fully known which genetic or epigenetic factors are involved in regulating virulence traits of T. gondii. There are on-going efforts to elucidate the mechanisms regulating the stage transition process via the application of high-throughput epigenomics, genomics and proteomics techniques. Given the range of experimental conditions and the typical yield from such high-throughput techniques, a new challenge arises: how to effectively collect, organize and disseminate the generated data for subsequent data analysis. Here, we describe toxoMine, which provides a powerful interface to support sophisticated integrative exploration of high-throughput experimental data and metadata, providing researchers with a more tractable means toward understanding how genetic and/or epigenetic factors play a coordinated role in determining pathogenicity of T. gondii. As a data warehouse, toxoMine allows integration of high-throughput data sets with public T. gondii data. toxoMine is also able to execute complex queries involving multiple data sets with straightforward user interaction. Furthermore, toxoMine allows users to define their own parameters during the search process that gives users near-limitless search and query capabilities. The interoperability feature also allows users to query and examine data available in other InterMine systems, which would effectively augment the search scope beyond what is available to toxoMine. toxoMine complements the major community database ToxoDB by providing a data warehouse that enables more extensive integrative studies for T. gondii. Given all these factors, we believe it will become an indispensable resource to the greater infectious disease research community. © The Author(s) 2015. Published by Oxford University Press.

  15. Warehouse hazardous and toxic waste design in Karingau Balikpapan

    Science.gov (United States)

    Pratama, Bayu Rendy; Kencanawati, Martheana

    2017-11-01

    PT. Balikpapan Environmental Services (PT. BES) is company that having core business in Hazardous and Toxic Waste Management Services which consisting storage and transporter at Balikpapan. This research starting with data collection such as type of waste, quantity of waste, dimension area of existing building, waste packaging (Drum, IBC tank, Wooden Box, & Bulk Bag). Processing data that will be done are redesign for warehouse dimension and layout of position waste, specify of capacity, specify of quantity, type and detector placement, specify of quantity, type and fire extinguishers position which refers to Bapedal Regulation No. 01 In 1995, SNI 03-3985-2000, Employee Minister Regulation RI No. Per-04/Men/1980. Based on research that already done, founded the design for warehouse dimension of waste is 23 m × 22 m × 5 m with waste layout position appropriate with type of waste. The necessary of quantity for detector on this waste warehouse design are 56 each. The type of fire extinguisher that appropriate with this design is dry powder which containing natrium carbonate, alkali salts, with having each weight of 12 Kg about 18 units.

  16. Unexpected levels and movement of radon in a large warehouse

    International Nuclear Information System (INIS)

    Gammage, R.B.; Espinosa, G.

    2004-01-01

    Alpha-track detectors, used in screening for radon, identified a large warehouse with levels of radon as high as 20 p Ci/l. This circumstance was unexpected because large bay doors were left open for much of the day to admit 1 8-wheeler trucks, and exhaust fans in the roof produced good ventilation. More detailed temporal and spatial investigations of radon and air-flow patterns were made with electret chambers, Lucas-cell flow chambers, tracer gas, smoke pencils and pressure sensing micrometers. An oval-dome shaped zone of radon (>4 p Ci/L) persisted in the central region of each of four separate bays composing the warehouse. Detailed studies of air movement in the bay with the highest levels of radon showed clockwise rotation of air near the outer walls with a central dead zone. Sub slab, radon-laden air ingresses the building through expansion joints between the floor slabs to produce the measured radon. The likely source of radon is air within porous, karst bedrock that underlies much of north-central Tennessee where the warehouse is situated

  17. What Information Does Your EHR Contain? Automatic Generation of a Clinical Metadata Warehouse (CMDW) to Support Identification and Data Access Within Distributed Clinical Research Networks.

    Science.gov (United States)

    Bruland, Philipp; Doods, Justin; Storck, Michael; Dugas, Martin

    2017-01-01

    Data dictionaries provide structural meta-information about data definitions in health information technology (HIT) systems. In this regard, reusing healthcare data for secondary purposes offers several advantages (e.g. reduce documentation times or increased data quality). Prerequisites for data reuse are its quality, availability and identical meaning of data. In diverse projects, research data warehouses serve as core components between heterogeneous clinical databases and various research applications. Given the complexity (high number of data elements) and dynamics (regular updates) of electronic health record (EHR) data structures, we propose a clinical metadata warehouse (CMDW) based on a metadata registry standard. Metadata of two large hospitals were automatically inserted into two CMDWs containing 16,230 forms and 310,519 data elements. Automatic updates of metadata are possible as well as semantic annotations. A CMDW allows metadata discovery, data quality assessment and similarity analyses. Common data models for distributed research networks can be established based on similarity analyses.

