BLUEFIELD STATE COLLEGE Cyberinfrastructure Class

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BLUEFIELD STATE COLLEGECyberinfrastructure
Class
October 6, 2006
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Agenda

• Introduction
• Cyberinfrastructure _at_ 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

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CyberinfrastructureRevolutionizing Science and
Engineering
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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
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Trans-Disciplinary Organization
Scientific Leadership Team
Domain Area Teams
Computational Biology
Genomics
Transciptomics
Proteomics
Metabolomics
Bioinformatics
Software Engineering
Outreach
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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
Develop- ment
QA/QC Release
Design Review
IOWG/ Community Standards
SWG/ Collaborator Interactions
Project Deliverables
Scientific Publications
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Agenda

• Introduction
• Cyberinfrastructure _at_ 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

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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)
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NIAID-Proteomics Centers
VBIPDC http//proteinbank.vbi.vt.edu/ProteinBank/
Admin Center http//proteomicsresource.org/
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VBIPDC Data Visualization Tools
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Agenda

• Introduction
• Cyberinfrastructure _at_ 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

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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

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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 O157H7 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

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Collaboration Tools
OpenGroupware
Vertabase
InSORs
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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.

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Training Future ScientistsCyberinfrastructure
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

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Agenda

• Introduction
• Cyberinfrastructure _at_ 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

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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/
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Acknowledgements CI Group _at_ VBI
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
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
Bioinformatics Eric Snyder, Ph.D. Zhangjun Fei,
Ph.D. Stephen Cammer, Ph.D. Darius Dziuda,
Ph.D. Yan Zhang, Ph.D.

• 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)