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      Taverna: a tool for building and running workflows of services

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          Abstract

          Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/.

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          Pfam: clans, web tools and services

          Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler … (2005)
          Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK (), the USA (), France () and Sweden ().
          Article 0 comments Cited 683 times – based on 0 reviews     Review now
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            BIND: the Biomolecular Interaction Network Database.

            Gary Bader, Doron Betel, Christopher W. V. Hogue (2003)
            The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display. We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions. An interaction network clustering tool has also been developed to help focus on regions of interest. Continued input from users has helped further mature the BIND data specification, which now includes the ability to store detailed information about genetic interactions. The BIND data specification is available as ASN.1 and XML DTD.
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              Creating a bioinformatics nation.

              Lincoln Stein (2002)
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (publisher-id): Nucleic Acids Research
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date Collection: 01 July 2006
                Publication date (Print): 01 July 2006
                Publication date (Electronic): 14 July 2006
                Volume: 34
                Issue: Web Server issue
                Pages: W729-W732
                Affiliations
                School of Computer Science, University of Manchester M13 9PL, UK
                1School of Computing Science, University of Newcastle NE1 7RU, UK
                2School of Chemistry, University of Manchester M60 1QD, UK
                3EMBL European Bioinformatics Institute, Hinxton Cambridge, CB10 1SD, UK
                Author notes
                *To whom correspondence should be addressed. Tel: +44 0 161 275 0677; Fax: +44 0 161 275 6204; Email: duncan.hull@ 123456cs.man.ac.uk
                Article
                DOI: 10.1093/nar/gkl320
                PMC ID: 1538887
                PubMed ID: 16845108
                SO-VID: 92120911-c202-47b6-9f4f-bc378e876ff0
                Copyright © © The Author 2006. Published by Oxford University Press. All rights reserved
                License:

                The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

                History
                Date received : 14 February 2006
                Date revision received : 01 March 2006
                Date accepted : 13 April 2006
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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