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Experience using web services for biological sequence analysis

H. Stockinger, T. Attwood, S. N. Chohan, R. Cote, P. Cudre-Mauroux, L. Falquet, P. Fernandes, R. D. Finn, T. Hupponen, E. Korpelainen, A. Labarga, A. Laugraud (+6 others)
2008 Briefings in Bioinformatics  
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

H.T. Gao, J.H. Hayes, H. Cai
2005 Computer  
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]

Patrick May, Hans-Christian Ehrlich, Thomas Steinke
2006 Lecture Notes in Computer Science  
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

Kumar Parijat Tripathi, Daniela Evangelista, Antonio Zuccaro, Mario Rosario Guarracino, Yu Xue
2015 PLoS ONE  
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

Natalio Krasnogor, Azhar Shah, Daniel Barthel, Piotr Lukasiak, Jacek Blazewicz
2008 Current Bioinformatics  
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

Yuanjun Wu, Xiaotong Mu, Danial Kahrizi
2020 Cellular and Molecular Biology  
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  
Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (  ...  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

Ching-Hsien Hsu, Chun-Yuan Lin, Ming Ouyang, Yi Ke Guo
2013 BioMed Research International  
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

Heiko Neuweger, Jan Baumbach, Stefan Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, Jörn Kalinowski, Sebastian Oehm, Alfred Pühler, Sven Rahmann, Jochen Weile, Alexander Goesmann
2007 BMC Systems Biology  
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

S Yarfitz, D S Ketchell
2000 Bulletin of the Medical Library Association  
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

Xiaorong Xiang, Gregory Madey, Jeanne Romero-Severson
2007 2007 40th Annual Hawaii International Conference on System Sciences (HICSS'07)  
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

Fernando Farfán, Jun Ma, Maureen A Sartor, George Michailidis, Hosagrahar V Jagadish
2012 BMC Bioinformatics  
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

J. A. Siepen, K. Belhajjame, J. N. Selley, S. M. Embury, N. W. Paton, C. A. Goble, S. G. Oliver, R. Stevens, L. Zamboulis, N. Martin, A. Poulovassillis, P. Jones (+6 others)
2008 Nucleic Acids Research  
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

Lin Dai, Xin Gao, Yan Guo, Jingfa Xiao, Zhang Zhang
2012 Biology Direct  
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]

Ibrokhim Y. Abdurakhmonov
2016 Bioinformatics - Updated Features and Applications  
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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