AmiGO 1 8
Status
Currently experimental. Expected to move into testing in the next couple of weeks.
- Testing:
[TODO] Run tanuki locally[TODO] Add fuzzing and psuedo-fuzzing to kappa(skip and later add to tanuki)- [TODO] General user testing on pre-production
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)
Current work
Frontend
Try and lighten up on some of the POSTs in AmiGO to make searches easier to trackFinish new term details pagefind way to avoid confusion with old viewTry different iconsTry dynamic lines to highlight ancestorsExplore text-based viewsConsensus reached, now polishingUse caching for gp counts?[bumped--necessary? will check with auto tester later]Default gp count valuesFix td downloads
Re-expose the buckets in slimmer[bumped--using new report on accordion]Update docs to most recent version (final item)
Backend
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]Setup production to produce their own indexes locally[will likely juggle frontend servers while producing indexes]See if association search index can be added/generated in a timely manner (talk to Tanya).[takes a while--will do more work on exp server.]
Bugs
- Slimmer bug [1]
Upload bug[2]Download GAF bug[3]Links and GO.xref_abbs fun[4] [Done.]To be fixed by direct download?[Yes. Done.]
Check and make sure that E. coli is done consistently (done first pass to 83333; need to check with Jim/upstream)
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
Deferred (alpha) features
Switch TE caching over from page render caching to data caching (currently evaluating sqlite3)[likely bumped in favor of new tools]- Term request client for SF (AKA ART) (XP term request)
- Could this be better done in wiki?
- Coannotation (possible coannotation interface)
- Advanced graph visualizations [5] [6]
- Early plugin framework done
- Heatmap and random plugin examples
- Workspaces, generalization of sessions (concept)
- Addition of ubiquitous completion in boxes
- Front page with completion (concept)
- xprods in 1.5
- xprods in 1.6
- Examples (all using experimental bp_xp_mouse_anatomy xps):
- heart
- heart development
- TAZ orthoset (notice heart in top right corner)
- Examples (all using experimental bp_xp_mouse_anatomy xps):
Plans and TBD
- 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?)