1. Biomedical and Bioscience Gateway to National Cyberinfrastructure John McGee Renaissance Computing Institute mcgee@renci.org

2. Meeting the needs of individuals Many individuals … No single science environment fits all patterns of R&E –Education and entry level research –Domain scientists with little large scale IT expertise –Domain scientists with significant IT expertise Integrating large scale National CI with science applications is often non-trivial –Policy, Technology, Security, History –Even for domain scientists with significant IT expertise

3. Meeting the needs of individuals RENCI is taking a four tier approach to Gateway activities: –Web Portal environment OGCE based –Workflow development environment with supporting deployed infrastructure Existing rich client application (Taverna) –Client applications that consume RENCI hosted TG enabled web services Custom client applications –Adaptation of a research team’s existing job management scripts Glue code only More than just a portal scenario - the Portal becomes a hosting environment for most of these collaborations

4. >140 Bioscience Applications Simple form fill and submit to run bioscience jobs on TeraGrid Guided tour through popular Bioscience applications Most successful with Education segment. Used in two graduate level Biology courses. Completed workflows embedded into the portal are beginning to pique the interest of research teams.

5. Application Suites –EMBOSS European Molecular Biology Open Software Suite –GLIMMER gene identification in microbial DNA –HMMER Hidden Markov Model program for profile- based sequence analysis –NCBI diverse set of tools –PHYLIP PHYLogeny Inference Package for inferring phylogenies –ClustalW, FASTA Standard bioinformatics databases –NCBI Aggregate (300 GB) –PDB (6.3 GB) –Prints (72 MB) –RepBase (8.6 MB) –UniProt (28 GB) –PFam (8.7 GB) –ProSite (16 MB) –TransFac (36 MB) Current Bioportal Applications

6. Tiered Portal System user with a Web Browser web server computational services mySQL Biological Data Sets OGCE Chef https GRAM, GridFTP Tomcat Velocity Turbine Jetspeed scheduler ClientWeb Application Execution Services myProxy JAVA COG

7. Bioportal Architecture PISE Application XML description HTML files Bioportal Gatekeeper GridFTP MyProxy OGCE User Databases Job History Database Application Processing Interface Generator Velocity files Application Processing Command files Authentication, Grid credential User Profile Job submission Job records Remote File Access Grid Framework User Workspace Application Framework Security and Account Management Workflow Processing Application Services

8. Adapting NC Bioportal for TeraGrid Gateway launched on May-19 –www.tgbioportal.org Community Account Credentials –All Gateway users are mapped to a single credential for operation on the TeraGRid RP Administrator Portlet and web service –Access to portal user and job information Integration with Auditing and Accounting Software/data deployment and maintenance

9. Adapting NC Bioportal for TeraGrid - cont’d Resource selection –RP submission target is selected from pool of active RPs. User can manually change. Bio application code platform compatibility –heterogeneous environment –NMI Build and test –reflect availability of the applications Packaging for broad deployment –licensing issues on some apps/data

10. Workflow and Web Service Hosting Taverna BioMart BioMoby Hosted Web Services Deploy, config, maintain Bioscience backend compute/data components on TG

11. TeraGrid Taverna RENCI Hosted Web Services (BioMoby, BioMart, domain specific strong data types, etc) RENCI Hosted Web Services (BioMoby, BioMart, domain specific strong data types, etc) BioScience Applications BioScience Data Sets RENCI Developed Workflows TeraGrid User Info Services WS Registry Portal Web Interface NextGen RENCI Bioportal Job Mgmt, Audit, Acctng, … MetaScheduling