Quest: AI for Science Tools Landscape

Quest: AI for Science Tools Landscape

ID: q-ai-tools-landscape Layer: Forge Priority: 75 Status: active Depends-on: Forge quest, Tools quest

Goal

Maintain a living catalog of AI-for-science tools, platforms, agents, and
benchmarks. Help researchers discover the best tools for their work. Help
SciDEX track what to integrate next.

Design decisions

Why wiki entity_type='ai_tool' (not a separate table)

• Reuses existing wiki infrastructure: search, cross-linking, KG edges
• Frontmatter JSON provides structured fields for filtering
• Agents can create/update entries using existing wiki workflows
• Excluded from /wiki neuroscience pages by entity_type filter

Keeping it current

• Agent scanning: recurring task scans arXiv, tech news, Product Hunt

for new AI-for-science launches. Creates draft entries.

• Staleness flag: entries with last_reviewed > 90 days get "needs review" badge
• Community updates: future: let visitors suggest edits / new entries
• Inspirations page: remains hand-curated highlights; landscape is comprehensive

Not polluting the wiki

• entity_type='ai_tool' is EXCLUDED from /wiki search + /wiki listing
• Dedicated browsing page at /forge/landscape
• Links TO neuroscience wiki (tools that study X → link to X's wiki page)
• Links FROM wiki TO landscape (wiki pages can reference relevant tools)

Frontmatter schema for ai_tool entries

{
  "tool_category": "platform|agent|model|benchmark|database|library|framework",
  "specializations": ["drug_discovery","protein_engineering","genomics",
                       "literature_synthesis","hypothesis_generation",
                       "clinical_trials","single_cell","imaging","multi_agent"],
  "pricing": "free|freemium|paid|enterprise|open_source",
  "open_source": true,
  "url": "https://example.com",
  "github_url": "https://github.com/org/repo",
  "paper_url": "https://arxiv.org/abs/XXXX.XXXXX",
  "paper_title": "Paper Title (Year)",
  "benchmarks_run": ["SWE-bench","BixBench","BioML-bench"],
  "benchmark_scores": {"BixBench": "17%", "SWE-bench": "33%"},
  "founded_year": 2024,
  "funding_stage": "seed|series_a|series_b|public|academic",
  "funding_amount": "$10M",
  "team_size": "10-50",
  "key_people": ["Jane Doe (CEO)", "John Smith (CTO)"],
  "data_sources": ["PubMed","UniProt","AlphaFold"],
  "scidex_integration": "integrated|planned|none",
  "scidex_tool_ids": ["pubmed_search","uniprot_lookup"],
  "last_reviewed": "2026-04-06",
  "maturity": "research|beta|production|deprecated",
  "tags": ["multi-agent","web-based","api-available"]
}

Page: /forge/landscape

Filters

• Category dropdown (platform, agent, model, benchmark, ...)
• Specialization tags (multi-select)
• Pricing filter (free, open-source, paid)
• Maturity filter
• SciDEX integration status
• Text search across title + description

Display

• Grid or table view toggle
• Each card: logo/icon, name, one-line description, category badge, tags
• Expandable: full description, benchmarks, key people, links
• Sort by: name, category, recently reviewed, funding

Sections

Platforms & Agents — end-to-end AI scientist systems

Models & Methods — foundation models, specialized architectures

Databases & Knowledge Graphs — data infrastructure

Benchmarks — evaluation suites

Libraries & Frameworks — open-source building blocks

Seed data

Migrate ~30 entries from /docs/inspirations (AI for Science sections) into
ai_tool wiki entries with structured frontmatter. These become the initial
catalog.

