Difference between revisions of "AmiGO 1 8"

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[[Category:Software]]
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[[Category:AmiGO]]
 
= Status =
 
= Status =
  
Currently [http://amigo.berkeleybop.org/cgi-bin/amigo/go experimental]. Expected to move into testing in the next couple of weeks.
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Currently in [http://amigo1.geneontology.org production] (as of 20013-10-17).
  
* Testing:
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See [[AmiGO 2]] for the future beta.
** [TODO] Run tanuki locally
 
** [TODO] Add fuzzing and psuedo-fuzzing to kappa
 
** [TODO] General user testing on pre-production
 
  
 
= New features =
 
= New features =
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* Rapid searching ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=live_search live search])
 
* Rapid searching ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=live_search live search])
 
* New term details with improved graph view ([http://amigo.berkeleybop.org/cgi-bin/amigo/term_details?term=GO:0022008 term details for GO:0022008])
 
* New term details with improved graph view ([http://amigo.berkeleybop.org/cgi-bin/amigo/term_details?term=GO:0022008 term details for GO:0022008])
 
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* Speed--new caching sub-system for several components (see above for example)
= Current work =
 
 
 
== Frontend==
 
 
 
* <strike>Try and lighten up on some of the POSTs in AmiGO to make searches easier to track</strike>
 
* <strike>Finish new term details page</strike>
 
** <strike>find way to avoid confusion with old view</strike>
 
** <strike>Try different icons</strike>
 
** <strike>Try dynamic lines to highlight ancestors</strike>
 
** <strike>Explore text-based views</strike>
 
** <strike>Consensus reached, now polishing</strike>
 
** <strike>Use caching for gp counts?</strike> [bumped--necessary? will check with auto tester later]
 
** <strike>Default gp count values</strike>
 
** <strike>Fix td downloads</strike>
 
* <strike>Re-expose the buckets in slimmer</strike> [bumped--using new report on accordion]
 
* Update docs to most recent version (final item)
 
 
 
== Backend ==
 
 
 
* <strike>Work out CVS to SVN transition one way or another (this will be done by June first; give production plenty of heads-up during transition) [transitioning now; seth is testing]</strike>
 
* <strike>Setup production to produce their own indexes locally</strike> [will likely juggle frontend servers while producing indexes]
 
* <strike>See if association search index can be added/generated in a timely manner (talk to Tanya).</strike> [takes a while--will do more work on exp server.]
 
 
 
== Bugs ==
 
 
 
* Slimmer bug [https://sourceforge.net/tracker/index.php?func=detail&aid=2996853&group_id=36855&atid=908269]
 
* <strike>Upload bug</strike> [https://sourceforge.net/tracker/?func=detail&aid=2962252&group_id=36855&atid=908269]
 
* <strike>Download GAF bug</strike> [https://sourceforge.net/tracker/?func=detail&aid=2821450&group_id=36855&atid=908269]
 
* <strike>Links and GO.xref_abbs fun</strike> [https://sourceforge.net/tracker/?func=detail&aid=2996856&group_id=36855&atid=908269] [Done.]
 
** <strike>To be fixed by direct download?</strike> [Yes. Done.]
 
* <strike>Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream)</strike>
 
  
 
= New experimental (beta) features =
 
= New experimental (beta) features =
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** Start with term enrichment and work out
 
** Start with term enrichment and work out
  
= Deferred (alpha) features =
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= Known issues =
 
 
* Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)
 
* Term request client for SF (AKA ART) ([http://amigo.berkeleybop.org/cgi-bin/amigo/xp_term_request XP term request])
 
** Could this be better done in wiki?
 
* Coannotation (possible [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=gp_with_2_terms coannotation] interface)
 
* Advanced graph visualizations [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers_graph] [http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=layers2_graph]
 
** Early plugin framework done
 
** Heatmap and random plugin examples
 
* Workspaces, generalization of sessions ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=workspace_client concept])
 
* Addition of ubiquitous completion in boxes
 
** Front page with completion ([http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=front_page concept])
 
** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/go.cgi xprods in 1.5]
 
** [http://berkeleybop.org/alpha/goxprod/go.cgi xprods in 1.6]
 
***Examples (all using experimental bp_xp_mouse_anatomy xps):
 
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-assoc.cgi?term=MA:0000072 heart]
 
**** [http://toy.lbl.gov:9012/cgi-bin/go_xprod/term-details.cgi?term=GO:0007507&session_id=159amigo1208881634 heart development]
 
**** [http://berkeleybop.org/alpha/goxprod/amigo?mode=homolset_graph&set=1 TAZ orthoset] (notice heart in top right corner)
 
  
== Plans and TBD ==
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Please see the [https://sourceforge.net/tracker/?group_id=36855&atid=908269 tracker].
 
 
* Migrate peripheral pages to new framework (ongoing)
 
* Migrate core pages over to the new framework (ongoing)
 
* Cross-product and inter-ontology link support (may be punted until following release, but we will start on necessary infrastructure changes)
 
* Organizing annotation results by qualifier
 
* Expand the scope of community annotation (depending on user feedback).
 
* RSS update on terms and gps (could be tied to GONUTs for timeliness?)
 
* Looking at other ways to supply search results (perl clucene (apache) vs. lucene (tomcat) vs. solr (tomcat or jetty) vs. perl/xapian (apache) vs. ruby/ferret (apache))
 
** Look at ways of solving "*ase" problem (if it is) (e.g. reverse indexing and merge results)
 
 
 
[[Category:Software]]
 
[[Category:AmiGO]]
 

Latest revision as of 14:56, 22 May 2014

Status

Currently in production (as of 20013-10-17).

See AmiGO 2 for the future beta.

New features

  • Centralized internal testing (kappa)
  • GOOSE integrated into framework (GOOSE)
  • Rapid searching (live search)
  • New term details with improved graph view (term details for GO:0022008)
  • Speed--new caching sub-system for several components (see above for example)

New experimental (beta) features

  • [New] Static version of the Lucene search for fallback (term gene product).
  • Matrix tool (nmatrix)
  • Integrate new RG views from Sven (may be deferred) (phylotree)
    • Check licensing of JS tree viewer (ntree)
  • Relation filtering (may be bumped to deferred)
    • Start with term enrichment and work out

Known issues

Please see the tracker.