openscientist-hypothesislisted

# 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