Dannon is running the weekly BRC-Analytics meeting this week. The plan is to open with a brief narrative retro of the past 7 days, ask about blockers, and then walk through the GitHub project board (galaxyproject/projects/56) as a group.
Week of Mar 9: 12 non-merge commits (3 contributors), 10 PRs merged, ~6.2K code LOC (excl. generated data), 10 issues closed — all workflow-first flow. Streak: 3 active days (Mon–Wed). Quiet since Thursday.
| Metric | Value |
|---|---|
| Commits to main (non-merge) | 12 |
| Contributors | 3 (Danielle, Fran, Dannon) |
| PRs merged | 10 |
| Total insertions | ~6.2K code + 79K generated JSON |
| Total deletions | ~1.3K code + 79K generated JSON |
| Issues closed | 10 |
| Active days | 3 (Mon Mar 10 – Wed Mar 12) |
| Days since last commit to main | 4 (since Mar 12) |
Note: raw git stats show 186K+/79K- but ~79K on each side is workflow-assembly-mappings.json regeneration, not real code churn.
This was a workflow-first week. The entire week was dominated by shipping the new workflow-first analysis flow — the ability to start from a workflow and then select assemblies, rather than the other way around. This was a multi-PR coordinated effort between Fran and Danielle, with Dannon handling infrastructure PRs.
The week had a burst pattern: all activity concentrated Mon–Wed (Mar 10–12), then silence. Three active days, zero commits since Wednesday.
Fran McDade — Ship of the week. Landed the massive #1183 (workflows entity page & workflow-first analysis flow, 3038+/620-, 135 files) plus 6 supporting PRs: reference assembly selection step, sidebar assembly details, stepper integration, GA2 workflows, no-results state, taxonomy filtering. This is easily 5K+ LOC of new UI work across the entire workflow-first experience. Also has 2 open draft PRs continuing this work (strandedness support, human-friendly taxonomy filters).
Danielle Callan — Followed up Fran's UI work with the data plumbing: built the workflow-assembly mapping system that validates which workflows are compatible with which assemblies at build time (#1187). Generated QC reports, added build-time mapping JSON, and filtered the workflows page to only show valid assemblies. 7 non-merge commits across 2 days.
Dannon — Infrastructure: merged #1096 (env config fallback) and #1118 (mypy type checking for Python). Cut the v0.24.0 release (#1185).
feat: 7 (58%) ██████████████████████████████
fix: 2 (17%) ████████
refactor: 1 ( 8%) ████
chore: 2 (17%) ████████
Healthy feat-dominant mix. Low fix ratio — this was greenfield feature work, not firefighting.
4x catalog/build/ts/build-workflow-mappings.ts
4x app/views/WorkflowsView/utils.ts
3x catalog/build/ts/build-catalog.ts
3x app/views/WorkflowsView/workflowsView.tsx
3x scripts/sync-api-brc-analytics.sh
All workflow-related. Very focused work.
#1183 — Workflows Entity Page & Workflow-First Analysis Flow (Fran McDade) 3038+/620- across 135 files. New entity page for workflows, explore view with filters, workflow configuration page, reference assembly selection with full modal, assembly selector table, assembly summary, data selector, and truncated text utility. This is the foundation for the new workflow-first UX.
- Coordinated multi-PR feature delivery — Fran broke the massive workflow-first feature into logical, reviewable chunks (#1161 → #1176 → #1178 → #1179 → #1183). Danielle followed with validation. Clean sequencing.
- Build-time safety — The workflow-assembly mapping system catches incompatible workflow/assembly combos at build time rather than letting users discover them at runtime. Good defensive design.
- Infrastructure hygiene — Dannon snuck in mypy and env config improvements while the feature train was running. Low-risk, high-value.
- 4 days of silence — Nothing has landed since Wednesday. Are PRs stuck in review? Is everyone context-switching?
- Open review queue growing — 4 non-draft PRs awaiting review (#1194, #1174, #1159, #1069). Some of these are straightforward.
- Generated data in git — The 79K-line JSON files in
catalog/output/create noisy diffs. Worth discussing whether there's a better approach long-term.
| Column | Count |
|---|---|
| In Progress | 20 |
| Todo | 24 |
| Done | 391 |
| (no status) | 65 |
500 items total — the board is at the GitHub project item limit. Some cleanup of Done items may be needed.
