{"quest":{"id":"q-ai-tools-landscape","name":"AI Tools Landscape","description":"Living catalog of AI-for-science tools, platforms, agents, and benchmarks. Uses wiki entity_type='ai_tool' with structured frontmatter (category, specializations, pricing, benchmarks, open-source status). Browsing page at /forge/landscape with filters by category, specialization, pricing. Seeded with 23 entries from inspirations page. Kept current via agent scanning + staleness badges. Spec: docs/planning/specs/q-ai-tools-landscape_spec.md","layer":"Forge","priority":64,"status":"paused","created_at":"2026-04-06T13:25:19.757994+00:00","updated_at":"2026-04-10T14:44:10.355870+00:00"},"tasks":[{"id":"c6a6770f-3d79-48a9-a5f5-af7c16446db5","title":"[Landscape] Comparison view: side-by-side tool evaluation","description":"Add /forge/landscape/compare?tools=slug1,slug2 page showing side-by-side comparison of 2-3 tools: features, benchmarks, pricing, integrations. Uses frontmatter fields.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"open","priority":52,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-07 02:14:20","updated_at":"2026-04-25T07:47:19.794436+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: ORPHAN_BRANCH — 1 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"safety\": 8}}"},{"id":"4be33a8a-4095-401e-8223-990b9d29283b","title":"[Forge] Curate AI-for-science tool landscape — priority tiers 1-3","description":"Curate AI-for-science tool landscape pages. Create wiki_pages with entity_type='ai_tool' for each.\n\nPRIORITY TIER 1 (directly competitive/complementary to SciDEX):\n- Biomni (Stanford, 150+ tools) — DONE\n- FutureHouse (Robin, PaperQA2, Aviary, Kosmos) — DONE\n- ScienceClaw (MIT multi-agent discovery) — DONE\n- Inference.bio / Variant Bio — DONE\n- Google AI co-scientist\n- OpenAI Deep Research\n- Owkin K-Navigator / OwkinZero — DONE\n- K-Dense (scienceclaw-based, Claude skills)\n- Autoscience (Carl autonomous scientist)\n- BenchSci LENS\n- Causaly agentic research\n\nPRIORITY TIER 2 (relevant platforms):\n- Mithrl (NGS lifecycle) — DONE\n- Recursion/Exscientia (merged, virtual cells)\n- Converge Bio (biotech LLM hub)\n- ScienceMachine / Sam AI Bioinformatician\n- Tag.bio (Parkinson's Foundation partner)\n- Kepler AI (TahoeDive, perturbation data)\n- Pluto Bio (multi-omics AI agents)\n- Synthesize Bio (GEM-1 gene expression model)\n- Elucidata (multi-omics data platform)\n\nPRIORITY TIER 3 (agent frameworks / benchmarks):\n- The AI Scientist (Sakana AI)\n- Agent Laboratory\n- STORM (Stanford, literature synthesis)\n- OctoTools (Stanford, extensible agent tools)\n- BioDiscoveryAgent (Stanford, genetic perturbation)\n- RE-Bench / MLE-Bench / BioML-Bench / CureBench\n- GAIA benchmark / DABStep\n\nEach page should have: URL, category, key features, relevance to SciDEX, last reviewed date.\nUse entity_type=\"ai_tool\" so pages don't pollute /wiki neuroscience content.\nTrack progress by updating this spec with which tools have been covered.","status":"blocked","priority":92,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T05:55:50.359740+00:00","updated_at":"2026-04-24T13:13:27.340450+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4be33a8a_4095_forge_curate_ai_science_tool_landscape_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"completion_shas\": [\"6570061c8c0ab8a0bb9112eb40e34d578575c857\", \"3fe2b90c6710ec9b40e9fb1ffa7eb42600a105cd\", \"9c23d41f33a7f6cfb5600df9a6183ffa64cf3bf9\", \"27cf88fe91a30928e2c103544a231db09c9ae4f4\", \"84d3f89e41fcd43e04c764ba2f2d5c513b82213b\", \"ca46257815b7334467b718f0c152ce3a496731a1\", \"f34158d3b38fccaa379ecc25e135558b02786011\", \"05db6f017f10044da09f36c4fc43c4339419c3a9\", \"cf2ebfd23f4b985084b736c05b4e57cb7c3410e3\"], \"completion_shas_checked_at\": \"2026-04-13T05:55:50.345969+00:00\", \"completion_shas_missing\": [\"311a2347e5bdebca1c4c97a35d43670dae44f5ea\", \"ccf118f34c28b3e575428b2c0cf69e9975405e83\", \"5cc0f48d987cc33d8792562c72a984156e25edc1\", \"d9e65786694a97bfd67cb5b4aee51f4926292e27\", \"ab72f1346494395bec0b7a81d7b83abd6560dc6f\", \"c5288e9c95e1da2b534fee5ec420df998e577854\", \"cb6cedd8b12660ea5188816357f127e17f5454c9\"]}"},{"id":"f2f6629a-1f40-4f3e-aba1-126f58b17fb5","title":"[Landscape] Auto-discovery agent: scan arXiv + GitHub for new AI-for-science tools","description":"Recurring task: weekly scan of arXiv cs.AI/q-bio, GitHub trending, and tech news for new AI-for-science platforms/tools/benchmarks. Create draft ai_tool wiki entries with structured frontmatter. Flag entries over 90 days since last_reviewed as stale.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"closed","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-06 13:49:33","updated_at":"2026-04-13 20:36:44","summary":"","completion_notes":"","last_error":"Audit reopened: ORPHAN_BRANCH — 1 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"b837ce33-4343-49cd-ac77-f34dfed301f7","title":"[Landscape] Expand catalog to 50+ entries with complete metadata","description":"Add missing tools: Genentech BALM, Insilico Medicine, Recursion Pharma, BenevolentAI, Isomorphic Labs, OpenFold, ESM (Meta), RoseTTAFold, scGPT, CellTypist, etc. Ensure each has complete frontmatter: URL, pricing, benchmarks, key people, specializations.