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Public web-based services from the European Bioinformatics Institute

N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen, R. Lopez
2004 Nucleic Acids Research  
The mission of the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL) in Heidelberg, is to ensure that the growing body of information from molecular  ...  To fulfil this mission, the EBI provides a wide variety of free, publicly available bioinformatics services.  ...  ACKNOWLEDGEMENTS We would like to thank our parent organization, the European Molecular Biology Laboratory; the Commission of the European Union, which provides funding through the TEMBLOR grant (QLRI-  ... 
doi:10.1093/nar/gkh405 pmid:15215339 pmcid:PMC441543 fatcat:3q4of4kokrff7pyrexa6wxhx3u

Web Services at the European Bioinformatics Institute

A. Labarga, F. Valentin, M. Anderson, R. Lopez
2007 Nucleic Acids Research  
Sequence analysis The European Bioinformatics Institute also provides Web Services for sequence similarity tools (WSFasta, WSWUBlast, WSNCBIBlast, WSMPsrch, WSScanPS, WSScanWise); protein analysis (WSInterProScan  ...  , or retrieve data from the ArrayExpress public repository at the EBI.  ... 
doi:10.1093/nar/gkm291 pmid:17576686 pmcid:PMC1933145 fatcat:tc6mwelg3rbnpgqjfqr26v3y5i

Information resources for the bioinformatician

J. C. Ison
2000 Briefings in Bioinformatics  
A World-Wide Web site called The Bioinformatics Resource has been created containing a comprehensive set of information resources of use to the bioinformatician.  ...  The collaborative computing project in biosequence and structure analysis (CCP11) was established to foster bioinformatics in the broad community and the UK research community in particular.  ...  Acknowledgement The author gratefully acknowledges the support of the MRC.  ... 
doi:10.1093/bib/1.3.229 pmid:11465034 fatcat:acr5ozdylbhnjd3ccfuaso3xfu

Jalview: Visualization and Analysis of Molecular Sequences, Alignments, and Structures

Andrew Waterhouse, Jim Procter, David A Martin, Geoffrey J Barton
2005 BMC Bioinformatics  
Jalview is also able to access web based alignment, secondary structure prediction and sequence database services provided by the the European Bioinformatics Institute (EBI), and the University of Dundee  ...  exchange, web service discovery and interaction.  ... 
doi:10.1186/1471-2105-6-s3-p28 fatcat:nlbbus7r6rghbnuo43suiktosy

Exploring reference data through existing computing services for the bioinformatics community

Yosra Sanaa, Gilles Mathieu, Christophe Blanchet, Pietro Mandreoli, Marco Antonio Tangaro, Giacinto Donvito, Nadina Foggetti, Marica Antonacci, Laura Burlot, Jonathan Lorenzo, Daniele Colombo, Federico Zambelli (+2 others)
2021 Zenodo  
EOSC-Pillar's work package 6 focuses on scientific demonstrators that show the added value of EOSC services Learn more about Use case 6.6: https://www.eosc-pillar.eu/use-cases/exploring-reference-data-through-existing-computing-services-bioinformatics-community  ...  EOSC-Pillar is a European Commission Horizon 2020 funded research and innovation project. EOSC aims to provide researchers with access to data/results that are currently fragmented.  ...  different Galaxy deployments An open, web-based platform for accessible, reproducible, » Facilitating the deployment of Galaxy  ... 
doi:10.5281/zenodo.5764786 fatcat:z6jv2jaxpzbgxlyenhk6umtsf4

Guest Editorial: Special Section on Grid, Web Services, Software Agents, and Ontology Applications for Life Sciences

Luciano Milanesi, Giuliano Armano, Vincent Breton, Paolo Romano
2007 IEEE Transactions on Nanobioscience  
Armano et al. describe an agent-based system able to retrieve scientific publications from the web throughout a text categorization process.  ...  Others are concerned with advanced techniques and methodologies, like Web services and agent-based systems.  ... 
doi:10.1109/tnb.2007.897434 fatcat:kihmne4uazcivazs5vgh36c6py

KBWS: an EMBOSS associated package for accessing bioinformatics web services

Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita
2011 Source Code for Biology and Medicine  
The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use.  ...  In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular  ...  This research was supported by the Grant-in-Aid for Young Scientists No.222681029 from the Japan Society for the Promotion of Science (JSPS), and by funds from the Yamagata Prefectural Government and Tsuruoka  ... 
doi:10.1186/1751-0473-6-8 pmid:21529350 pmcid:PMC3101651 fatcat:fwomop332zd2xnojjyntnu2v5a