All workflow-first related:
- #1186 Validate workflow-assembly compatibility (d-callan)
- #1180 Add workflows to GA2 (frano-m)
- #1177 Compare/filter workflow taxonomy id (frano-m)
- #1175 No workflows message (frano-m)
- #1150 Remaining stepper integration (NoopDog/frano-m)
- #1149 Sidebar assembly details (NoopDog/frano-m)
- #1148 Assembly selection modal (NoopDog/frano-m)
- #1147 Reference assembly selection step (NoopDog/frano-m)
- #1146 Workflow configuration page (NoopDog/frano-m)
- #1144 Workflows entity page (NoopDog/frano-m)
P1 (High Priority):
| # | Title | Assignee(s) | Notes |
|---|---|---|---|
| #723 | ENA picker refinements | MFM, NoopDog, frano-m | 3 assignees — who's point? Recent activity? |
| #783 | Link from NCBI to BRC Analytics | d-callan | Status update? |
| #709 | Roadmap | NoopDog | Ongoing |
| #710 | Regularly updatable DB Backend | jdavcs | Status? |
| #982 | Learn section updates | scottcain | Status? |
P2:
| # | Title | Assignee(s) | Notes |
|---|---|---|---|
| #582 | scRNA-Seq workflow errors | mvdbeek | Long-running — stalled? |
| #537 | Galaxy pages integration | NoopDog | Depends on mockups (#703 in Todo) |
| #315 | Build diploid variant calling workflow | mvdbeek | Long-running — stalled? |
| #804 | Integrate LoganSearch | dannon, Smeds | Status? |
| #765 | LLM prompt on home page | dannon, NoopDog, d-callan | Status? |
| #766 | LLM prompt for SRA picker | dannon, NoopDog, d-callan | Status? |
| #809 | Fungal RNAseq workflow | nekrut | Status? |
| #815 | Mission/vision statements | NoopDog, d-callan | Status? |
| #816 | Define/track key metrics | d-callan | Status? |
Potentially Stalled / Needs Attention:
| # | Title | Assignee(s) | Concern |
|---|---|---|---|
| #691 | Fungal gene models from VEuPathDB | unassigned | No priority, no assignee — should this be in progress? |
| #718 | feat: create range filter (#382) | unassigned | Appears to be a PR/issue duplicate of #382 — clean up? |
| #129 | Mirror track data from VEuPathDB/UCSC | scottcain | Old issue — still active? |
| #382 | Create range filter | MFM | Has open draft PR #718 — check progress |
| #523 | Review workflows for additional filters | mvdbeek | No priority set |
| #736 | Gene models and community annotations to UCSC | scottcain | P3, long-running |
Ready to pick up?
| # | Title | Assignee(s) | Priority |
|---|---|---|---|
| #812 | Login/Access to users Galaxy API | dannon | P1 — Dannon's. Ready to start? |
| #803 | Integrate LexicMap | dannon, Smeds, kbeavers | P1 |
| #726 | Expose ENA text search on picker | unassigned | P1 — needs an owner |
| #802 | Add featured workflow runs | unassigned | P2 — needs an owner |
Stale / Needs Triage:
| # | Title | Notes |
|---|---|---|
| #190 | Conferences to target on 2025 | Year is wrong — still relevant? |
| #475 | Redo analysis of Pv4 dataset | nekrut — old, still needed? |
| #257 | Specs for "Comparative page" | nekrut — long-lived design item |
| #577 | More detail when accessions don't produce results | unassigned — still relevant with new workflow-first flow? |
| #579 | Stepper allows accessions not appropriate | NoopDog — possibly addressed by new workflow work? |
Unassigned items in Todo (need owners):
- #792 [GA2] Create help/forum page
- #577 More detail in workflow stepper
- #692 Add entry for how to request new genomes
- #705 Create an assembly (P3)
- #811 Integrate workflow reports (P2)
- #817 Define initial target user communities (P1)
Ready for review (not draft):
| PR | Author | Title | Status |
|---|---|---|---|
| #1194 | frano-m | fix: remove coming soon flag on workflows page | Needs review |
| #1174 | d-callan | feat: add more VGP phase 1 assemblies to ga2 | Needs review |
| #1159 | dannon | feat: add MCP server for catalog and ENA data | Needs review |
| #1069 | d-callan | feat: updating eukaryote assemblies | Needs review — been open a while |
Draft PRs (FYI):
| PR | Author | Title | Notes |
|---|---|---|---|
| #1195 | frano-m | make workflow taxonomy filters human-friendly | Active — continues workflow work |
| #1184 | frano-m | add strandedness support to DE workflow form | Active |
| #1141 | scottcain | adding youtube section to learn | Draft since ? |
| #1051 | Smeds | working jbrowse embedding | Long-running draft |
| #940 | github-actions | update data catalog 2025-11-02 | Stale — 4+ months old |
| #904 | Smeds | add ga2 bucket file | Long-running draft |
| #894 | dannon | Galaxy tool execution integration demo | Draft/experimental |
| #718 | frano-m | create range filter | Long-running draft |
#804 — Integrate LoganSearch (P2, with Smeds)
- Created Sep 2025, last updated Oct 2025. Empty body, 1 comment.