Acceptance criteria

Future extensions

• Comparison view: side-by-side tool comparison ✓ done 2026-04-06
• Benchmark leaderboard: tools ranked by benchmark scores
• Integration roadmap: which tools SciDEX plans to integrate
• User ratings/reviews
• Auto-discovery agent scanning arXiv + GitHub trending

Work Log

Already Resolved — 2026-04-27 17:00:00Z

The /forge/landscape/compare route is live on origin/main via commit 223a3b165.
Evidence: curl http://localhost:8000/forge/landscape/compare returns 200 with "Side-by-Side Tool Comparison" content.
Comparison with 3 real tools (ai-tool-4paradigm-biomed,ai-tool-absciai,ai-tool-agent-laboratory) returns the comparison table with overflow-x:auto wrapper.
Original work was committed in orphan 9d39cf649 ([Landscape] Add /forge/landscape/compare …); the code landed on main through the large squash merge in 223a3b165 (2026-04-27).

2026-04-06 — Comparison view [task:c6a6770f-3d79-48a9-a5f5-af7c16446db5]

Implemented /forge/landscape/compare?tools=slug1,slug2[,slug3]:

• New FastAPI route GET /forge/landscape/compare accepting comma-separated slugs (up to 3)
• Side-by-side comparison table with 15 fields: category, maturity, pricing, open source, specializations, SciDEX integration, benchmarks, benchmark scores, funding, team size, data sources, tags, last reviewed, description
• Differences highlighted (slightly tinted rows); same values shown in muted style
• Tool selector dropdowns (3 slots) with auto-submit JS to swap tools
• Added "Compare Tools" entry to Forge nav dropdown
• Added "+ Compare" button on each landscape card; JS tracks up to 3 selected tools; sticky compare bar shows selected tools and links to compare URL
• Tested: Python syntax OK; route renders with selector form when no tools provided

2026-04-06 — Auto-discovery scan #1 [task:f2f6629a-1f40-4f3e-aba1-126f58b17fb5]

Weekly scan of arXiv cs.AI/q-bio, GitHub trending, and tech news.
Script: scripts/landscape_scan_2026_04_06.py

12 new entries added (catalog now 35 total):

Slug	Title	Category	Maturity
ai-tool-ai-scientist-v2	AI Scientist-v2 (Sakana AI)	agent	research
ai-tool-google-ai-co-scientist	Google AI Co-Scientist (DeepMind)	platform	beta
ai-tool-evo2	Evo 2 (Arc Institute / NVIDIA / Stanford)	model	production
ai-tool-boltz2	Boltz-2 (MIT / Recursion)	model	beta
ai-tool-openfold3	OpenFold3 (OpenFold Consortium)	model	beta
ai-tool-allen-bkp	Allen Institute Brain Knowledge Platform	database	production
ai-tool-drugclip	DrugCLIP (Tsinghua / Peking University)	model	production
ai-tool-agent-laboratory	Agent Laboratory (Schmidgall)	framework	beta
ai-tool-frontierscience-bench	FrontierScience Benchmark (OpenAI)	benchmark	production
ai-tool-fairchem-v2	FAIRChem v2 / UMA (Meta FAIR Chemistry)	framework	production
ai-tool-sciscigpt	SciSciGPT (Northwestern / Dashun Wang Lab)	agent	beta
ai-tool-ai-researcher-hkust	AI-Researcher (HKUST / novix.science)	agent	beta

Staleness check: 0 entries flagged (all reviewed within 90 days).

Highlights for SciDEX:

• Evo 2: 40B DNA model — direct relevance for variant effect prediction in APOE, MAPT, LRRK2
• Allen Institute BKP: 34M cells / 22 species, Alzheimer's + Parkinson's data — Atlas integration candidate
• DrugCLIP: 10M× faster virtual screening (Science 2026) — Forge tool candidate
• Google AI Co-Scientist: multi-agent Gemini debate system mirrors SciDEX Agora architecture
• Boltz-2 + OpenFold3: open structure + binding affinity prediction — drug discovery pipeline

2026-04-06 — Catalog expansion to 50+ entries [task:b837ce33-4343-49cd-ac77-f34dfed301f7]

Expanded catalog from 35 to 53 entries with complete metadata.
Script: scripts/landscape_expand_2026_04_06.py

