PATHEMA-Burkholderia
     A CLADE SPECIFIC
BIOINFORMATICS RESOURCE
         CENTER

     http://pathema.jcvi.org
What is Pathema?
 Pathema (http://pathema.jcvi.org)

 A NIAID Bioinformatics Resource Center designed to
  support bio-d...
What is Pathema?
    An extensive library of literature and manually curated data
•
    A customized suite of sophisticate...
All Entamoeba (3)
                                                                      E. histolytica
                   ...
What is the future of Pathema?
 We are relying on your feedback!
   Data exchange & integration
   Genome sequence anal...
Acknowledgements
P.I.:      Granger Sutton
Funding:    NIAID
Subcontract: University of Maryland Baltimore, IGS
Informatic...
Jamboree Overview
Day 1:
 Prokaryotic Annotation Methodologies
  • Gene Model & Functional Curation
 Introduction to Man...
Introductions
 Bioinformatics Project Manager
   Lauren Brinkac              lbrinkac@jcvi.org

 Burkholderia Investigat...
Pathema Burkholderia Annotation Jamboree: Introduction to Annotation Jamboree
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Pathema Burkholderia Annotation Jamboree: Introduction to Annotation Jamboree

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Conference: Sept 24 - 26, 2008 at the JCVI Rockville, MD Campus
Presenters: Ramana Madupu, Lauren Brinkac, Derek Harkins

Published in: Technology, Health & Medicine
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Pathema Burkholderia Annotation Jamboree: Introduction to Annotation Jamboree

  1. 1. PATHEMA-Burkholderia A CLADE SPECIFIC BIOINFORMATICS RESOURCE CENTER http://pathema.jcvi.org
  2. 2. What is Pathema?  Pathema (http://pathema.jcvi.org)  A NIAID Bioinformatics Resource Center designed to support bio-defense and infectious disease research.  Pathema provides detailed curation of six target pathogens:  Category A priority pathogens: Bacillus anthracis, Clostridium botulinum  Category B priority pathogens: Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica
  3. 3. What is Pathema? An extensive library of literature and manually curated data • A customized suite of sophisticated bioinformatics software • Comparative analysis tools customized to retrieve, display, • and compute results relevant to ongoing bio-defense research Overarching Goal: to provide core resources that will accelerate scientific progress on understanding, detecting, diagnosing and treating Category A-C pathogens and other pathogens involved in new and re-emerging infectious diseases.
  4. 4. All Entamoeba (3) E. histolytica E. dispar E. invadens All Clostridium (25) All Burkholderia (28) All Bacillus (24) B. mallei (11) B. anthracis (17) C. perfringens (9) B. cereus (3) B. pseudomallei (10) C. botulinum (9) B. thuringiensis (2) B. thailandensis C. difficile B. cenocepacia B. subtilis C. thermocellum B. sp. B. pumilus C. acetobutylicum B. phages (4) C. tetani P. aeruginosa C. butyricum R. solanacearum C. novyi C. phytofermentans
  5. 5. What is the future of Pathema?  We are relying on your feedback!  Data exchange & integration  Genome sequence analysis  Custom data analysis  Custom tool development  New Genome Sequences & Annotation Data  Clade-specific Pathema Workshops  ! Clade-specific Annotation Jamborees !  Incorporate expert annotation & experimental references
  6. 6. Acknowledgements P.I.: Granger Sutton Funding: NIAID Subcontract: University of Maryland Baltimore, IGS Informatics Engineers Informatics Analysts Tanja Davidsen (manager) Scott Durkin (manager) Erin Beck Ramana Madupu Alex Richter Susmita Shrivastava Kevin Galinsky Bob Dodson Jay Sundarm Derek Harkins Seth Schobel Lis Caler Owen White (University of Maryland Baltimore) Anu Ganapathy YongMei Zhao Josh Orvis Aaron Gussman Kevin Galens Jonathon Crabtree
  7. 7. Jamboree Overview Day 1:  Prokaryotic Annotation Methodologies • Gene Model & Functional Curation  Introduction to Manatee Day 2:  Participant Presentations  Burkholderia Training Exercises  Burkholderia Annotation Day 3:  Burkholderia Annotation
  8. 8. Introductions  Bioinformatics Project Manager Lauren Brinkac lbrinkac@jcvi.org  Burkholderia Investigator Bill Nierman wnierman@jcvi.org  Bioinformatics Analyst Ramana Madupu rmadupu@jcvi.org  Bioinformatics Analyst Derek Harkins dharkins@jcvi.org  Pathema-Burkholderia burkholderia@jcvi.org

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