  18. Routing orderpickers in a warehouse: a comparison between optimal and heuristic solutions

    OpenAIRE

    Koster, René; Poort, van der, Edo

    1998-01-01

    textabstractThe problem of finding efficient orderpicking routes is studied for both conventional warehouses, where pickers have a central depot for picking up and depositing carts and pick lists, and modern warehouses, where orderpicking trucks can pick up and deposit pallets at the head of every aisle without returning to the depot. Such environments can be found in many warehouses where paperless picking is performed from pallet locations with pickers having mobile terminals receiving inst...

  19. Configuring Simulation Models Using CAD Techniques: A New Approach to Warehouse Design

    OpenAIRE

    Brito, A. E. S. C.

    1992-01-01

    The research reported in this thesis is related to the development and use of software tools for supporting warehouse design and management. Computer Aided Design and Simulation techniques are used to develop a software system that forms the basis of a Decision Support System for warehouse design. The current position of simulation software is reviewed. It is investigated how appropriate current simulation software is for warehouse modelling. Special attention is given to Vi...

  20. DIVERGENOME: a bioinformatics platform to assist population genetics and genetic epidemiology studies.

    Science.gov (United States)

    Magalhães, Wagner C S; Rodrigues, Maíra R; Silva, Donnys; Soares-Souza, Giordano; Iannini, Márcia L; Cerqueira, Gustavo C; Faria-Campos, Alessandra C; Tarazona-Santos, Eduardo

    2012-05-01

    Large-scale genomics initiatives such as the HapMap project and the 1000-genomes rely on powerful bioinformatics support to assist data production and analysis. Contrastingly, few bioinformatics platforms oriented to smaller research groups exist to store, handle, share, and integrate data from different sources, as well as to assist these scientists to perform their analyses efficiently. We developed such a bioinformatics platform, DIVERGENOME, to assist population genetics and genetic epidemiology studies performed by small- to medium-sized research groups. The platform is composed of two integrated components, a relational database (DIVERGENOMEdb), and a set of tools to convert data formats as required by popular software in population genetics and genetic epidemiology (DIVERGENOMEtools). In DIVERGENOMEdb, information on genotypes, polymorphism, laboratory protocols, individuals, populations, and phenotypes is organized in projects. These can be queried according to permissions. Here, we validated DIVERGENOME through a use case regarding the analysis of SLC2A4 genetic diversity in human populations. DIVERGENOME, with its intuitive Web interface and automatic data loading capability, facilitates its use by individuals without bioinformatics background, allowing complex queries to be easily interrogated and straightforward data format conversions (not available in similar platforms). DIVERGENOME is open source, freely available, and can be accessed online (pggenetica.icb.ufmg.br/divergenome) or hosted locally. © 2012 Wiley Periodicals, Inc.

  1. Research on Warehouse Target Localization and Tracking Based on KF and WSN

    Directory of Open Access Journals (Sweden)

    Guang-Rong BIAN

    2014-01-01

    Full Text Available This paper firstly established the model of warehouse targeting and tracking system based on Wireless Sensor Networks (WSN. The principle of Location and tracking is based on the maximum likelihood estimation method of multilateral measurement. According to monitoring motion trajectory of the same unknown target node within a continuous period of time, the motion equation can be established. It can achieve the effective tracking of warehouse target that KF algorithm is applied to carrying out the state estimation of warehouse target motion equation. Simulation results show that, while the warehouse target tracking system state equations are linear, using KF algorithm can obtain satisfactory tracking accuracy.

  2. Proposed Quality Evaluation Framework to Incorporate Quality Aspects in Web Warehouse Creation

    OpenAIRE

    Shah, Umm-e-Mariya; Shaikh, Maqbool Uddin; Shamim, Azra; Mehmood, Yasir

    2011-01-01

    Web Warehouse is a read only repository maintained on the web to effectively handle the relevant data. Web warehouse is a system comprised of various subsystems and process. It supports the organizations in decision making. Quality of data store in web warehouse can affect the quality of decision made. For a valuable decision making it is required to consider the quality aspects in designing and modelling of a web warehouse. Thus data quality is one of the most important issues of the web war...

