Turn a research question into a reviewable investigation.
A guided workspace for organising evidence, tracing mechanisms and drafting candidate hypotheses and experiment proposals. Generated artefacts stay separate from approved scientific knowledge — never auto-promoted to the curated graph. Literature ingest and advanced adapters remain partial / interface-only.
6WORKBENCH STEPS
5FRONTIER TOPICS
partialPHASE E
Workbench
Guided research flow (PRD FR-038–040): question → evidence → mechanism → hypothesis → experiment → review. Every artefact is labelled candidate · draft. Nothing auto-promotes into the curated graph or marks a claim experimentally supported.
Paste a literature project JSON, curation-candidate manifest, or a prior workbench export. No PMIDs or model scores are invented; rows stay draft candidates.
Phase C workflow — export candidates or send them into the workbench evidence step above (still drafts).
Literature intelligence (PRD FR-036/037): identify a source, validate metadata locally, extract candidate claims, map to canonical graph IDs, flag conflicts, then prepare records for human curation. Identifiers are optional and never invented. Accepted items stay candidates — they do not approve graph claims.
Live PubMed/Crossref verification runs in Citation curation after import — not in this browser scaffold.
Curation handoff
0 claim(s) accepted · 0 exportable row(s). Export a candidate manifest for Citation curation. Import adds unreviewed rows only — scientific claim approval stays a separate human step. This UI never writes approved evidence.
Phase D interfaces for future omics, structure, pMHC/epitope, genomics, and agent adapters. Status remains interface-only — see also Methods §4.
Advanced analysis adapters are modular contracts for omics, structure, pMHC/epitope, genomics, and agents. None are wired into production inference in this build — dry-run always returns typed not_available. Also documented on Methods & trust.
Not implemented; No structure prediction runtime in this app; UI documents the contract only; Never treat interface previews as fold/dock results
pMHC / epitopeNot implemented
Peptide–MHC / epitope predictors
Support vaccination and T-cell recognition exploration.
ID peptide-mhc · no runtime version · stub only · Interface contract only — no binding ranks.
Related concepts (navigation only): EG01
Inputs
Peptide sequences; HLA / MHC alleles
Outputs (documented)
Binding ranks; Candidate epitope list
Limitations
Not implemented; Predictor outputs must never be labelled as validated epitopes without lab confirmation; UI documents the contract only; Never treat interface previews as binding ranks
GenomicsNot implemented
Genomic variant analysis
Link coding variants to PID / HLA / pathway concepts in the graph.
ID genomic-variants · no runtime version · stub only · Interface contract only — no clinical variant caller.
Related concepts (navigation only): EG07, EG12
Inputs
Variant calls (VCF-like); Gene / HLA context
Outputs (documented)
Mapped immunogenetic concepts; Uncertainty flags
Limitations
Not implemented; No clinical interpretation pathway; UI documents the contract only; Never treat interface previews as clinical variant calls
AgentsNot implemented
Specialised scientific agents
Orchestrate retrieval → mechanism → hypothesis drafts under human review.
ID scientific-agents · no runtime version · stub only · Interface contract only — no agent runtime.
Related concepts (navigation only): C003, M001
Inputs
Scoped research question; Allowed tool list
Outputs (documented)
Candidate hypotheses; Experiment proposals marked as candidates
Limitations
Not implemented; Candidates are never established findings; UI documents the contract only; Never treat interface previews as agent conclusions
StructurePlanned
TCR–pMHC docking (molecular stub)
Future structural context for TCR recognition hypotheses under human review.
ID tcr-pmhc-dock · no runtime version · stub only · Planned molecular stub — contract only.
Related concepts (navigation only): EG01, C014
Inputs
TCR sequence or structure handle; Peptide–MHC complex identifier
Not implemented; Planned molecular stub — no docking engine, no scores, no poses; Must not be labelled as immunogenicity or clinical binder prediction; Promotion to implemented requires rights + held-out eval + tests
StructurePlanned
Cytokine–receptor MD refine (molecular stub)
Educational structural context for cytokine signalling hypotheses — never a dynamics result.
ID cytokine-receptor-md · no runtime version · stub only · Planned molecular stub — contract only.
Not implemented; Planned molecular stub — no MD engine or energy scores; UI documents a future contract only; Never treat previews as simulation trajectories
Implementation phases B–E
Status reflects shipped, testable code — not marketing claims. See also Methods & trust.
Phase Bpartial
Knowledge-layer gap fills
draft-ext-4 adds IVIG, pharmacogenetic HLA screen, herd-protection and post-infectious flare teaching drafts; domain coverage panel + gap queue on Evidence. Exemplar claim-review: TNF→RA on-path done; PD-1 partial; IFN→SLE still scaffold-ish — curator work, not silent graph completion.
New records live in extensions with draft:true at merge time.
Immunogenetics lesson + route appear in curriculum merges.
Graph release snapshot separates core vs draft counts; extensions version bumps.
Phase Cpartial
Scientific literature intelligence
Deepened local workflow + Research UI + curation-candidate export. Live PubMed/Crossref bulk ingest is still not shipped — identifier verification remains the existing server-side curation path after human import.
Browser-safe workflow module creates versioned candidate artefacts with conflict flags.
Review queue UI maps to graph IDs, sets claim_support, accept/reject/edit with candidate labelling.
Curation handoff export matches importManifest shape without auto-approving claims.
Phase Dpartial
Advanced model registry interfaces
Contracts + stub dry-run + request-shape validation + promotion gate + planned molecular stubs (TCR–pMHC dock, cytokine–receptor MD) on Research/Methods. Still no live predictors — implementedModels() empty.
MODEL_REGISTRY rendered with status badges, request-shape previews, inputs/outputs, limitations.
invokeModelStub / dryRunAllStubs refuse all current adapters with scientificClaimAllowed=false.
implementedModels() remains empty until a real adapter ships.
Phase Epartial
Scientific Workbench steps
Six-step machine with visit gating, Ask/lit/mechanism imports, Literature→Workbench handoff, curation-manifest import, local draft save, URL seeds, versioned export (wb-1). Still no lab execution, KG write-back, or auto-promotion.
Workbench UI first-class on Research layer (not a 13th nav item).
Hypothesis and experiment proposal artefacts stay candidate/draft_proposal.
Export includes schema + graph/extensions version identifiers and candidateFlags.
CD19 CAR-T produced drug-free remissions in refractory SLE, myositis and systemic sclerosis case series. Open questions: durability, toxicity, cost, and whether a reset is truly achieved.