18 new entries added (catalog now 53 total):

Slug	Title	Category	Maturity
ai-tool-insilico-medicine	Insilico Medicine (Chemistry42 / PandaOmics)	platform	production
ai-tool-recursion	Recursion Pharmaceuticals (Recursion OS)	platform	production
ai-tool-benevolentai	BenevolentAI	platform	production
ai-tool-isomorphic-labs	Isomorphic Labs (DeepMind spinout)	platform	production
ai-tool-genentech-balm	BALM — Genentech Biomedical Language Model	model	research
ai-tool-alphafold3	AlphaFold3 (Google DeepMind / Isomorphic Labs)	model	production
ai-tool-esm3	ESM-3 / ESMFold (Meta FAIR)	model	production
ai-tool-rosettafold2	RoseTTAFold2 / RoseTTAFold All-Atom (Baker Lab)	model	production
ai-tool-rfdiffusion	RFdiffusion (Baker Lab / UW IPD)	model	production
ai-tool-proteinmpnn	ProteinMPNN (Baker Lab / UW IPD)	model	production
ai-tool-scgpt	scGPT (University of Toronto)	model	production
ai-tool-celltypist	CellTypist (EMBL-EBI)	model	production
ai-tool-scfoundation	scFoundation (Tsinghua University)	model	production
ai-tool-elicit	Elicit (AI Research Assistant)	agent	production
ai-tool-consensus	Consensus (AI Academic Search)	agent	production
ai-tool-atomwise	Atomwise (AIMS Platform)	platform	production
ai-tool-genie2	Genie2 (Generate Biomedicines)	model	production
ai-tool-absciai	AbSci (Zero-Shot Antibody Design)	platform	production

Frontmatter completeness: All 18 entries include url, pricing, maturity, open_source, key_people, specializations, tags, last_reviewed. Entries for industry platforms (Insilico, Recursion, BenevolentAI, Isomorphic, Atomwise, AbSci, Genie2) include founded_year, funding_stage, funding_amount, team_size. Entries with papers include paper_url, paper_title.

Highlights for SciDEX (Neurodegeneration):

• ESM-3 + ProteinMPNN + RFdiffusion + RoseTTAFold2: Complete Baker Lab / EvolutionaryScale protein design toolkit
• AlphaFold3: Gold standard for neurodegeneration target structures (tau, amyloid, α-synuclein)
• scGPT + CellTypist + scFoundation: Single-cell foundation models for brain atlas analysis
• BenevolentAI: KG-driven ALS/Parkinson's programs — direct SciDEX neurodegeneration overlap
• Isomorphic Labs: DeepMind spinout ($2.9B+ pharma deals) — state-of-the-art structure-based drug design reference

2026-04-08 — Priority Tiers 1-3 complete [task:4be33a8a-4095-401e-8223-990b9d29283b]

Curated and created wiki pages for all remaining Priority Tier 1-3 tools.
Script: scripts/landscape_tiers_2026_04_08.py

23 new entries added (catalog now 82 total):

Slug	Title	Tier	Category
ai-tool-openai-deep-research	OpenAI Deep Research	T1	agent
ai-tool-autoscience-carl	Autoscience Carl	T1	agent
ai-tool-benchsci-lens	BenchSci LENS	T1	platform
ai-tool-causaly	Causaly	T1	platform
ai-tool-converge-bio	Converge Bio	T2	platform
ai-tool-sciencemachine-sam	ScienceMachine Sam	T2	agent
ai-tool-tag-bio	Tag.bio	T2	platform
ai-tool-kepler-ai	Kepler AI	T2	agent
ai-tool-pluto-bio	Pluto Bio	T2	platform
ai-tool-synthesize-bio	Synthesize Bio / GEM-1	T2	model
ai-tool-elucidata-polly	Elucidata Polly	T2	platform
ai-tool-receptor-ai	Receptor.AI	T2	platform
ai-tool-storm-stanford	STORM	T3	framework
ai-tool-octotools	OctoTools	T3	framework
ai-tool-biodiscoveryagent	BioDiscoveryAgent	T3	agent
ai-tool-re-bench	RE-Bench	T3	benchmark
ai-tool-mle-bench	MLE-Bench	T3	benchmark
ai-tool-curebench	CUREBench	T3	benchmark
ai-tool-gaia-benchmark	GAIA Benchmark	T3	benchmark
ai-tool-dabstep	DABStep	T3	benchmark
ai-tool-pdgrapher	PDGrapher	T3	model
ai-tool-origene	OriGene	T3	agent
ai-tool-eubiota	Eubiota	T3	agent

