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WP 12 - Infrastructure for Tools Integration

WP 12 - Infrastructure for Tools Integration. WP 12 - Description of Work. Starts by:

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WP 12 - Infrastructure for Tools Integration

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  1. WP 12 - Infrastructure for Tools Integration

  2. WP 12 - Description of Work Starts by: “The overall aim of this work package is to develop a dynamicstrategy for selecting, connecting and linking the highly diverse set of tools that at any one time makes up the methods from the domain of publicly available bioinformatics. The goal is in part to establish a strategy that will link important tools that are created by many different European groups and institutes and offer them to experimentalists within biology and medicine in a coherent, integrated fashion, and in part to address the recurrent issue of tools becoming obsolete as they are outperformed by newer approaches.” Finishes by: “(...)The key aspects to consider are mentioned above – overall WP12 should identify a strategy that will lead to in-dept coordination and sharing, while as the same time confronting the political issue of keeping some visibility for the National tool providers and their institutions. The strategy must secure that a pipeline for tool development is kept active in Europe; while at the same time securing that bioinformatics end-users will experience a much less fragmented and duplicated view of what bioinformatics can off them as assistance in their experimental efforts than today. (...)”

  3. WP12 Expert Committee Adam Godzik, Professor at the Burnham Institute, USA Christophe Blanchet,Pôle Bioinformatique de Lyon, France Ib Groth Clausen, AstraZeneca, Sweden Jan Christian Bryne, Bergen Center for Computational Science, Norway Niels Tolstrup, Exiqon, Denmark Paul Gordon, Calgary University, Canada Rodrigo Lopez, EBI, UK Francis Ouellette, Ontario Institute for Cancer Research, Canada

  4. Affiliation Academia Industry

  5. Geographically Europe Rest of the World

  6. Stakeholders Provider User Implementer

  7. What is a tool? • Tools add value to data • Database view (”EBI”): ”a tool produces data for distribution in a database”, e.g. ”pre-computed” annotation • Many tools are popular because they can be run on any data item (e.g. a sequence) no matter whether it is already incorporated in a database, has an accession number, is proprietary or public, complete or partial

  8. What is a tool? • Funding situation for tools is dramatically different from the database case because it is entirely distributed already – the main issues relate to their • visibility • interoperability • performance (benchmarking) • online or not ? • In Elixir the tool area should be sold to the funders as additional benefits from the substantial investments already made

  9. New ”generations” of tools • Datadriven updates and expansion is build into the tool • Potentially no lag phase between the underlying data becomes available and the new version of the tool is made available • May also involve new types of needs for supercomputer ressources

  10. NetPhorest.info – prediction of kinase association for experimentally determined phosphorylation sites Miller et al. Linear motif atlas for phosphorylation-dependent signaling. Science Signal. 2008 1:ra2.

  11. Draft ELIXIR WP 12 Roadmap Report Priorities mapped to time – short (2011-2012), medium (2013-2015), longer (2016+) Short term: Access: Programatic access, (traditional clickable interfaces, downloads) Basic infrastructure should work from the start in order to take off Not new webservice technologies – winning ones largely identified* Focus on accessibility, uptime, replication, testing and user scope Well-maintained catalogs AN-tagged data vs anonymous data Benchmarking frameworks (including sustainability) Definition issues of unique vs ubiquitous tools Training *WSDL/SOAP/Web service Interoperability Basic Profile 1.1 & REST/DAS

  12. Draft ELIXIR WP 12 Roadmap Report Priorities mapped to time: short (2011-2012), medium (2013-2015), longer (2016+) Medium term: User category-sensitive aspects Recommended hardware for WSs Advanced benchmarking and tool comparison Tool termination policies Long term: End-user data and tool integration Commercial tools adopt standards defined by public effort (long term goals hard to obtain from industry in particular big pharma)

  13. http://www.biocatalogue.org http://beta.biocatalogue.org Started June 2008. In first beta phase. Launch June 2009 at ISMB. Professor Carole Goble University of Manchester, UK Director myGrid Consortium

  14. Curation Model Attribution Tags Versioning Ratings Controlled vocabs Quantitative Content Semantic Content Searching Statistics Ontologies Free text Usage Statistics Operational Metrics Functional Capabilities Service Model Interfaces Operational Capabilities Community Standing Usage Policy Usable and Useful Understandable Provenance

  15. Elixir Tool integration marketing bait ”Parsed on arrival”

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