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Pathema Website Functionality
      Enhancements:
    Pathema gets its Sexy Back



       Tanja Davidsen, Ph.D.
       J....
Improved Front Page
Improved Front Page
Improved Searches using Lucene

• Improved speed and functionality of the search queries
  on Pathema
• An open source inf...
Improved Searches using Lucene

• Improves our search speed from 30+s to 1-3s
• Filters will allow us to let the users bui...
GBrowse (GMOD)

• The most popular GMOD viewer
• Used to replace and/or accompany our in
  house genome viewers
• Order an...
Gbrowse
ClosTox: The Clostridum Toxin DB

• The Clostridium community is primarily
  interested in the toxin genes
• We created a ...
ClosTox
Sybil: Comparative Genomic Region


• Compares a reference to selected
  comparison genomes by protein clusters
• Specify ...
Sybil: Comparative Genomic Region
Sybil: Synteny gradient display
• A color-coded display of conserved synteny
  between two or more sequences
• Select a re...
Sybil: Synteny Gradient Display
Pathway Tools
Pathway Tools
Abundance Profiler
New Data Types

• Virulence Factors
• Epitopes
• Experimentally characterized
  genes/proteins
• Multidrug transporters
• ...
Acknowledgements

•   PI: Granger Sutton (JCVI)
•   Subcontract: Owen White (University of Maryland, Baltimore, IGS)
•   P...
Pathema Website Functionality Enhancements
Pathema Website Functionality Enhancements
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Pathema Website Functionality Enhancements

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Conference: Annual BRC Meeting (BRC6), Oct 28-29, 2008 in Ft. Lauderedale, Florida.
Presenter: Tanja Davidsen

Published in: Technology
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Pathema Website Functionality Enhancements

  1. 1. Pathema Website Functionality Enhancements: Pathema gets its Sexy Back Tanja Davidsen, Ph.D. J. Craig Venter Institute
  2. 2. Improved Front Page
  3. 3. Improved Front Page
  4. 4. Improved Searches using Lucene • Improved speed and functionality of the search queries on Pathema • An open source information retrieval library supported by Apache • At the core of the Lucene logical architecture is a document containing fields of text, independent of file format • Prevents us from hitting the database for searches, especially helpful for inexact searches • Used by Wikipedia, Monster, SourceForge, UniProt and EBI
  5. 5. Improved Searches using Lucene • Improves our search speed from 30+s to 1-3s • Filters will allow us to let the users build even more complex queries: Search for all genes in organism B.anthracis starting  with the “dna” and assigned GO ID GO:0003677
  6. 6. GBrowse (GMOD) • The most popular GMOD viewer • Used to replace and/or accompany our in house genome viewers • Order and appearance of tracks are customizable by administrator and end-user • Supports third party annotation using GFF formats • Third-party feature loading • Customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers)
  7. 7. Gbrowse
  8. 8. ClosTox: The Clostridum Toxin DB • The Clostridium community is primarily interested in the toxin genes • We created a specialty toxin and neurotoxin associated proteins (NAPs) database for browsing on the Clostridium site • Data for the database provided by Clostridium researchers/community • Very successful debut at the last Botulism meeting
  9. 9. ClosTox
  10. 10. Sybil: Comparative Genomic Region • Compares a reference to selected comparison genomes by protein clusters • Specify how many clustered genes a non- reference sequence region must have in common to with the reference
  11. 11. Sybil: Comparative Genomic Region
  12. 12. Sybil: Synteny gradient display • A color-coded display of conserved synteny between two or more sequences • Select a reference sequence (bottom of the display) with the genes color-coded from the 5’ end to the 3’ end • Orthologs in the comparison genomes are shown in the color of the ortholog from the reference genome • As a result one can see large and small-scale rearrangements at a glance, in addition to regions that may be inserted in one sequence relative to another
  13. 13. Sybil: Synteny Gradient Display
  14. 14. Pathway Tools
  15. 15. Pathway Tools
  16. 16. Abundance Profiler
  17. 17. New Data Types • Virulence Factors • Epitopes • Experimentally characterized genes/proteins • Multidrug transporters • Genomic islands • Community requested databases (ClosTox)
  18. 18. Acknowledgements • PI: Granger Sutton (JCVI) • Subcontract: Owen White (University of Maryland, Baltimore, IGS) • Project Manager: Lauren Brinkac JCVI Informatics Engineers Analysts  Tanja Davidsen (manager) Scott Durkin (manager)  Erin Beck Ramana Madupu  Alex Richter Susmita Shrivastava  Kevin Galinsky Bob Dodson  Jay Sundaram Derek Harkins  Seth Schobel Lis Caler  IGS Informatics Engineers  Anu Ganapathy YongMei Zhao  Josh Orvis Aaron Gussman  Kevin Galens Jonathon Crabtree 

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