Manage and drive forward an ongoing project, tracked in projects/ dir
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See how to installReview the instructions the agent will receive before you install.
You should find either a file or a folder:
./PROJECT_NAME.md ./PROJECT_NAME/ <multiple materials>
A project doc typically will contain a list of genes, potentially prioritized. This should be in the form of a checkbox you can check off. The species for the gene (uniprot code or lowercase name like 'mouse') should be clear (if not, ask)
Review the genes in the priority order.
IMPORTANT: you MUST consult the annotation-reviewer.md subagent for this task.
If the user specifies a deep research provider(s), make sure to perform deep research using at least this provider(s), otherwise default to falcon.
E.g. just deep-research-falcon ORGANISM GENE_SYMBOL
You can edit the project doc, but try and make this incremental. After the main description have something like:
<checkboxes etc here; keep this up to date>
<get the date from date>
<todays notes, add here>
ONLY make PRs when asked.
The general procedure is:
just validate-allgh pr createif the user asks, build the static site and stats (just stats, just update-browser-data). Note it can be hard to disentangle derived
files, but you should be OK if there are no other local updates
besides the one for this project.
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Review AI Gene Review pull requests and curation changes for GO term quality, evidence support, core function identification, and annotation action justification. Use for PR review comments, review follow-up automation, and QA of gene review YAML.
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Use this agent when you need to systematically review existing GO annotations for a gene and make curation decisions based on literature evidence and functional analysis. This agent should be called after seeding the SPECIES/GENE/GENE-ai-review.yaml file, which seeds each annotation with `action: PENDING`; these should all be manually reviewed.
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Use this agent when you need to perform custom bioinformatics analyses on genes or proteins that go beyond standard database lookups. This includes situations where existing domain/family annotations from UniProt are insufficient, when you need to verify dubious annotations, or when you need to perform comparative analyses across gene sets. The agent creates reproducible analysis pipelines with proper dependency management and documentation.
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Work with BioReason-Pro predictions and reasoning traces for protein function. Use when: comparing BioReason outputs against curated reviews, converting web exports to YAML, reviewing reasoning trace quality, or running the SFT/RL comparison. Triggers: "bioreason", "GO-GPT predictions", "reasoning trace review", "bioreason comparison", "SFT vs RL".
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Use ONLY when the user explicitly asks to orchestrate parallel external agents (Codex or Claude Code) in tmux sessions via tp (tmux-pilot). Or when a user tells you that you're the boss or orchestrator. You can also use this if you are an operclaw agent. NEVER auto-invoke for a generic "do this in parallel" request. For in-process subagents, use superpowers:dispatching-parallel-agents instead.
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Use this agent when you need to synthesize and distill the core functions of a gene from multiple information sources (textual summaries, reviewed annotations, bioinformatics analysis) and populate the `core_functions` section of a gene review YAML file. This agent should be called after completing the gene research, annotation review, and bioinformatics analysis phases of a gene review project.
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