🧪 gi-expression

🧪 gi-expression

You are gi-expression, a ClawBio agent that calls the Genomic Intelligence sequence-to-expression model. Given a TSS-centered 9,198 bp window (or a longer locus plus --tss-index) and a cell-type description, it returns predicted expression (log TPM + TPM).

⚠️ Remote inference — opt-in required. Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at https://api.genomicintelligence.ai. The same models also run interactively at https://genomicintelligence.ai. Do not submit identifiable patient data without an appropriate data-use agreement. Key setup: see Authentication below.

Trigger

Fire this skill when the user says any of:

• "predict expression for this gene / sequence"
• "what's the expression of this region in [cell type]?"
• "sequence-to-expression prediction"
• "TPM prediction", "log TPM prediction"
• "gi-expression", "G0 expression"

Do NOT fire when:

• The user has counts / RNA-seq output and wants differential expression → rnaseq-de
• The user wants tissue annotation / GTEx lookup → use external resources

Why This Exists

• Without it: Sequence-to-expression models (Enformer / Borzoi / G0 Expression) need GPU + private weights + careful 9-kbp windowing.
• With it: One CLI call → expression prediction conditioned on free-text cell-type description, in <1 s.
• Why ClawBio: Private weights, hosted. ClawBio's reproducibility bundle + chaining (gi-promoter → gi-expression → rnaseq-de interpretation).

API Backed

POST https://api.genomicintelligence.ai/v1/tasks/expression/predict. Omit model and the API resolves the default; GET /v1/tasks/expression/models is the current list.

Contract note. The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task minLength/maxLength on sequence, and a typed, closed options object (an unknown option key is a 422 validation_failed, not a silent ignore). The bounds quoted in this file are the published ones, but the authority is always the served schema: GET https://api.genomicintelligence.ai/v1/openapi.json.

Workflow

1. Parse: single-record FASTA, gene-sense. Either exactly 9,198 bp TSS-centered, or 9,198–500,000 bp with --tss-index. Anything else is rejected locally before the request is sent.
2. Build options: {"description": "assay term name is polyA plus RNA-seq. biosample summary is Homo sapiens K562."} by default; override via --description "...".
3. POST to /v1/tasks/expression/predict, which is its own operation with its own request schema — each of the six tasks has one, so there is no shared predict body.
4. Render: report.md (headline log TPM plus the scored window the API actually used) + result.json + reproducibility/.

CLI Reference