  3. Two warehouse inventory model for deteriorating item with exponential demand rate and permissible delay in payment

    Directory of Open Access Journals (Sweden)

    Kaliraman Naresh Kumar

    2017-01-01

    Full Text Available A two warehouse inventory model for deteriorating items is considered with exponential demand rate and permissible delay in payment. Shortage is not allowed and deterioration rate is constant. In the model, one warehouse is rented and the other is owned. The rented warehouse is provided with better facility for the stock than the owned warehouse, but is charged more. The objective of this model is to find the best replenishment policies for minimizing the total appropriate inventory cost. A numerical illustration and sensitivity analysis is provided.

  4. Deteksi Outlier Transaksi Menggunakan Visualisasi-Olap Pada Data Warehouse Perguruan Tinggi Swasta

    Directory of Open Access Journals (Sweden)

    Gusti Ngurah Mega Nata

    2016-07-01

    Full Text Available Mendeteksi outlier pada data warehouse merupakan hal penting. Data pada data warehouse sudah diagregasi dan memiliki model multidimensional. Agregasi pada data warehouse dilakukan karena data warehouse digunakan untuk menganalisis data secara cepat pada top level manajemen. Sedangkan, model data multidimensional digunakan untuk melihat data dari berbagai dimensi objek bisnis. Jadi, Mendeteksi outlier pada data warehouse membutuhkan teknik yang dapat melihat outlier pada data yang sudah diagregasi dan dapat melihat dari berbagai dimensi objek bisnis. Mendeteksi outlier pada data warehouse akan menjadi tantangan baru.        Di lain hal, Visualisasi On-line Analytic process (OLAP merupakan tugas penting dalam menyajikan informasi trend (report pada data warehouse dalam bentuk visualisasi data. Pada penelitian ini, visualisasi OLAP digunakan untuk deteksi outlier transaksi. Maka, dalam penelitian ini melakukan analisis untuk mendeteksi outlier menggunakan visualisasi-OLAP. Operasi OLAP yang digunakan yaitu operasi drill-down. Jenis visualisasi yang akan digunakan yaitu visualisasi satu dimensi, dua dimensi dan multi dimensi menggunakan tool weave desktop. Pembangunan data warehouse dilakukan secara button-up. Studi kasus dilakukan pada perguruan tinggi swasta. Kasus yang diselesaikan yaitu mendeteksi outlier transaki pembayaran mahasiswa pada setiap semester. Deteksi outlier pada visualisasi data menggunakan satu tabel dimensional lebih mudah dianalisis dari pada deteksi outlier pada visualisasi data menggunakan dua atau multi tabel dimensional. Dengan kata lain semakin banyak tabel dimensi yang terlibat semakin sulit analisis deteksi outlier yang dilakukan. Kata kunci — Deteksi Outlier,  Visualisasi OLAP, Data warehouse

  5. 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

  6. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN

    Science.gov (United States)

    2010-01-01

    Background 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. Results 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. Conclusions Bioinformatics curation and ontological

  7. REDfly: a Regulatory Element Database for Drosophila.

    Science.gov (United States)

    Gallo, Steven M; Li, Long; Hu, Zihua; Halfon, Marc S

    2006-02-01

    Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.

  8. The Visit-Data Warehouse: Enabling Novel Secondary Use of Health Information Exchange Data

    Science.gov (United States)

