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