Projects update meeting 2022-02-16
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Attendees
- Present: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
- Regrets:
Announcement
David & Kimberly out next Wednesday
Finalize GOC meeting date
https://doodle.com/poll/nhwsxa4e8kaxfxgd
Decision:
- Tuesday April 26 to Thursday April 28, 7AM-11AM Pacific time
- Virtual meeting (with possibility of local nodes)
- SAB in the fall (may be uncoupled form GOC meeting?)
Projects update
Procedure for project management
- From the broader grant aims, PIs/managers select a list of ACTIVE projects
- Active projects have a PI, PO, TL, and necessary resources
- Active projects have a Project in GitHub with a set list of tasks (tickets).
- The list of tasks is reviewed with the entire team (including PI and PO) to define/restrict the scope of the project. A 'future' project may be created for longer-term tasks.
- Tasks can be added/removed in the course of a project, but it is expected that major changes and addition of time-consuming tasks are reviewed with the PI/PO and to approve the new scope.
- Because it is difficult to estimate a delivery date, projects are reviewed every 6-8 weeks, sooner if needed (or upon completion).
Current active projects: (adapted from Paul's list and from Seth's matrix)
| Project name | Link to GH project | Resources: PI, PO, TL, Other resources | Next review | Follow up review | Aligned with Matrix? | Notes |
|---|---|---|---|---|---|---|
| Software improvement | ||||||
| Finalize AmiGO default relation change (Aim 3) | AmiGO default relation GH project | PI: Chris, PO:Chris, TL: Seth, Others: Seth | 2022-02-16 | 2022-03-02 or 2022-03-16 | Yes | To review and close after the next release |
| Software improvements (to prioritize between API or pipeline) ++ Seth: specify (Seth would like to remove unneeded code) | PLANNING Pipeline cleanup & PLANNING GO API | PI: Chris, PO:??, TL: Seth, Others: Seth, Dustin, Sujay? | 2022-02-23 - Review specs | Needs to be better specified | ||
| Alliance software support | Alliance software support | PI: , PO:??, TL: Seth, Others: | No | |||
| Noctua improvement and maintenance | Noctua 2021 & Noctua 2020 | PI: Paul , PO: Kimberly, TL: Seth, Others: Tremayne, Jim | No | |||
| Ongoing data QC and pipeline maintenance | Ongoing data QC and pipeline maintenance | PI: Chris, PO:Pascale, TL: Seth, Others: Seth, Dustin, Sujay, Jim? | 2022-02-23 - Review project status | Not applicable | ||
| Essential software maintenance | Essential software maintenance | PI: Chris, PO:Pascale, TL: Seth, Others: Seth, Dustin, Sujay, Jim? | Ad hoc if there is a big bug? | Not applicable | ||
| Remove some main roadblocks for GO-CAM models curation (Aim 2) | ||||||
| NEO load of new sequences | NEO load GH project | PI: Chris, PO: Pascale , TL:, Seth Others: Sujay | 2022-03-16 | Yes | ||
| New visual editor (Tremayne) -> ready to push to Noctua dev? | Visual Pathway editor GH project | PI: Paul, PO: Paul, TL:, Others: Tremayne | 2022-03-02 | Yes | Software call: OK to move to development; Need to define plan for next phase: testing, which bugs/features need to be fixed/added | |
| Model copy | PLANNED Old Shallow Model Copy GH project | PI: Paul, PO: Kimberly, TL: Jim, Others: Tremayne | 2022-03-02 - Review specs | No - was supposed to be Feb | ||
| Noctua output | GPAD output | PI: Chris, PO: Kimberly, TL:?, Others: Jim | 2022-03-30 - Review specs | +/- : Planned for March, but project not yet defined or resourced | ||
| Simple version of automation of Noctua updates (planned) | PI: Chris, PO: TBD, TL: Seth, Others: | 2022-02-23 - Review specs | No | |||
| Complete MOD imports (Aim 2) | ||||||
| Define specific remaining tasks for MOD imports + choose priorities for this period | To be created - MGI - WB - SGD | PI: Chris, PO: Kimberly, TL: Seth, Others: David, Suzi, Dustin | 2022-03-23 | No | ||
| Annotation Extension Relation Review | Annotation Extension Relation Review | PI: , PO: Kimberly, TL: , Others: David, Dustin, Pascale | ||||
| Integrate YeastPathways in GO Cam | Yeast Pathways | PI: Paul, PO: , TL: Dustin, Others: | No | |||
| Ontology (Aim 1) | ||||||
| Phylogenetic taxon constraints | TC GH project - ontology repo | PI: Paul, PO: Pascale, TL: Jim, Others: | 2022-04-20 | Yes | ||
| Outreach/usability (Aim 3) | ||||||
| Switch to “species” for download outputs | PLANNED Improved Downloads ???? | PI: , PO:, TL:, Others: | 2022-03-23 - Review specs | No | ||
| Outreach - collect teaching materials in Google drive? | PI: Mike , PO: Suzi, TL:, Others: | 2022-04-xx before the GOC meeting | No | |||
| Noctua training material | Noctua training Project | PI: Mike , PO: Suzi, TL: NA, Others: David | 2022-04-xx before the GOC meeting | No | ||
| Other projects | ||||||
Annotation of protein-containing complexes in Noctua
- There is a new bug with entering Complex Portal IDs as enablers in Noctua Form
- This was introduced with a change in how protein-containing complexes are typed, and thus affected what is available in the autocomplete
- Current workaround is to use the 'Add Individual' functionality in the graph editor
- This and other issues that have arisen regarding annotating to complexes in Noctua made us realize we need to review current practice
- Can SGD curators meet the week of March 7th to let us know how they annotate complexes
- Note that we don't currently have a mechanism to derive and export complex annotations onto individual genes
- Also note that we are not up to the standards of IMEX/ComplexPortal for creation of complexes, so we have a parallel, albeit probably less stringent, way of assigning genes to complexes