    Fleischman, William; Lowry, Tina; Shapiro, Jason

    2014-01-01

    Introduction/Objectives: Health Information Exchange (HIE) efforts face challenges with data quality and performance, and this becomes especially problematic when data is leveraged for uses beyond primary clinical use. We describe a secondary data infrastructure focusing on patient-encounter, nonclinical data that was built on top of a functioning HIE platform to support novel secondary data uses and prevent potentially negative impacts these uses might have otherwise had on HIE system performance. Background: HIE efforts have generally formed for the primary clinical use of individual clinical providers searching for data on individual patients under their care, but many secondary uses have been proposed and are being piloted to support care management, quality improvement, and public health. Description of the HIE and Base Infrastructure: This infrastructure review describes a module built into the Healthix HIE. Healthix, based in the New York metropolitan region, comprises 107 participating organizations with 29,946 acute-care beds in 383 facilities, and includes more than 9.2 million unique patients. The primary infrastructure is based on the InterSystems proprietary Caché data model distributed across servers in multiple locations, and uses a master patient index to link individual patients’ records across multiple sites. We built a parallel platform, the “visit data warehouse,” of patient encounter data (demographics, date, time, and type of visit) using a relational database model to allow accessibility using standard database tools and flexibility for developing secondary data use cases. These four secondary use cases include the following: (1) tracking encounter-based metrics in a newly established geriatric emergency department (ED), (2) creating a dashboard to provide a visual display as well as a tabular output of near-real-time de-identified encounter data from the data warehouse, (3) tracking frequent ED users as part of a regional-approach to

  9. The visit-data warehouse: enabling novel secondary use of health information exchange data.

    Science.gov (United States)

    Fleischman, William; Lowry, Tina; Shapiro, Jason

    2014-01-01

    Health Information Exchange (HIE) efforts face challenges with data quality and performance, and this becomes especially problematic when data is leveraged for uses beyond primary clinical use. We describe a secondary data infrastructure focusing on patient-encounter, nonclinical data that was built on top of a functioning HIE platform to support novel secondary data uses and prevent potentially negative impacts these uses might have otherwise had on HIE system performance. HIE efforts have generally formed for the primary clinical use of individual clinical providers searching for data on individual patients under their care, but many secondary uses have been proposed and are being piloted to support care management, quality improvement, and public health. This infrastructure review describes a module built into the Healthix HIE. Healthix, based in the New York metropolitan region, comprises 107 participating organizations with 29,946 acute-care beds in 383 facilities, and includes more than 9.2 million unique patients. The primary infrastructure is based on the InterSystems proprietary Caché data model distributed across servers in multiple locations, and uses a master patient index to link individual patients' records across multiple sites. We built a parallel platform, the "visit data warehouse," of patient encounter data (demographics, date, time, and type of visit) using a relational database model to allow accessibility using standard database tools and flexibility for developing secondary data use cases. These four secondary use cases include the following: (1) tracking encounter-based metrics in a newly established geriatric emergency department (ED), (2) creating a dashboard to provide a visual display as well as a tabular output of near-real-time de-identified encounter data from the data warehouse, (3) tracking frequent ED users as part of a regional-approach to case management intervention, and (4) improving an existing quality improvement program

  10. A central repository for gridded data in the MeteoSwiss Data Warehouse

    Science.gov (United States)

    Grueter, E.

    2010-09-01

    The significance of gridded data in meteorology and climatology has increased remarkably over the last years. New products of observing systems such as radars, improved interpolation techniques, spatial analyses or modeling procedures have already led to a proliferated amount of available grid data within the meteorological and climatological community. Since these products are generated by different systems the format in which they are delivered can vary quite much. To facilitate the combined use of different gridded data sets (f. ex. rain accumulation based on radar data and interpolated rainfall based on observations) MeteoSwiss decided to incorporate them in one central data repository. It's been the strategy of MeteoSwiss over the last ten years to store and manage all of its data in a single central data platform - the MeteoSwiss Data Warehouse - which is completely metadata driven. After the integration of all kind of historical and current surface data the system was extended in 2009 to store different types of upper air data. The last release of this Data Warehouse project focuses on grid data to complete MeteoSwiss' data integration strategy. This release comprises both the storage of different types of gridded datasets being delivered in various data formats into one single grid database and its data management. Here from datasets, which have originally been created in different data formats (f. ex. gif and netCDF), can be exported in whatever format is supported by the system. This procedure facilitates to a great extent the combined analyses of grid data originating in different data sources. Additionally interfaces to other software packages such as R allow direct access to the grid database. Web applications are implemented to allow users to carry out predefined spatial analyses such as spatial aggregation for a user specified extent of the dataset. After evaluating different solutions MeteoSwiss decided to implement its system using existing GIS

  11. Benefits of a clinical data warehouse with data mining tools to collect data for a radiotherapy trial

    International Nuclear Information System (INIS)