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"closed","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-06 14:04:23","updated_at":"2026-04-13 20:36:44","summary":"","completion_notes":"","last_error":"Audit reopened: ORPHAN_BRANCH — 1 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"178a2a47-dbfd-478b-bbd1-071c16d88451","title":"[Landscape] Integration roadmap: track which tools to add to SciDEX","description":"Surface tools with scidex_integration='planned' prominently. Link to Orchestra tasks for integration work. Track progress: planned → in-progress → integrated. Helps prioritize Forge development.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n   spec and the relevant files on origin/main NOW. The original task\n   may have been written against a state of the code that no longer\n   exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n   has evolved past the need for this work (different architecture,\n   different priorities), close the task with reason \"obsolete: <why>\"\n   instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep='<task-id>'`\n   and read the related commits. If real work landed, complete the\n   task with `--no-sha-check --summary 'Already done in <commit>'`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n   agents have been working on this codebase. Before committing, run\n   `git log --since='24 hours ago' -- <files-you-touch>` to see what\n   changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n   refactor, do not \"fix\" unrelated issues, do not add features that\n   weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"closed","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-06 13:58:58","updated_at":"2026-04-13 20:36:44","summary":"","completion_notes":"","last_error":"Audit reopened: ORPHAN_BRANCH — 1 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"}],"reviews":[],"effectiveness":{},"commits":[{"hash":"59405c7c5","message":"docs: AGENTS.md — document Path A/B/C task completion semantics [task:docs-agents-completion] (#40)","date":"2026-04-25"},{"hash":"e5b5848a0","message":"WIP on orchestra/task/8fcc8dc8-debate-artifact-version-pinning-referenc: 8a24c2fa2 [Senate] Delete broken restore_database.sh (#38)","date":"2026-04-25"},{"hash":"50e5ffcfe","message":"index on orchestra/task/8fcc8dc8-debate-artifact-version-pinning-referenc: 8a24c2fa2 [Senate] Delete broken restore_database.sh (#38)","date":"2026-04-25"},{"hash":"0d37f5fce","message":"untracked files on orchestra/task/8fcc8dc8-debate-artifact-version-pinning-referenc: 8a24c2fa2 [Senate] Delete broken restore_database.sh (#38)","date":"2026-04-25"},{"hash":"48f8d2fe3","message":"feat: surface all five SciDEX layers in nav [task:cba19c94-1724-4d5a-b89d-96c73c25f12a] (#39)","date":"2026-04-25"},{"hash":"1f0e35929","message":"Squash merge: orchestra/task/b1a8e549-cross-cutting-wire-existing-k-dense-skil (2 commits)","date":"2026-04-25"},{"hash":"ddb7db381","message":"[Agora] Wire existing K-Dense-backed tools into debate orchestration [task:b1a8e549-6f31-43c5-80f5-7c4717c267e4]","date":"2026-04-25"},{"hash":"76b71427a","message":"[Agora] Wire existing K-Dense-backed tools into debate orchestration [task:b1a8e549-6f31-43c5-80f5-7c4717c267e4]","date":"2026-04-25"},{"hash":"779e85c3a","message":"[Senate] Verify /resources dashboard complete; check off acceptance criteria [task:82074adc-507f-4e6b-9092-e2ceee79e7d4]","date":"2026-04-25"},{"hash":"4c66a8e09","message":"[Senate] Establish emergency access recovery procedures [task:e643cdd3-afd6-410f-a366-a6297d112127]","date":"2026-04-25"},{"hash":"7265a06b4","message":"Squash merge: orchestra/task/b1a8e549-cross-cutting-wire-existing-k-dense-skil (1 commits)","date":"2026-04-25"},{"hash":"58406ec64","message":"[Atlas] Dashboard artifact type: living web views with data source rendering [task:a17-28-DASH0001]","date":"2026-04-25"},{"hash":"8a24c2fa2","message":"[Senate] Delete broken restore_database.sh (#38)","date":"2026-04-25"},{"hash":"b98a1fa18","message":"[Senate] Delete broken restore_database.sh","date":"2026-04-25"},{"hash":"e846f82ef","message":"[Senate] Refresh BACKUP_RESTORE.md + docs/runbooks/emergency_restore.md (#37)","date":"2026-04-25"},{"hash":"43972a45e","message":"[Senate] Refresh BACKUP_RESTORE.md + docs/runbooks/emergency_restore.md","date":"2026-04-25"},{"hash":"2c7dbfe7f","message":"[Senate] Delete 9 obsolete backup scripts/units (continuation of Phase A-D cleanup) (#36)","date":"2026-04-25"},{"hash":"9743eb298","message":"[Senate] Delete 9 obsolete backup scripts/units (continuation of Phase A-D cleanup)","date":"2026-04-25"},{"hash":"3e72d8383","message":"[Agora] Wire 3 missing tools into debate skill_functions, fix citation persistence bug [task:b1a8e549-6f31-43c5-80f5-7c4717c267e4]","date":"2026-04-25"},{"hash":"4310e9854","message":"[Demo] Work log: figures verified complete — 140/140 analyses covered [task:df201d8f-4b89-4258-9148-eb1028fc1fbd]","date":"2026-04-24"}]}