OpenScientist Hypothesis Workflow

Use this skill for AIGR work that runs, stages, or maintains OpenScientist hypothesis jobs for gene function review.

Core Rules

• Treat OpenScientist as an independent bioinformatics scientist exploring a hypothesis: gene G has function F.
• For existing annotations, prefer the neutral function-assignment mode: --as-function-hypothesis.
• Do not feed existing local *-bioinformatics/RESULTS.md analyses into OpenScientist prompts. Those are holdout evidence for post-run comparison.
• It is acceptable to pass bounded non-holdout review context, especially the selected term, original evidence reference, and a small number of relevant literature/deep-research references.
• Avoid sending every function for genes with large reviews; select the specific hypothesis being tested.

Running Jobs

• Use the just recipes, not raw deep-research-client, for AIGR hypothesis jobs. The justfile carries project defaults such as OpenScientist iteration count.
• Be patient with OpenScientist. Jobs may run quietly for a long time before the local report is written.
• Do not interrupt a real OpenScientist run merely because the local wrapper is silent or the child process is sleeping.
• Check completed and running jobs at https://www.openscientist.io/jobs before deciding a job is stuck.
• One-iteration OpenScientist runs are smoke tests only. Real hypothesis jobs should use the project default of at least 3 iterations unless the user explicitly asks otherwise.

Timeouts

• Give analyses ample time. Real 3-iteration runs commonly take ~50-70 minutes, and structural / fold-discovery jobs can run longer; they are cancelled mid-analysis if the timeout is too short (observed: a job cancelled at the upstream 3600s default after producing nothing).
• The just recipes now inject the maximum OpenScientist job timeout (--param timeout=7200, i.e. 2h) alongside --param max_iterations=3, and the wrapper's subprocess wall (--timeout-seconds, default 8100s) is kept above the job timeout so the child process is not killed first. If you ever bypass just and call the script directly, pass both: e.g. -- --param max_iterations=3 --param timeout=7200 plus --timeout-seconds 8100. The two timeouts are independent — raising one without the other still cancels the run.
• 7200s is the API ceiling: OpenScientistParams.timeout is validated le=7200, so a larger value fails fast with a pydantic less_than_equal error and writes nothing. Do not exceed it.
• Do not lower these to "save time"; a too-short timeout wastes the whole run.
• When a job still hits the 7200s ceiling (common for human proteins asked a multi-faceted question), the fix is scope, not time: re-run with a single decisive analysis in the hypothesis (e.g. "Foldseek fold assignment" alone, not fold + disorder + motif + targeting) and/or --param max_iterations=2. Observed: C18orf21 7200s timeout -> 2708s when narrowed to Foldseek-only; HSPA12A/DNAJC28 likewise completed once narrowed. The paralog of a job that did finish (e.g. HSPA12B at 5208s) will usually finish on a plain retry — variance, not a hard limit.
• Scoping each hypothesis to one computable question up front (rather than a broad "characterize this gene") both avoids timeouts and gives cleaner, more decisive provenance.

Failure Modes

• A job can exit 0 yet write no report. Always confirm openscientist.md (and the openscientist_artifacts/ dir) actually exist before treating a run as done; an empty hypothesis directory means it failed.
• Two distinct failure signatures seen, both leaving an empty output dir:
  • detail=... timed out after Ns ... has been cancelled -> raise the timeout (see above) and re-run.
  • detail=... Request ID: req_... -> a transient OpenScientist-internal LLM error (their server-side agent call failed; the id is for their debugging). Re-run; if the same gene fails this way repeatedly, treat it as a persistent upstream issue, move on, and report it rather than retrying indefinitely.
• Remove the empty GENE-hypotheses/<slug>/ directory before re-running so a failed attempt does not masquerade as a completed one.

After Completion

• Verify the generated report does not include withheld local bioinformatics paths or RESULTS.md content.
• Compare the OpenScientist conclusion against the held-out local bioinformatics result after the run.
• Keep operational lessons in skills or agent instructions, not in user-facing project pages.

Wiring Verdicts Into Reviews

• A refuted proposal must be deleted, not set to REMOVE. Validation enforces that annotations absent from GOA carry action: NEW (they are AI proposals, identifiable by having no original_reference_id). If a run refutes such a proposal, delete the annotation block and any core_functions entry built on it, and record the refutation in the description + an OpenScientist file: reference. action: REMOVE is only for real GOA annotations and will fail validation on a not-in-GOA term ("Found N annotations not in GOA").
• Gate findings that depend on uncacheable references. When a run's conclusion rests on very recent papers not in publications/ (so their supporting_text cannot be verbatim-verified) and that you cannot otherwise confirm, record it as a clearly-labelled lead — keep the conservative existing annotation, note "not yet verified / PMIDs not cached", and cite the OpenScientist file: report — rather than asserting a new annotation. Verify, don't trust. (Example: C18orf21 -> RMP24 / RNase MRP, left as a lead pending primary-literature caching.)
• Don't overstate disagreements. Before wiring "the run overturns the prior review", check the primary data: the two analyses often agree on the facts (e.g. residues present) and differ only on interpretation (e.g. a PROSITE signature failure). Wire genuine standoffs as UNDECIDED with both lines of evidence and the decisive experiment, and do not import the run's secondary claims (e.g. a named degenerate paralog) unless corroborated by repo data.
• Verbatim supporting_text gotchas: plain (unquoted) YAML scalars cannot contain ": " — single-quote any quote containing a colon-space (e.g. "Foldseek: zero ..."). The pre-edit hook catches these.

Job Hygiene

• Background jobs are killed on container restart; the harness reports which. Check the GENE-hypotheses/<slug>/ dir — if empty, clean it and re-launch.
• Check whether the API key is already set before assuming it is not: printenv OPENSCIENTIST_API_KEY (it is exported in some environments, so the just recipes work directly). Only if it is absent, pass OPENSCIENTIST_API_KEY inline when calling the script directly, and wire it into the environment/setup config for reproducible just runs.