    Roelofs, Erik; Persoon, Lucas; Nijsten, Sebastiaan; Wiessler, Wolfgang; Dekker, André; Lambin, Philippe

    2013-01-01

    Introduction: Collecting trial data in a medical environment is at present mostly performed manually and therefore time-consuming, prone to errors and often incomplete with the complex data considered. Faster and more accurate methods are needed to improve the data quality and to shorten data collection times where information is often scattered over multiple data sources. The purpose of this study is to investigate the possible benefit of modern data warehouse technology in the radiation oncology field. Material and methods: In this study, a Computer Aided Theragnostics (CAT) data warehouse combined with automated tools for feature extraction was benchmarked against the regular manual data-collection processes. Two sets of clinical parameters were compiled for non-small cell lung cancer (NSCLC) and rectal cancer, using 27 patients per disease. Data collection times and inconsistencies were compared between the manual and the automated extraction method. Results: The average time per case to collect the NSCLC data manually was 10.4 ± 2.1 min and 4.3 ± 1.1 min when using the automated method (p < 0.001). For rectal cancer, these times were 13.5 ± 4.1 and 6.8 ± 2.4 min, respectively (p < 0.001). In 3.2% of the data collected for NSCLC and 5.3% for rectal cancer, there was a discrepancy between the manual and automated method. Conclusions: Aggregating multiple data sources in a data warehouse combined with tools for extraction of relevant parameters is beneficial for data collection times and offers the ability to improve data quality. The initial investments in digitizing the data are expected to be compensated due to the flexibility of the data analysis. Furthermore, successive investigations can easily select trial candidates and extract new parameters from the existing databases

  12. Benefits of a clinical data warehouse with data mining tools to collect data for a radiotherapy trial.

    Science.gov (United States)

    Roelofs, Erik; Persoon, Lucas; Nijsten, Sebastiaan; Wiessler, Wolfgang; Dekker, André; Lambin, Philippe

    2013-07-01

    Collecting trial data in a medical environment is at present mostly performed manually and therefore time-consuming, prone to errors and often incomplete with the complex data considered. Faster and more accurate methods are needed to improve the data quality and to shorten data collection times where information is often scattered over multiple data sources. The purpose of this study is to investigate the possible benefit of modern data warehouse technology in the radiation oncology field. In this study, a Computer Aided Theragnostics (CAT) data warehouse combined with automated tools for feature extraction was benchmarked against the regular manual data-collection processes. Two sets of clinical parameters were compiled for non-small cell lung cancer (NSCLC) and rectal cancer, using 27 patients per disease. Data collection times and inconsistencies were compared between the manual and the automated extraction method. The average time per case to collect the NSCLC data manually was 10.4 ± 2.1 min and 4.3 ± 1.1 min when using the automated method (pdata collected for NSCLC and 5.3% for rectal cancer, there was a discrepancy between the manual and automated method. Aggregating multiple data sources in a data warehouse combined with tools for extraction of relevant parameters is beneficial for data collection times and offers the ability to improve data quality. The initial investments in digitizing the data are expected to be compensated due to the flexibility of the data analysis. Furthermore, successive investigations can easily select trial candidates and extract new parameters from the existing databases. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  13. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

    Science.gov (United States)

    Rigden, Daniel J.; Fernández-Suárez, Xosé M.; Galperin, Michael Y.

    2016-01-01

    The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases. PMID:26740669

  14. Column-Oriented Databases, an Alternative for Analytical Environment

    Directory of Open Access Journals (Sweden)

    Gheorghe MATEI

    2010-12-01

    Full Text Available It is widely accepted that a data warehouse is the central place of a Business Intelligence system. It stores all data that is relevant for the company, data that is acquired both from internal and external sources. Such a repository stores data from more years than a transactional system can do, and offer valuable information to its users to make the best decisions, based on accurate and reliable data. As the volume of data stored in an enterprise data warehouse becomes larger and larger, new approaches are needed to make the analytical system more efficient. This paper presents column-oriented databases, which are considered an element of the new generation of DBMS technology. The paper emphasizes the need and the advantages of these databases for an analytical environment and make a short presentation of two of the DBMS built in a columnar approach.

