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BLUEFIELD STATE COLLEGE Cyberinfrastructure Class

BLUEFIELD STATE COLLEGE Cyberinfrastructure Class. October 6, 2006. Agenda. Introduction Cyberinfrastructure @ VBI Biodefense data, curation, and integration Curation of the pathogens and their genomes ‘omic databases for PathoSystems Biology Cyberinfrastructure Outreach Program

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BLUEFIELD STATE COLLEGE Cyberinfrastructure Class

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  1. BLUEFIELD STATE COLLEGECyberinfrastructure Class October 6, 2006

  2. Agenda • Introduction • Cyberinfrastructure @ VBI • Biodefense data, curation, and integration • Curation of the pathogens and their genomes • ‘omic databases for PathoSystems Biology • Cyberinfrastructure Outreach Program • Collaborative Research • Training current scientists • Training future scientists • Bioinformatics Software System • ToolBus/PathPort Project • Web based analysis resources • Conclusions

  3. Daniel E. Atkins, et. al. • http://www.communitytechnology.org/nsf_ci_report/ Cyberinfrastructure:Revolutionizing Science and Engineering

  4. Cyberinfrastructure Mission Knowledge Management Health Productivity Quality Target Discovery Biological Research Knowledge Generation Analysis Algorithms, Comparative Genomics, Pathways, Post-sequence data Data Management Information Storage, Queries, Curation & DB Management

  5. Trans-Disciplinary Organization Scientific Leadership Team Domain Area Teams Computational Biology Genomics Transciptomics Proteomics Metabolomics Bioinformatics Software Engineering Outreach

  6. Formalized Process Management Funded Project Requirements Scientific Goals Domain Area Team Charters Standard Operating Procedures Management Oversight & Review Resource- Loaded Schedules Use Cases Requirements Competitive Analysis Usability Engineering Design Review Develop- ment QA/QC Release IOWG/ Community Standards SWG/ Collaborator Interactions Project Deliverables Scientific Publications

  7. Agenda • Introduction • Cyberinfrastructure @ VBI • Biodefense data, curation, and integration • Curation of the pathogens and their genomes • ‘omic databases for PathoSystems Biology • Cyberinfrastructure Outreach Program • Collaborative Research • Training current scientists • Training future scientists • Bioinformatics Software System • ToolBus/PathPort Project • Web based analysis resources • Conclusions

  8. PATRIC: PathoSystems Resource Integration Center • Bioinformatics Resource Centers for Biodefense and Emerging/Re-emerging Infectious Diseases • 8 Bioinformatics Resource Centers (BRCs) established (2004) • Genome analysis and curation • CDC category B and C pathogens • 3 genera of bacteria • 5 categories of viruses www.patric.vbi.vt.edu NIH-NIAID-DMID-04-34 (2003)

  9. NIAID-Proteomics Centers VBIPDC: http://proteinbank.vbi.vt.edu/ProteinBank/ Admin Center: http://proteomicsresource.org/

  10. VBIPDC: Data Visualization Tools

  11. Agenda • Introduction • Cyberinfrastructure @ VBI • Biodefense data, curation, and integration • Curation of the pathogens and their genomes • ‘omic databases for PathoSystems Biology • Cyberinfrastructure Outreach Program • Collaborative Research • Training current scientists • Training future scientists • Bioinformatics Software System • ToolBus/PathPort Project • Web based analysis resources • Conclusions

  12. Cyberinfrastructure Outreach Program • Mid-Atlantic Regional Center of Excellence in Biodefense • Hands on training for analysis of ‘omic data • Collaborative Research Analysis • CI-TEAM: NSF Funded Cyberinfrastructure Outreach • Training of next-generation scientists for CI