All entries include: URL, category, key features, relevance to SciDEX, last_reviewed date, structured frontmatter with tool_category, specializations, pricing, maturity, open_source, key_people, data_sources, tags, and scidex_integration status. Entries with papers include paper_url and paper_title. Industry entries include founded_year, funding_stage, funding_amount, team_size.

Highlights for SciDEX:

• Causaly: 70M causal relationships — benchmark for SciDEX Atlas KG scale
• BenchSci LENS: 400M+ entity KG with structured evidence extraction — reference for Atlas
• Tag.bio: Direct Parkinson's Foundation partner (PD GENEration data)
• Eubiota: Gut-brain axis microbiome discovery — directly relevant to neurodegeneration
• OriGene: 600+ tools multi-agent system — closest architectural parallel to SciDEX
• PDGrapher: Inverse perturbation prediction for therapeutic targets (Zitnik Lab)

2026-04-08 — DeSci & Token Economy + new tools [task:a8e1228c-8a2c-40c6-84aa-e8c483b92808]

Completed the DeSci & Token Economy section and added notable new tools.
Script: scripts/landscape_desci_2026_04_08.py

7 new entries added (catalog now 89 total):

Slug	Title	Section	Category
ai-tool-bio-protocol	Bio Protocol / BioAgents (elizaOS)	DeSci	platform
ai-tool-molecule-protocol	Molecule Protocol (IP-NFTs)	DeSci	platform
ai-tool-scinet	SciNet (Decentralized Science Platform)	DeSci	platform
ai-tool-vitadao	VitaDAO (Longevity Research DAO)	DeSci	platform
ai-tool-labdao	LabDAO (Decentralized Compute)	DeSci	platform
ai-tool-nvidia-bionemo	NVIDIA BioNeMo	Tier 4	platform
ai-tool-gyde	GYDE (Protein Design)	Tier 4	platform

All entries include: URL, category, key features, relevance to SciDEX, last_reviewed date, structured frontmatter with tool_category, specializations, pricing, maturity, open_source, key_people, data_sources, tags, and scidex_integration status. DeSci entries include founded_year, funding_stage, funding_amount, team_size where applicable. Open-source entries include github_url.

Highlights for SciDEX:

• Bio Protocol/BioAgents: Direct architectural parallel — multi-agent fleet + knowledge graph + hypothesis generation. $36.9M+ funded, 1,000+ hypotheses on-chain
• Molecule Protocol: Reference implementation for tokenized scientific IP. Founded VitaDAO + Bio Protocol
• VitaDAO: $55M+ treasury, Pfizer-backed, longevity focus overlaps neurodegeneration
• NVIDIA BioNeMo: Infrastructure layer for AI drug discovery — Lilly $1B co-innovation lab, open Clara models
• GYDE: Open-source protein design platform — could integrate for neurodegeneration target analysis

Tool Inventory (2026-04-08)

Covered (wiki pages created)

Priority Tier 1 — COMPLETE

Priority Tier 2 — COMPLETE

Priority Tier 3 — COMPLETE

DeSci & Token Economy — COMPLETE

New Tools (Tier 4 — notable 2026 launches)

File: q-ai-tools-landscape_spec.md

Modified: 2026-04-28 03:24

Size: 16.7 KB