Gi Expression

🧪 gi-expression

You are gi-expression, a ClawBio agent that calls the Genomic Intelligence sequence-to-expression model. Given at least 9,198 bp around a TSS (--tss-index unless it is exactly 9,198 bp) 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 at least 4,599 bp from each end. 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

# Demo — HBB in K562
python skills/gi-expression/gi_expression.py --demo --output /tmp/gi-expression-demo

# Custom cell-type description
python skills/gi-expression/gi_expression.py \
  --input my_tss_window.fa \
  --description "assay term name is polyA plus RNA-seq. biosample summary is Homo sapiens liver." \
  --output report_dir

# Whole locus: the model reads around --tss-index
# (0-based offset into the sequence, counted after whitespace is stripped)
python skills/gi-expression/gi_expression.py \
  --input my_locus_50kb.fa --tss-index 24000 \
  --output report_dir

# Via ClawBio runner
python clawbio.py run gi-expression --demo

Authentication

The skill requires a Genomic Intelligence partner key in GI_API_KEY. Resolution order:

1. --api-key <value> CLI flag (explicit override).
2. GI_API_KEY environment variable.
3. Otherwise: the skill raises a RuntimeError pointing here.

Quick start — ClawBio hackathon key

A shared hackathon-tier key ships in .env.example at the repo root (opt-in only). Caps are per-key and are not published as a fixed number — read RateLimit-Limit / RateLimit-Remaining on any /v1/tasks/ response for the live allowance. The runner keeps them for you: they are in result.json under rate_limit, and a 429 names them on the error line. From wherever the ClawBio files live on your machine:

# Repo root (git clone) — or ~/.claude/plugins/cache/clawbio/clawbio/<version>/ for plugin installs
cp .env.example .env
set -a && source .env && set +a

Production / heavier use

Request an individual key at contact@genomicintelligence.ai, then:

export GI_API_KEY=gi_yourkeyhere

Demo

python clawbio.py run gi-expression --demo

Bundled fixture is HBB centered on its canonical TSS, RC'd to gene-sense, scored with the skill's default K562 description.

Read the predicted value from your own run rather than from this page. Absolute predictions move when the model checkpoint changes, so any figure written here becomes a false claim. What is stable is the relative signal — gene-sense scores far above the genomic strand, and highly-expressed genes score above silent ones in the same cell context. Do not build assertions on an absolute value read from documentation.