1. IXodus a knowledge discovery process based on the SIMDAT-Pharma GRID technologies Richard Kamuzinzi Université Libre de Bruxelles – Bioinformatics June, 5 – 7th 2007 World Wide Workflow GRID ASIA 2007 Singapore

2. SIMDAT Facts EU Information Society Technologies (IST) GRID Project Duration: 4 years Start date: September 1st 2004 26 partners

3. Scope Product and Process Development (automobiles, aircraft, drugs, meteorological services) is –Complex –Involves several independent organizations at different locations Complexity management in one site is too expensive => cost/risk sharing with partners => GRID

4. Strategic objectives to test and enhance Data Grid technology for product development and production process design, to develop federated versions of problem- solving environments by leveraging enhanced Grid services, to exploit Data Grids as a basis for distributed knowledge discovery, to promote defacto standards for these enhanced Grid technologies across a range of disciplines and sectors as well as to raise awareness of the advantages of Data Grids in important industrial sectors

5. Project organization (SIMDAT-Pharma) NEC, GSK, Inpharmatica, ULB, Fraunhofer SCAI-Bio and UKA

6. IXodus – The scientific problem Lyme disease: significant source of human and animal pathology in temperate areas of the world (identified in 90s) Caused by the bite of a tick of genus IXodes, infected by the pathogen bacterium Borrelia burgdorferi the study of host-parasite interactions is an active research as ~20% ticks have been found infected by the bacterium IXodus scientific protocol: designed to deal with characterisations of genes expressed in the salivary gland of the tick IXodes ricinus at various stage of the host-parasite interaction process

7. IXodus – Workflow design (1) From IXodus scientific protocol to IXodus workflow (WF) design, we identify 2 uses cases: 1.“New cDNA sequences”: the workflow is daily feeded with a batch of nucleic sequences from the systematic sequencing of thousands of salivary gland cDNAs 2.“Databank update”: whenever a new version of relevant biological databank appears, the core workflow analysis is re- enacted to discover potentially new information

8. IXodus design (2) Use Case 1 Sequences Gathering part Pre-processing part Main analysis part

9. IXodus design (3) Use Case 2 Event processing part

10. IXodus – Implementation Workflow technology platform: InforSense TM KDE Implementation is tightly coupled with the deployment environment, which is mainly driven by 2 kind of constraints: –GRID approach –Semantic Web (SW) approach

11. IXodus implementation - The test-bed GRID approach Knowledge DB IXodus Internet EMBL -services ULB NEC – Semantic Broker ULB -services EMBL - services Main properties  Federated data and services with redundancy  Privacy, AuthZ, AuthN, non repudiation  Intellectual Proprietary (IPR) preservation by traceability (digital signatures)  Users profiles management to optimise resources availability

12. Internet ULB EMBLNEC IXodus implementation - The test-bed SW approach Main properties  Semantic-enabled service annotation  Semantic-enabled service discovery “Which service instance can operate on the latest version of the EMBL databank?”  Dynamic update of already annotated services Service advertising Semantic Broker

13. IXodus implementation – InforSense KDE The complete Workflow

14. IXodus implementation – InforSense KDE User sequences gathering

15. IXodus implementation – InforSense KDE Management of sequences overlapping

16. IXodus implementation – InforSense KDE Main analysis flow (Bioinformatics tools)

17. IXodus implementation – InforSense KDE Service instance selection & launching

18. IXodus - General benefits Workflow tool maturity: design of complex WF to support demanding problem in a reasonable delivery- time is a reality (RWD vs. RAD) WF on GRID approach is really valuable and provides the confidence we need to front the data/services “tsunami” in Life sciences… the good news is …

19. IXodus - General benefits (2)...thanks to WF technologies, the scientists no more scares the vertiginous “beast” (data/services explosion)…

20. IXodus – Remaining challenges B2A Grids: we still need precise understanding of strategic benefits from both (“win-win”) side WF technologies: need better distinction between “abstract” WF and “operational” WF: –How to decouple? –Runtime service selection using the concept of rules? At design phase: the designer would appreciate semantics approach to search for services From WF to Service: –Partial (∑args) vs. Complete(∑args) –Different profiles of user From WF to UI: –At design phase: need to define how WF actors interact with the whole system To leverage the WF log in order to generate textual information that would support scientific papers/notebooks writing (who, service_name, service_version, database_version, …)

21. SIMDAT - Major outcomes to expect SIMDAT approach will provide state-of-the-art components To enable industry-strength environment for e- Science activities To support the academia/industry collaborations in R&D activities (B2B & B2A Grids) –B2A Grids: how the “win-win” model is precisely configured? To help build up virtual organisations that federate data, services and scientific expertise

22. Thank you ! Web: http://www.simdat.orghttp://www.simdat.org Contact: richard.kamuzinzi@ulb.ac.be Acknowledgments  co-author: Robert Herzog, Université Libre de Bruxelles (ULB)  Scientific expert: Valérie Ledent, ULB  Edmond Godfroid & Bernard Couvreur: Laboratory of Applied Genetics, ULB  SIMDAT colleagues: Joseph Mavor (ULB), Falk Zimmermann (NEC), Changtao Qu (NEC), Nabeel Azam (InforSense), Moustapha Ghanem (InforSense), Kai Kumpf (SCAI-Bio)