gi-expression

name	gi-expression
description	Predict tissue / cell-type expression (log TPM + TPM) from a 9,198 bp TSS-centered DNA sequence using the Genomic Intelligence G0 Expression model, via the hosted /v1/tasks/expression/predict API. The model is conditioned on a free-text cell-type / assay description.
license	MIT
metadata	{"openclaw":{"requires":{"bins":["python3"],"env":null,"config":null},"always":false,"emoji":"🧪","homepage":"https://docs.genomicintelligence.ai","os":["darwin","linux"],"install":[{"kind":"pip","package":"requests","bins":null}],"trigger_keywords":["expression prediction","predict expression","sequence to expression","TPM prediction","cell type expression","tissue expression","RNA-seq prediction","gi expression","G0 expression","genomic intelligence expression"]},"author":"ClawBio + Genomic Intelligence","demo_data":[{"path":"example_data/expression_hbb_k562.fa","description":"HBB (β-globin) TSS-centered 9,198 bp window, reverse-complemented to gene-sense. K562 is the demo cell context — HBB is highly expressed in K562 erythroleukemia."}],"dependencies":{"python":">=3.10","packages":["requests>=2.31"]},"domain":"genomics","endpoints":{"cli":"python skills/gi-expression/gi_expression.py --input {input_file} --output {output_dir}"},"inputs":[{"name":"input_file","type":"file","format":["fa","fasta","fna"],"description":"Single-record FASTA. The expression model expects exactly 9,198 bp centered on the TSS, gene-sense (RC minus-strand genes).","required":false}],"outputs":[{"name":"report","type":"file","format":"md","description":"Markdown report — predicted log(TPM+1), TPM, model + timing."},{"name":"result","type":"file","format":"json","description":"Full `{data, meta}` response."},{"name":"reproducibility","type":"directory","description":"command.sh + environment.json."}],"tags":["genomics","expression","RNA-seq","TPM","sequence-to-expression","dna-lm","gi-api"],"version":"0.1.0"}

🧪 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 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. Prefer a browser? The same models 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 — default model g0-expression.

Workflow

1. Parse: single-record FASTA (must be 9,198 bp, TSS-centered, gene-sense).
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.
4. : (headline log TPM) + + .