Web services at the European Bioinformatics Institute-2009

H. Mcwilliam, F. Valentin, M. Goujon, W. Li, M. Narayanasamy, J. Martin, T. Miyar, R. Lopez
2009 Nucleic Acids Research  
The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997.  ...  From the user's point of view, these Web Services provide the same functionality as the browser-based forms.  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge all software developers, database administrators, data curators and users at the EMBL-EBI and elsewhere, who have provided extremely valuable feedback and  ... 
doi:10.1093/nar/gkp302 pmid:19435877 pmcid:PMC2703973 fatcat:5kah2noaqjhjbd477rxenbrxvu

SOAP-based services provided by the European Bioinformatics Institute

S. Pillai, V. Silventoinen, K. Kallio, M. Senger, S. Sobhany, J. Tate, S. Velankar, A. Golovin, K. Henrick, P. Rice, P. Stoehr, R. Lopez
2005 Nucleic Acids Research  
THE TECHNOLOGIES The European Bioinformatics Institute (EBI) has tried and tested standards such as CORBA (http://www.corba.org) and Web Services.  ...  at: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 ISD, UK.  ... 
doi:10.1093/nar/gki491 pmid:15980463 pmcid:PMC1160251 fatcat:2odbedc7xzfnnldtxk7spoqxry

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

Heinz Stockinger, Adrian M. Altenhoff, Konstantin Arnold, Amos Bairoch, Frederic Bastian, Sven Bergmann, Lydie Bougueleret, Philipp Bucher, Mauro Delorenzi, Lydie Lane, Philippe Le Mercier, Frédérique Lisacek (+12 others)
2014 Nucleic Acids Research  
The SIB Swiss Institute of Bioinformatics (www.isbsib.ch) was created in 1998 as an institution to foster excellence in bioinformatics.  ...  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.  ...  INTRODUCTION The SIB Swiss Institute of Bioinformatics was formally founded in 1998 but prior bioinformatics services initiated in the 1980s, such as Swiss-Prot (1) (now UniProtKB/Swiss-Prot), ExPASy (  ... 
doi:10.1093/nar/gku380 pmid:24792157 pmcid:PMC4086091 fatcat:ps6txa3xijhpxbpl2radc6dvdi

One Health EJP Annual Scientific Meeting Satellite Workshop 2021 Abstract Book [article]

Matthias Filter, Esther M. Sundermann, Yvonne Mensching
2021 Zenodo  
Seven out of the ten innovative digital solutions introduced in this abstract book were presented at the virtual event that took place on 7th June 2021.  ...  book for the One Health EJP Annual Scientific Meeting (ASM) Satellite Workshop 2021 Online Software Fair.  ...  in the data curation process.  ... 
doi:10.5281/zenodo.4923179 fatcat:qepr2hnd4baxznbrl2mkqfhw24

The EMBL Nucleotide Sequence Database

G. Stoesser
2002 Nucleic Acids Research  
EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK.  ...  Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European  ...  INTRODUCTION The European Bioinformatics Institute (EBI) is an Outstation of the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany.  ... 
doi:10.1093/nar/30.1.21 pmid:11752244 pmcid:PMC99098 fatcat:d4m5pk36dvcvxivcuvskxwn3oe

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
2021 Zenodo  
As the national infrastructure of bioinformatics and the French node of the European infrastructure ELIXIR, the Institut Français de Bioinformatique (IFB, alias ELIXIR-FR) is at the crossroads of these  ...  the National Research Agency, and a strong commitment of our supporting institutions to open permanent positions.  ...  >> Detailed report of the survey  ... 
doi:10.5281/zenodo.5324333 fatcat:py5xp6q7ungkdevdqx25zxfwmq

The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck (+93 others)
2015 Nucleic Acids Research  
A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day.  ...  Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores  ...  WEB SERVICE The BioMart Community Portal handles queries from several interfaces such as: r PERL API r Java API r Web interfaces r URL based access r RESTful web service r SPARQL For more detailed description  ... 
doi:10.1093/nar/gkv350 pmid:25897122 pmcid:PMC4489294 fatcat:vg2axbtz5rauti5yac74id57k4

A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years

Ágnes Ősz, Lőrinc Sándor Pongor, Danuta Szirmai, Balázs Győrffy
2017 Briefings in Bioinformatics  
Three major bioinformatics centres, the US National Centre for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/), the European Bioinformatics Institute (EMBL-EBI, http://www.ebi.ac.uk/) and  ...  Both Nucleic Acids Research and Bioinformatics request a 2-year maintenance of the published services from the authors after publication (Table 1) .  ... 
doi:10.1093/bib/bbx159 pmid:29228189 fatcat:7jjht7qpcfbwdhotbrqcncqqqy
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