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Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
Lee Apollo Bosc2008
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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 <ul><li>Official relational database schema for GMOD </li></ul><ul><li>Highly sophisticated </li></ul><ul><li>http://gmod.org/wiki/index.php/Chado </li></ul>
  • 10. Chado
  • 11. GFF3 <ul><li>Generic Feature Format Version 3 </li></ul><ul><li>Extension to previous GFF formats </li></ul><ul><li>Sequence Ontology compliant </li></ul><ul><li>Used by many communities </li></ul><ul><li>http://www.sequenceontology.org/gff3.shtml </li></ul>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 <ul><li>Redesign the data model to reflect the Chado schema </li></ul><ul><li>Enable communication with analysis servers that provide access to popular sequence analysis tools (e.g., NCBI BLAST, WU-BLAST, ePCR) </li></ul><ul><li>Integration with GMOD’s GBrowse </li></ul>
  • 19. Downloading Apollo <ul><li>http://apollo.berkeleybop.org </li></ul><ul><li>Source tarball from SourceForge </li></ul><ul><li>Source from SourceForge CVS </li></ul><ul><ul><li>http://gmod.cvs. sourceforge .net/gmod/apollo </li></ul></ul>Platform Optionally bundled JRE Windows Yes Mac OS X No Linux Yes Solaris Yes (x86 version) Unix No
  • 20. Acknowledgements <ul><li>Lawrence Berkeley National Laboratory </li></ul><ul><ul><li>Suzanna Lewis (project PI) </li></ul></ul><ul><ul><li>Nomi Harris </li></ul></ul><ul><ul><li>Mark Gibson </li></ul></ul><ul><li>Wellcome Trust Sanger Institute </li></ul><ul><ul><li>Steven Searle </li></ul></ul><ul><li>The Arabidopsis Information Resource </li></ul><ul><ul><li>Raymond Chetty (new MSA viewer) </li></ul></ul><ul><li>Apollo community </li></ul><ul><li>The National Institute of General Medical Sciences (NIGMS) for funding (NIH grant 1R01GM080203-01) </li></ul>

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