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Experience using web services for biological sequence analysis
2008
Briefings in Bioinformatics
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of biological sequence analysis. ...
In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context ...
We thank Eric Jain and Jan Christian Bryne for useful discussions and feedback. ...
doi:10.1093/bib/bbn029
pmid:18621748
pmcid:PMC2989672
fatcat:pw4vx7rf5bfi7jtgkc5izrwrjq
Integrating biological research through Web services
2005
Computer
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Figure 1 shows the three Web services in the scenario and the data-analysis path to discover drug targets using these services. ...
Components a, b, and c are three service providers that provide Web services for the data analysis related to drug discovery. The numbered lines are the steps in the analysis path. ...
doi:10.1109/mc.2005.97
fatcat:pf7xaxiywjhlnki44smlbmd6x4
ZIB Structure Prediction Pipeline: Composing a Complex Biological Workflow Through Web Services
[chapter]
2006
Lecture Notes in Computer Science
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We will present the status of our efforts for the realization of an automated protein prediction pipeline as an example for a complex biological workflow scenario in a Grid environment based on Web services ...
The efficient management and use of these data, and its transformation into knowledge are basic requirements for biological research. ...
We would like to thank Falko Krause and Jonas Maaskola for their implementation of local Web services, and the Triana group at Cardiff University for their support. ...
doi:10.1007/11823285_121
fatcat:v2njy3wcurhdxobexljnlu3paa
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA
2015
PLoS ONE
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This pipeline uses the web services available for BLAST (Basis Local Search Alignment Tool), QuickGO and DAVID (Database for Annotation, Visualization and Integrated Discovery) tools. ...
RNA-seq is a new tool to measure RNA transcript counts, using high-throughput sequencing at an extraordinary accuracy. ...
Gennaro Oliva for the computational support and maintenance of the interomics cluster at ICAR-CNR and for his constant help in low level software installation and configuration. ...
doi:10.1371/journal.pone.0140268
pmid:26581084
pmcid:PMC4651556
fatcat:wnu6uvpljza4pfuonwyw6mpgu4
Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review
2008
Current Bioinformatics
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Semantic Web (section 2.1.1 [22-33]) Web Services (section 2.1.2 [34-42]) Web Agents (section 2.1.3 [57-60]) Grid-enabled Applications (section 2.2.1 [75-77]) Grid-based BioPortals (section 2.2.2 [66-70 ...
The use of computational and networking resources is thus unavoidable. ...
Technology Semantic Grid
(In-silico experiments)
HT Sequencing
HT Expression Analysis
HT Proteomics
HT Structure Analysis
Classical Grid Technology
(Pre-Web Service architecture)
Genome
Functional ...
doi:10.2174/157489308783329850
fatcat:thpj6eywwvg5tfdqvbw5nch3ty
Design of biological gene information collection system based on data mining technology
2020
Cellular and Molecular Biology
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The information analysis module analyzes the biological gene information and stores the information in the gene web analysis database. ...
The system hardware stores the biochip information in the virtual chip set model through the gene expression spectrum data analysis model uses the gene expression similarity analysis model to analyze the ...
(B) The system uses the web biological information analysis model based on multi-layer architecture to study biological information. ...
doi:10.14715/cmb/2020.66.7.15
fatcat:alei6mrkoneevfak2ncfie247m
The EMBL-EBI search and sequence analysis tools APIs in 2019
2019
Nucleic Acids Research
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Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+ ...
The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities ...
We would like to also thank all EMBL-EBI teams for their invaluable help in providing biological data, applications and expertise. ...
doi:10.1093/nar/gkz268
pmid:30976793
pmcid:PMC6602479
fatcat:ojioxdg3pna2bdvgeea5zhj5sm
Biocloud: Cloud Computing for Biological, Genomics, and Drug Design
2013
BioMed Research International
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We are grateful to all authors for their contributions and for undertaking two-cycle revisions of their manuscripts, without which this special issue could not have been produced. ...
Acknowledgments The guest editors would like to express sincere gratitude to numerous reviewers for their professional effort, insight, and hard work put into commenting on the selected articles which ...