  13. Collaborative research – 'omic data analysis BAA, Global Pathogen Science Portal: Common Asset for Biological Security – Dr. Sekowski, U.S. Army Edgewood Chemical Biological Center Expression profiling of M. musculus upon its infection with B. anthracis – Dr. DaSilva, US Army Medical Research Institute of Infectious Diseases Expression profiling of early response to hemorrhagic fever in Rhesus macaque – Dr. Salvato, Univ. of Maryland Epithelial cell response to enterohemorrhagic E. coli O157:H7 infection – Dr. Kaper, Univ. of Maryland Expression profiling of E. histolytica during its infection of mouse – Drs. Petri and Gilchrist, Univ. of Virginia Comparison of transcriptomes among different E. histolytica strains – Dr. Nozaki, Japan Gene expression associated with hepatic enzyme activity – Dr. Lewis, Virginia Tech Univ. Differential expression of pig arteries in response to different flow pattern – Dr. Egersdotter, Virginia Tech Univ. Transcriptome changes of Malaria patients in response to stimulation by different pools of peptides – Dr. Sztein, Univ. of Maryland

  14. Collaboration Tools OpenGroupware Vertabase InSORs

  15. Training Current Scientists:Genomic Tools • 11 sessions have been conducted with over 80 participants representing 7 institutions. • The “portable classroom” sessions are held at locations near the researchers.

  16. Training Future Scientists:Cyberinfrastructure Demonstration Through Project-Centric Bioinformatics • flexible and sustainable outreach program to be implemented by the high-schools and colleges. • to prepare the future scientific workforce for a trans-disciplinary approach to solving scientific problems. • a project-centric approach to introduce the problem to the students, who in turn apply the principles of various disciplines with the help of the experts to derive solutions

  17. Agenda • Introduction • Cyberinfrastructure @ VBI • Biodefense data, curation, and integration • Curation of the pathogens and their genomes • ‘omic databases for PathoSystems Biology • Cyberinfrastructure Outreach Program • Collaborative Research • Training current scientists • Training future scientists • Bioinformatics Software System • ToolBus/PathPort Project • Web based analysis resources • Conclusions

  18. ToolBus/PathPort System Software and Data Analysis • Federation of best available tools through web services • Development of new tools and visualization interfaces • Connection to best data sources • Interoperability among tools and across domains http://pathport.vbi.vt.edu/

  19. Software Team • Dana Eckart, Ph.D. • Boyu Yang, Ph.D. • Eric Nordberg • Chengdong Zhang, Ph.D. • Pradhuman Jhala • Prasuna Chennupati • Abhishek Agrawal • Chaitanya Kommidi • Maulik Shukla • Nithiwat Kampanya • Tony Zhang • Nishant Vaghela • Kiran Indukuri • Jian Li • Jeetendra Soneja • Yongjian Guo • Qiang Yu • Ranjan Jha • Deborah Hix, Ph.D. • Balaji Rajagopalan • Joseph Gabbard • Hui Liu, Ph.D. • Mark Scott • Tian • Yuying Tian Acknowledgements: CI Group @ VBI • Key Personnel • Bruno Sobral (PI) • Oswald Crasta (PI, Co-Director, CB) • Ron Kenyon (Co-Director, Management) • Rebecca Will (Co-Director, SW Group) • Bruce Sharp (Project Manager) • Mike Czar (Project Manager) • Curation Team • Rebecca Wattam, Ph.D. • Kelly Williams Ph.D. • Georgiy Abramochkin PhD • Herman Formadi • Chitti Dharmonalla • Anjan Purkayastha. Ph.D. • GongXin Yu, Ph.D. • Yongqun He, Ph.D., D.V.M. • Joshua Shallom, Ph.D. • Nataraj Dongre, Ph.D. • Mark Hance • Funding: - DoD Contract PathPort project W911SR-04-C-0045 (Sobral) • NIAID / NIH BRC Contract HHSN266200400035C (Sobral) • NIAID / NIH PRC Sub-Contract (Sobral) • MARCE BGRC (Sobral) • NSF CI-TEAM Award (O. Crasta) • Bioinformatics • Eric Snyder, Ph.D. • Zhangjun Fei, Ph.D. • Stephen Cammer, Ph.D. • Darius Dziuda, Ph.D. • Yan Zhang, Ph.D.

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