  15. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  16. Bioinformatic analysis of whole genome sequencing data

    OpenAIRE

    Maqbool, Khurram

    2014-01-01

    Evolution has shaped the life forms for billion of years. Domestication is an accelerated process that can be used as a model for evolutionary changes. The aim of this thesis project has been to carry out extensive bioinformatic analyses of whole genome sequencing data to reveal SNPs, InDels and selective sweeps in the chicken, pig and dog genome. Pig genome sequencing revealed loci under selection for elongation of back and increased number of vertebrae, associated with the NR6A1, PLAG1,...

  17. Top considerations for creating bioinformatics software documentation.

    Science.gov (United States)

    Karimzadeh, Mehran; Hoffman, Michael M

    2017-01-14

    Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others. © The Author 2017. Published by Oxford University Press.

  18. 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.

  19. 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.

  20. 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.

  1. CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

    Directory of Open Access Journals (Sweden)

    Baumbach Jan

    2007-11-01

    Full Text Available Abstract Background Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user can be analyzed in the context of known

  2. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases such...

  3. Biofuel Database

    Science.gov (United States)

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  4. The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses

    Directory of Open Access Journals (Sweden)

    Sarah Torres

    2010-06-01

    Full Text Available Over the past 30 years, genomic and bioinformatic analysis of human adenoviruses has been achieved using a variety of DNA sequencing methods; initially with the use of restriction enzymes and more currently with the use of the GS FLX pyrosequencing technology. Following the conception of DNA sequencing in the 1970s, analysis of adenoviruses has evolved from 100 base pair mRNA fragments to entire genomes. Comparative genomics of adenoviruses made its debut in 1984 when nucleotides and amino acids of coding sequences within the hexon genes of two human adenoviruses (HAdV, HAdV–C2 and HAdV–C5, were compared and analyzed. It was determined that there were three different zones (1-393, 394-1410, 1411-2910 within the hexon gene, of which HAdV–C2 and HAdV–C5 shared zones 1 and 3 with 95% and 89.5% nucleotide identity, respectively. In 1992, HAdV-C5 became the first adenovirus genome to be fully sequenced using the Sanger method. Over the next seven years, whole genome analysis and characterization was completed using bioinformatic tools such as blastn, tblastx, ClustalV and FASTA, in order to determine key proteins in species HAdV-A through HAdV-F. The bioinformatic revolution was initiated with the introduction of a novel species, HAdV-G, that was typed and named by the use of whole genome sequencing and phylogenetics as opposed to traditional serology. HAdV bioinformatics will continue to advance as the latest sequencing technology enables scientists to add to and expand the resource databases. As a result of these advancements, how novel HAdVs are typed has changed. Bioinformatic analysis has become the revolutionary tool that has significantly accelerated the in-depth study of HAdV microevolution through comparative genomics.

  5. A web services choreography scenario for interoperating bioinformatics applications.

    Science.gov (United States)

    de Knikker, Remko; Guo, Youjun; Li, Jin-Long; Kwan, Albert K H; Yip, Kevin Y; Cheung, David W; Cheung, Kei-Hoi

    2004-03-10

    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. 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 with these web services using a web

  6. 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

  7. A web services choreography scenario for interoperating bioinformatics applications

    Science.gov (United States)

    de Knikker, Remko; Guo, Youjun; Li, Jin-long; Kwan, Albert KH; Yip, Kevin Y; Cheung, David W; Cheung, Kei-Hoi

    2004-01-01

    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 with these web

  8. Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course.

    Science.gov (United States)

    Luo, Jingchu

    2014-11-01

    With the development of the Internet and the growth of online resources, bioinformatics training for wet-lab biologists became necessary as a part of their education. This article describes a one-semester course 'Applied Bioinformatics Course' (ABC, http://abc.cbi.pku.edu.cn/) that the author has been teaching to biological graduate students at the Peking University and the Chinese Academy of Agricultural Sciences for the past 13 years. ABC is a hands-on practical course to teach students to use online bioinformatics resources to solve biological problems related to their ongoing research projects in molecular biology. With a brief introduction to the background of the course, detailed information about the teaching strategies of the course are outlined in the 'How to teach' section. The contents of the course are briefly described in the 'What to teach' section with some real examples. The author wishes to share his teaching experiences and the online teaching materials with colleagues working in bioinformatics education both in local and international universities. © The Author 2013. Published by Oxford University Press.