- Theme: "Improve data discovery and access." Co-assigned with Smeds.
- Talking point: What's the current status? Is Smeds actively working on this or is it blocked? Does this need to be deprioritized given other work?
#765 — LLM prompt on the home page (P2, with NoopDog, d-callan)
- Created Aug 2025, last updated Sep 2025. Has mockups but 0 comments.
- Shows a search-style LLM interface on the homepage for querying BRC data.
- Talking point: This overlaps with the MCP server work (#1159) and the AI assistant PR (#1155, already merged). Worth discussing whether the MCP approach changes the scope of this issue — the backend is largely built, it's the frontend UX that needs design work.
#766 — LLM prompt for SRA picker (P2, with NoopDog, d-callan)
- Created Aug 2025, 1 comment. Has mockups showing text-based search for SRA data.
- Talking point: Same as #765 — the MCP/assistant infrastructure could serve this. Is this still the right UX direction or has thinking evolved?
#812 — Login/Access to users Galaxy API (P1, solo)
- Created Sep 2025, 6 comments, last updated Jan 2026. Well-scoped issue with detailed requirements covering user identity, Galaxy API access, and use cases (listing histories, workflow status, user profile).
- You already did significant research on this (Keycloak auth testbed, branch
keycloak-auth-testbed, documented in~/.claude/plans/keycloak-auth-testbed/). - Talking point: Ready to move to In Progress? What's the timeline? Are there dependencies on Galaxy-side Keycloak/OIDC work?
PR #1159 — feat: add MCP server for catalog and ENA data (open since Feb 27)
- 1541+/5-, 8 files. Embeds an MCP server at
/api/v1/mcpin the backend. - 12 tools: 10 catalog (organisms, assemblies, workflows, compatibility) + 2 ENA search.
- 2 comments, 0 reviews. Updated Mar 12.
- Talking point: This needs a reviewer. It's self-contained (backend only, no frontend changes). Could demo it live if helpful — anyone with Claude Desktop can point at the endpoint.
PR #894 — Galaxy tool execution integration demo (draft)
- Experimental/demo work. Mention if relevant but don't need to drive discussion on it.
1. Narrative Retro (5 min) — Dannon presents
- "This was a workflow-first week. Fran shipped the entire workflow entity page and workflow-first analysis flow across 7 PRs. Danielle followed with workflow-assembly mapping validation that ensures only compatible workflows show up. Dannon did infrastructure (mypy, env config, v0.24.0 release). 10 issues closed, all workflow-related."
- "All activity was Mon–Wed, nothing since. 4 non-draft PRs sitting in the review queue."
2. Blockers Check (2 min)
- "Anyone blocked on anything right now?"
3. Review Queue (5 min)
- Walk through the 4 open non-draft PRs. Assign reviewers or decide to merge.
- Flag the stale PRs (#940, #904) — close or keep?
4. Board Walk-through (15 min)
- In Progress: Check each item for movement. Flag the 6 potentially stalled items listed above.
- Todo: Any items ready to move to In Progress? Assign owners to unassigned P1/P2 items.
- Housekeeping: Board is at 500 items. Consider archiving completed items.
5. Wrap-up (3 min)
- Confirm priorities for the coming week
- Any items for next meeting?
Before the meeting:
- Pull up the project board: https://github.com/orgs/galaxyproject/projects/56
- Have this document open for reference
- Open the PR list: https://github.com/galaxyproject/brc-analytics/pulls
- Note:
originremote points to your fork (dannon/brc-analytics),upstreamis galaxyproject — recent merges only show onupstream/main