|
|
(15 intermediate revisions by 2 users not shown) |
Line 1: |
Line 1: |
| | [[Category:Software]] |
| | [[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. | | Currently in [http://amigo1.geneontology.org production] (as of 20013-10-17). |
|
| |
|
| * Testing:
| | See [[AmiGO 2]] for the future beta. |
| ** <strike>[TODO] Run tanuki locally</strike>
| |
| ** <strike>[TODO] Add fuzzing and psuedo-fuzzing to kappa</strike>(skip and later add to tanuki)
| |
| ** [TODO] General user testing on pre-production
| |
|
| |
|
| = New features = | | = New features = |
Line 15: |
Line 14: |
| * 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) | | * 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]
| |
| * <strike>Update docs to most recent version (final item)</strike>
| |
|
| |
| == 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 = |
Line 57: |
Line 24: |
| ** Start with term enrichment and work out | | ** Start with term enrichment and work out |
|
| |
|
| = Deferred (alpha) features = | | = Known issues = |
| | |
| * <strike>Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)</strike> [likely bumped in favor of new tools]
| |
| * 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 ==
| | 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)
| |
| * Relations for TE
| |
| * Slimmer rebuild
| |
| * Lucene
| |
| ** Replace traditional search with lucene-backed
| |
| ** Everything to consume Solr service
| |
| * Trying Galaxy
| |
| ** In and out from AmiGO
| |
| ** Sessions via local Galaxy install
| |
| * 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?)
| |
| | |
| [[Category:Software]]
| |
| [[Category:AmiGO]]
| |