  9. 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…

  10. Database Administrator

    Science.gov (United States)

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  11. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

    Science.gov (United States)

    Babbitt, Patricia C; Bagos, Pantelis G; Bairoch, Amos; Bateman, Alex; Chatonnet, Arnaud; Chen, Mark Jinan; Craik, David J; Finn, Robert D; Gloriam, David; Haft, Daniel H; Henrissat, Bernard; Holliday, Gemma L; Isberg, Vignir; Kaas, Quentin; Landsman, David; Lenfant, Nicolas; Manning, Gerard; Nagano, Nozomi; Srinivasan, Narayanaswamy; O'Donovan, Claire; Pruitt, Kim D; Sowdhamini, Ramanathan; Rawlings, Neil D; Saier, Milton H; Sharman, Joanna L; Spedding, Michael; Tsirigos, Konstantinos D; Vastermark, Ake; Vriend, Gerrit

    2015-01-01

    During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

  12. Bioinformatics tools for predicting GPCR gene functions.

    Science.gov (United States)

    Suwa, Makiko

    2014-01-01

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

  13. 27 CFR 24.126 - Change in proprietorship involving a bonded wine warehouse.

    Science.gov (United States)

    2010-04-01

    ... involving a bonded wine warehouse. 24.126 Section 24.126 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS WINE Establishment and Operations Changes Subsequent to Original Establishment § 24.126 Change in proprietorship involving a bonded wine warehouse...

  14. Routing orderpickers in a warehouse: a comparison between optimal and heuristic solutions

    NARCIS (Netherlands)

    M.B.M. de Koster (René); E. Poort, van der (Edo)

    1998-01-01

    textabstractThe problem of finding efficient orderpicking routes is studied for both conventional warehouses, where pickers have a central depot for picking up and depositing carts and pick lists, and modern warehouses, where orderpicking trucks can pick up and deposit pallets at the head of every

  15. Routing orderpickers in a warehouse : a comparison between optimal and heuristic solutions

    NARCIS (Netherlands)

    De Koster, R; Van der Poort, E

    In this paper the problem of finding efficient orderpicking routes is studied for both conventional warehouses, where pickers have a central depot for picking up and depositing carts and pick lists, and modern warehouses, where orderpicking trucks can pick up and deposit pallets at the head of every

  16. Protocol for a national blood transfusion data warehouse from donor to recipient

    NARCIS (Netherlands)

    van Hoeven, Loan R; Hooftman, Babette H; Janssen, Mart P; de Bruijne, Martine C; de Vooght, Karen M K; Kemper, Peter; Koopman, Maria M W

    2016-01-01

    INTRODUCTION: Blood transfusion has health-related, economical and safety implications. In order to optimise the transfusion chain, comprehensive research data are needed. The Dutch Transfusion Data warehouse (DTD) project aims to establish a data warehouse where data from donors and transfusion

  17. On the question of the capacity of warehouses of packaged-piece cargoes

    Directory of Open Access Journals (Sweden)

    Ilesaliev D.I.

    2017-06-01

    Full Text Available Mathematical models are proposed that establish interrelations between the individual parameters of a warehouse of packaged piece cargo. The models were used in the study of the mutual influence of the parameters on each other, also the capacity of the warehouses of packaged cargo

  18. 27 CFR 28.244a - Shipment to a customs bonded warehouse.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Shipment to a customs... Export Consignment § 28.244a Shipment to a customs bonded warehouse. Distilled spirits and wine withdrawn for shipment to a customs bonded warehouse shall be consigned in care of the customs officer in charge...

  19. 27 CFR 28.27 - Entry of wine into customs bonded warehouses.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Entry of wine into customs... TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS EXPORTATION OF ALCOHOL Miscellaneous Provisions Customs Bonded Warehouses § 28.27 Entry of wine into customs bonded warehouses. Upon filing of the application or...

  20. 27 CFR 44.266 - Return of cigars from export warehouses.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 2 2010-04-01 2010-04-01 false Return of cigars from... CIGARETTE PAPERS AND TUBES, WITHOUT PAYMENT OF TAX, OR WITH DRAWBACK OF TAX Withdrawal of Cigars From Customs Warehouses Return of Shipment § 44.266 Return of cigars from export warehouses. Where cigars are...