Apollo: A Sequence Annotation Editor Ed Lee Lawrence Berkeley National Laboratory
User Community
Workflow
Main Window
Annotation Info Editor
Architecture
Data Layer
Supported Formats
Chado <ul><li>Official relational database schema for GMOD </li></ul><ul><li>Highly sophisticated </li></ul><ul><li>http:/...
Chado
GFF3 <ul><li>Generic Feature Format Version 3 </li></ul><ul><li>Extension to previous GFF formats </li></ul><ul><li>Sequen...
GFF3
Style Wizard
Types Wizard
Multiple Alignment Transcript Viewer and Editor
Continuous Data Display
Undo
Future Plans <ul><li>Redesign the data model to reflect the Chado schema </li></ul><ul><li>Enable communication with analy...
Downloading Apollo <ul><li>http://apollo.berkeleybop.org </li></ul><ul><li>Source tarball from SourceForge </li></ul><ul><...
Acknowledgements <ul><li>Lawrence Berkeley National Laboratory </li></ul><ul><ul><li>Suzanna Lewis (project PI) </li></ul>...
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Lee Apollo Bosc2008

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Lee Apollo Bosc2008

  1. 1. Apollo: A Sequence Annotation Editor Ed Lee Lawrence Berkeley National Laboratory
  2. 2. User Community
  3. 3. Workflow
  4. 4. Main Window
  5. 5. Annotation Info Editor
  6. 6. Architecture
  7. 7. Data Layer
  8. 8. Supported Formats
  9. 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. 10. Chado
  11. 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. 12. GFF3
  13. 13. Style Wizard
  14. 14. Types Wizard
  15. 15. Multiple Alignment Transcript Viewer and Editor
  16. 16. Continuous Data Display
  17. 17. Undo
  18. 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. 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. 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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