2. Carole Goble - University of Manchester


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  • Outercurve Software Freedome Conservacy
  • is a provider of open source bioinformatics software and community services (Taverna, BioCatalogue, myExperiment, SysMO-SEEK, RightField), working closely with, and driven by the needs of, life science researchers. Taverna usable by long tail People wanted to use! Fully featured, extensible and scalable scientific workflow management system And built lots that wasn’t useful or used. Scientific Workflow Management System Suite of components: engine, GUI, server, platform, activities, repository and catalogue integrations, activity packs desktop, server and cloud Adopted by ~400 organisations in 41 countries All kinds of scientific data-intensive pipelines cloud-resident NGS sequence annotation, model building, data integration, prediction analytics, parameter sweeps, data cleaning…blah blah blah Specialism in linking third party public resources and web services in the wild First release 2004. New release every 3-4 months. Open Source LGPL
  • Working on Full OSGi and
  • Where
  • Software and Tools Alternative to ISACreator Inspired by MCISB Key Results initiative and SBRML [Paton et al] Harvest standards e.g. MIAME (MIBBI.org) Analyse consortium schemas and spreadsheets JERMs for each data type – microarray, metabolomics, proteomics .... Map project data sources to JERMs. Distribute JERM spreadsheet templates
  • Academic, Industry Vendor lockin Societal South Africa, Thailand, Open Source Software (& Open Access Services)
  • Academic, Industry Vendor lockin Societal South Africa, Thailand, epilepsy
  • PhD students Galaxy Taverna Workflow Management System KNIME GMOD EMBOSS CytoScape R and Bioconductor Bioclipse, http://www.bioclipse.net/ http://homepages.fh-giessen.de/~tmth07/tools.html
  • A PhD student ssticking something onto
  • New challenges in science and software All interlinked issues
  • E-Lab and Taverna – all my software - elephants ---- elephant in the room, blind men and elephants, danger of being white elephants? SysMO And other e-Science projects Each of these apply to all our projects. Just one of them is not enough. Not even for Taverna. To sustain it as a service we must sustain the software and the content in its repositories
  • balancing technical research agendas, stable and adopted infrastructure and scientific research Split teams Platform (the virtuous circle slide)
  • Norman missing! And olga. And wei.
  • Computer science research Software engineering Computational scientists Scientists Sponsors PALs Advocates & scouts Community builders Extreme collaborators Co-shaping partners Privileged users PhDs and post-docs only Protected by champions Embed Refresh Listening Act Local, think Global The Long Tail Data is the Next Intel Inside Users Add Value Network Effects by Default Some Rights Reserved The Perpetual Beta Cooperate, Don't Control Beyond a Single Device
  • Unknown are plugin and customisers Porting Tvaerna onto infrastrtcutres done by others
  • For every project For each of the projects The reseachand he applciations keep the production going. Because noone else does.
  • EPSRC, ESRC, BBSRC, NERC, JISC EU FP7, EU Innovative Medicine Initiative NIH NCI Industry (Microsoft, Eli Lilly) Core projects - OMII effectively VC and software engineering team not research team FP7 projects fund infrastructure BBSRC fund infrastructure NERC But EPSRC doesn’t (except for OMII)
  • E Software engineers <-> Computer Science researchers Developers <-> Bioinformaticians Each application brings its own deliverables and special requirements
  • Semantics in an out Riding out the cycles
  • BBSRC’s Tools & Resources and Biological and Bioinformatics Resource funds honourable mention. Funding and Social structures Are against shareable reusable software/ontology/database/thing Self-promotion Publish a new thing; can’t publish of reuse pre-existing thing . Novelty Research councils fund new, shiny things BBSRC’s Tools & Resources and Biological and Bioinformatics Resource funds honourable mention. Research vs Production Confusion How do you get funding for production software other than claiming to be researching stuff? How do you get a publication out of a bit of research software without claiming a potential user-base? I don’t want to be a long-term service/software provider!
  • Aggregate into products, Production-level quality and stability Certify products on a wide variety of platforms. Predictable, structured release schedule Guarantee support for each new version Professional documentation and training Localize software and documentation for major languages. Expertise that can be called upon Technical support SLAs to meet enterprise IT requirements Indemnify companies against potential IP infringement. Technical support SLAs to meet enterprise IT requirements Expertise that can be called upon Support desk Community self-help SSI keholders – users, developers, sys admin St Construct conditions for mutual self-advantage – collaborate to compete. Shifting funds in HEI too for local adoption. Jam today and jam tomorrow – ROI Reinvention is rife – not making best use of our assets.(and wastes tax payers money) Participatory design is expensive. Participatory advice Ramp – incremental adoption. Reward for software development for using other peoples software for your data being used rather than reinventing.
  • Picture of a policeman directing traffic The ltter one is for for
  • Chemspider complain about slowdown KNIME too expensive
  • A PhD student ssticking something onto
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