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Chemical Informatics and Cyberinfrastructure Collaboratory

Join us at the Chemical Informatics and Cyberinfrastructure Collaboratory Project Meeting on Oct. 28, 2005, at IU Bloomington, led by Geoffrey Fox from Indiana University Bloomington. Explore the general approach, principles, and comments on integrating chemistry, bioinformatics, and grid technology. Establish requirements and opportunities, compile resources, define projects, and aim for a joint action plan by January 2006.

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Chemical Informatics and Cyberinfrastructure Collaboratory

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  1. Chemical Informatics and Cyberinfrastructure Collaboratory Project Meeting, IU Bloomington Oct. 28 2005 Geoffrey Fox Computer Science, Informatics, Physics Pervasive Technology Laboratories Indiana University Bloomington IN 47401 gcf@indiana.edu http://www.infomall.org

  2. General Approach – “Chemistry/Bio” • Establish CICC requirements and opportunities from applications including • Chemo (Informatics and simulation) and Bio (informatics and complexity) • Industry, Government, Research • Existing related projects • International scope • Compile resources/sources of insight • Define useful taxonomy to group requirements • Abstract and iterate requirements with CS/Grid • Define and start early projects November 05 • Aim at first draft of joint Chemo/Bio-CS-Grid-Informatics status of field/action plan for CICC January 2006 • Need to have few recognized successes and a good plan a year from now to write a good full proposal

  3. BioInformatics Grid Chemical Informatics Grid Sequencing Tools Biocomplexity Simulations BIS … … HTS Tools Quantum CalculationsCIS Domain Specific Grids/Services Compute/Supercomputer Information/Knowledge Portals Services Collaboration MIS Instrument/Sensor Application Services Policy Data Access/Storage Metadata Discovery Core Low Level Grid Services Security Messaging Workflow Management Physical Network M(B,C)IS is Molecular (Bio, Chem) Information System supportingspecific metadata (CML, CellML, SBML) and physical representations/visualizations

  4. General Approach – “CS/Grid” • Divide 15 areas below the “red lines” among CS/Grid/Informatics participants • Evaluate existing Chemo/Bio Grids and IT including open source relevant software • Compare with other fields • Abstract and iterate technology choices/priorities/gaps with Chemo/Bio • Strongly prefer “standards” such as WS-*, WS-I, OGSA, GT4 • Stress interoperability with other Grids of relevance • Identify near term “low-hanging fruit/urgent requirements and opportunities” early November • Need Portal, Taverna evaluation …………. • Aim at first draft of joint Chemo/Bio-CS/Grid/Informatics status of field/action plan for CICC January 2006

  5. General Approach – Principles • How do we fold in research activities into education • Chemists educate Informatics researchers in project (and vice-versa) • How do we engage broader community such as internal biocomplexity, outside collaborators who can identify important requirements but where insufficient funds for an explicit project • Stress international quality and enabling broad participation through standard (adherence/development) and technology • Community (virtual organization) Grids • Link to (335) Minority-Serving Institutions Cyberinfrastructure Institute How do we best engage external advisors • Need to organize into working groups • Any other organizational structure needed • Who (people, communities, organizations) else should we engage • What changes in plans are needed e.g. to exploit today’s comments and hoped for existence of UK center • What are our strengths and weaknesses • What are greatest risks that full center proposal will not be written well/funded

  6. Comments on Grid Components • Support GT4 and WS-I+(+); Support Java and .NET • Portals – all services will have a portlet interface • Compute Grid -- This is some sort of Condor Grid (as used by Cambridge) • Supercomputer Grid -- (extended) TeraGrid • Workflow, Metadata, Information Management – learn from Taverna, link with BPEL style workflow, link with other Semantic Grid/metadata services • Instruments – learn from CIMA/Reciprocal Net, compare with Sensors in LEAD/SERVOGrid • MIS/CIS – See if idea sensible – in any case need CML, LSID, Molecular visualization • Application Services – Need a wizard. Support “filters” (Wild) and loosely coupled simulations (Baik) • Data – Link to PubChem and Bioinformatics – link to Baik database • Discovery – Extended UDDI • Security – review any special requirements and status of PubChem, caBIG, myGrid etc, • Collaboration, Management, Messaging, Policy -- nothing special needed

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