Lee Apollo Bosc2008
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Transcript

  • 1. Apollo: A Sequence Annotation Editor Ed Lee Lawrence Berkeley National Laboratory
  • 2. User Community
  • 3. Workflow
  • 4. Main Window
  • 5. Annotation Info Editor
  • 6. Architecture
  • 7. Data Layer
  • 8. Supported Formats
  • 9. Chado
    • Official relational database schema for GMOD
    • Highly sophisticated
    • http://gmod.org/wiki/index.php/Chado
  • 10. Chado
  • 11. GFF3
    • Generic Feature Format Version 3
    • Extension to previous GFF formats
    • Sequence Ontology compliant
    • Used by many communities
    • http://www.sequenceontology.org/gff3.shtml
    D. melanogaster C. elegans S. cerevisiae Dictyostelium A. thaliana D. rerio M. musculus H. sapiens S. pombe E. coli R. norvegicus
  • 12. GFF3
  • 13. Style Wizard
  • 14. Types Wizard
  • 15. Multiple Alignment Transcript Viewer and Editor
  • 16. Continuous Data Display
  • 17. Undo
  • 18. Future Plans
    • Redesign the data model to reflect the Chado schema
    • Enable communication with analysis servers that provide access to popular sequence analysis tools (e.g., NCBI BLAST, WU-BLAST, ePCR)
    • Integration with GMOD’s GBrowse
  • 19. Downloading Apollo
    • http://apollo.berkeleybop.org
    • Source tarball from SourceForge
    • Source from SourceForge CVS
      • http://gmod.cvs. sourceforge .net/gmod/apollo
    Platform Optionally bundled JRE Windows Yes Mac OS X No Linux Yes Solaris Yes (x86 version) Unix No
  • 20. Acknowledgements
    • Lawrence Berkeley National Laboratory
      • Suzanna Lewis (project PI)
      • Nomi Harris
      • Mark Gibson
    • Wellcome Trust Sanger Institute
      • Steven Searle
    • The Arabidopsis Information Resource
      • Raymond Chetty (new MSA viewer)
    • Apollo community
    • The National Institute of General Medical Sciences (NIGMS) for funding (NIH grant 1R01GM080203-01)