The performance experiment shows that it is desirable for molecular biologists to investigate the protein structure and function analysis under reasonable time constraints by using our cloud service. ...
doi:10.1155/2013/909470
fatcat:xngyf4ec55dell72yjxnjzssuu
CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome data
2007
BMC Systems Biology
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Results: To facilitate the analysis of gene-regulatory networks, we have developed CoryneCenter, a web-based resource for the systematic integration and analysis of genome, transcriptome, and gene regulatory ...
The introduction of high-throughput genome sequencing and post-genome analysis technologies, e.g. ...
The authors further wish to thank Ralf Nolte for technical support. ...
doi:10.1186/1752-0509-1-55
pmid:18034885
pmcid:PMC2212648
fatcat:f5vtl5tginb3vd64wiltwdkfvu
A library-based bioinformatics services program
2000
Bulletin of the Medical Library Association
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Outcomes of this program include bioinformatics consultation services, library-based and graduate level courses, networking of sequence analysis tools, and a biological research Web site. ...
Support for molecular biology researchers has been limited to traditional library resources and services in most academic health sciences libraries. ...
ACKNOWLEDGMENTS The authors thank Catherine Burroughs for assistance with the Bioinformatics Series evaluation survey and helpful comments on the manuscript, and Doug Schaad for help with the analysis ...
pmid:10658962
pmcid:PMC35196
fatcat:pmauxzs5czcevemqhwibjk7jpe
A Service-Oriented Data Integration and Analysis Environment for In Silico Experiments and Bioinformatics Research
2007
2007 40th Annual Hawaii International Conference on System Sciences (HICSS'07)
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In this paper, we present a practical experiment of building a service-oriented system upon current web services technologies and bioinformatics middleware. ...
This can be difficult to accomplish using manual search tools since sequence data is rapidly accumulating. ...
Introduction As biological research is becoming increasingly data driven, scientists are conducting experiments using the cyberinfrastructure (in silico experiments) to gather information in public online ...
doi:10.1109/hicss.2007.33
dblp:conf/hicss/XiangMR07
fatcat:mjxqebq3cbdn3dwtc3w4wiygpy
THINK Back: KNowledge-based Interpretation of High Throughput data
2012
BMC Bioinformatics
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Our methods perform a thorough and rigorous analysis of biological pathways, using complex factors such as the topology of the pathway graph and the frequency in which genes appear on different pathways ...
, gene sequences, and next-generation sequences. ...
Glenn Tarcea for his valuable support and guidance during the development stages of the THINK-Back Web Services suite. ...
doi:10.1186/1471-2105-13-s2-s4
pmid:22536867
pmcid:PMC3375631
fatcat:jor24o4a2zb4dng5pi5kx6pfd4
ISPIDER Central: an integrated database web-server for proteomics
2008
Nucleic Acids Research
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ACKNOWLEDGEMENTS The authors thank the Biotechnology and Biological Sciences Research Council (BBSRC) for support, in the form of the ISPIDER grant to all (refs, BBSB17239, BBSB17220, BBSB17204), technical ...
support from Dr Nick Gresham and Eric W Deutsch of the ISB Seattle for assistance with PeptideAtlas. ...
invoke biological web services to add value to the identifications. ...
doi:10.1093/nar/gkn196
pmid:18440977
pmcid:PMC2447780
fatcat:hsrupcbi4zehxdhvvgnibenk7m
Bioinformatics clouds for big data manipulation
2012
Biology Direct
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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 ...
Jun Yu and Ang Li for their valuable comments on this work. ...
doi:10.1186/1745-6150-7-43
pmid:23190475
pmcid:PMC3533974
fatcat:plt5x7aqpbcofiddfyk23fl4gm
Bioinformatics: Basics, Development, and Future
[chapter]
2016
Bioinformatics - Updated Features and Applications
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and design; building biological networks; development of databases and data management systems; development of software and analysis tools; bioinformatics services and workflow; mining of biomedical literature ...
analysis of large volumes of molecular sequences of DNA, RNA, proteins, and metabolites. ...
There are several basic bioinformatics services, for example, "Sequence Search Services" (SSS), "Multiple Sequence Alignment" (MSA), and "Biological Sequence Analysis" (BSA) [2, 128] . ...
doi:10.5772/63817
fatcat:otwfgrcmgfdglibb5afk2oktce
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