myExperiment: a repository and social network for the sharing of bioinformatics workflows

myExperiment (http://www.myexperiment.org) is an online research environment that supports the social sharing of bioinformatics workflows. These workflows are procedures consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results. As a public repository of workflows, myExperiment allows anybody to discover those that are relevant to their research, which can then be reused and repurposed to their specific requirements. Conversely, developers can submit their workflows to myExperiment and enable them to be shared in a secure manner. Since its release in 2007, myExperiment currently has over 3500 registered users and contains more than 1000 workflows. The social aspect to the sharing of these workflows is facilitated by registered users forming virtual communities bound together by a common interest or research project. Contributors of workflows can build their reputation within these communities by receiving feedback and credit from individuals who reuse their work. Further documentation about myExperiment including its REST web service is available from http://wiki.myexperiment.org. Feedback and requests for support can be sent to bugs@myexperiment.org.

[1]  Martijn J. Schuemie,et al.  Structuring and extracting knowledge for the support of hypothesis generation in molecular biology , 2009, BMC Bioinformatics.

[2]  Anders Krogh,et al.  miRMaid: a unified programming interface for microRNA data resources , 2010, BMC Bioinformatics.

[3]  Rodrigo Lopez,et al.  Web services at the European Bioinformatics Institute-2009 , 2009, Nucleic Acids Res..

[4]  Robert D. Finn,et al.  Experience using web services for biological sequence analysis , 2008, Briefings Bioinform..

[5]  Norman W. Paton,et al.  Fine-grained and efficient lineage querying of collection-based workflow provenance , 2010, EDBT '10.

[6]  Steve Pettifer,et al.  An active registry for bioinformatics web services , 2009, Bioinform..

[7]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[8]  Carole Goble,et al.  Lessons from myExperiment: Research Objects for Data Intensive Research , 2009 .

[9]  M. Kappler Software for rapid prototyping in the pharmaceutical and biotechnology industries. , 2008, Current opinion in drug discovery & development.

[10]  Carole A. Goble,et al.  The design and realisation of the myExperiment Virtual Research Environment for social sharing of workflows , 2009, Future Gener. Comput. Syst..

[11]  Renate Kania,et al.  SABIO-RK: Integration and Curation of Reaction Kinetics Data , 2006, DILS.

[12]  Carole A. Goble,et al.  Taverna: a tool for building and running workflows of services , 2006, Nucleic Acids Res..

[13]  Jill P Mesirov,et al.  Accessible Reproducible Research , 2010, Science.

[14]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[15]  Maliha Aziz,et al.  ProtocolDB: classifying resources with a domain ontology to support discovery , 2008, iiWAS.

[16]  Carole A. Goble,et al.  Towards open science: the myExperiment approach , 2010, Concurr. Comput. Pract. Exp..

[17]  Jiren Wang,et al.  Soap-HT-BLAST: high throughput BLAST based on Web services , 2003, Bioinform..

[18]  Douglas B. Kell,et al.  Automated manipulation of systems biology models using libSBML within Taverna workflows , 2008, Bioinform..

[19]  Mark D. Wilkinson,et al.  BioMOBY: An Open Source Biological Web Services Proposal , 2002, Briefings Bioinform..

[20]  Supporting data , 2010, Nature Medicine.

[21]  W.M.P. van der Aalst,et al.  Don't go with the flow: web services composition standards exposed , 2003 .

[22]  Carole A. Goble,et al.  Recycling workflows and services through discovery and reuse , 2007, Concurr. Comput. Pract. Exp..

[23]  Mitch Waldrop,et al.  Big data: Wikiomics , 2008, Nature.

[24]  Carole Goble,et al.  BioCatalogue: A Curated Web Service Registry For The Life Science Community , 2009 .

[25]  Hideaki Sugawara,et al.  Web API for biology with a workflow navigation system , 2009, Nucleic Acids Res..

[26]  Bertram Ludäscher,et al.  Kepler: an extensible system for design and execution of scientific workflows , 2004, Proceedings. 16th International Conference on Scientific and Statistical Database Management, 2004..

[27]  Carole A. Goble,et al.  Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data , 2008, BMC Bioinformatics.

[28]  Robert Stevens,et al.  A systematic strategy for large-scale analysis of genotype–phenotype correlations: identification of candidate genes involved in African trypanosomiasis , 2007, Nucleic acids research.