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

1. PATHEMA-Burkholderia
A CLADE SPECIFIC
BIOINFORMATICS RESOURCE
CENTER
http://pathema.jcvi.org

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. 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. 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

6. 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

7. 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

8. 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

9. 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