--- name: gi-chromatin-68cfe355cfa5 description: Predict chromatin state โ€” histone marks, DNase, TF binding โ€” across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API. license: MIT metadata: openclaw: requires: bins: - python3 env: null config: null always: false emoji: ๐Ÿงถ homepage: https://docs.genomicintelligence.ai os: - darwin - linux install: - kind: pip package: requests bins: null trigger_keywords: - chromatin - chromatin state - chromatin annotation - histone mark - histone modification - DNase - ATAC - TF binding - transcription factor binding - DeepSEA - epigenome - gi chromatin - genomic intelligence chromatin author: ClawBio + Genomic Intelligence demo_data: - path: example_data/chromatin_active_promoter_chr19.fa description: Chr19 active-promoter region โ€” bundled real human reference sequence. dependencies: python: '>=3.10' packages: - requests>=2.31 domain: genomics endpoints: cli: python skills/gi-chromatin/gi_chromatin.py --input {input_file} --output {output_dir} inputs: - name: input_file type: file format: - fa - fasta - fna description: Single-record FASTA, 200โ€“500,000 bp (whitespace stripped); the API windows automatically. required: false outputs: - name: report type: file format: md description: Markdown report โ€” windows processed, total annotations across tracks, model + timing. - name: result type: file format: json description: Full `{data, meta}` response with per-window per-track predictions. - name: reproducibility type: directory description: command.sh + environment.json. tags: - genomics - chromatin - histone - DNase - ATAC - TF-binding - deepsea - dna-lm - gi-api version: 0.1.0 --- # ๐Ÿงถ gi-chromatin You are **gi-chromatin**, a ClawBio agent that calls the **Genomic Intelligence** chromatin-annotation model (DeepSEA-style, 919 tracks: histone marks + DNase + TF binding across ENCODE cell types). > โš ๏ธ **Remote inference โ€” 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 . **Do not submit identifiable patient data** without an appropriate data-use agreement. Key setup: see [Authentication](#authentication) below. ## Trigger **Fire this skill when the user says any of:** - "predict chromatin state for this sequence" - "histone mark prediction", "DNase prediction", "ATAC prediction" - "TF binding prediction" - "DeepSEA" - "gi-chromatin", "predict epigenome" - "is this region accessible?" **Do NOT fire when:** - The user asks specifically about enhancer activity โ†’ `gi-enhancer` - The user asks for promoter prediction โ†’ `gi-promoter` ## Why This Exists - **Without it**: Running DeepSEA / similar locally needs custom torch envs + weight wrangling. - **With it**: One CLI call โ†’ 919 track predictions per window, in seconds. - **Why ClawBio**: Hosted G0 DeepSEA inference plus ClawBio reproducibility and chaining. ## API Backed `POST https://api.genomicintelligence.ai/v1/tasks/chromatin/predict`. Omit `model` and the API resolves the default โ€” a 919-track DeepSEA-style prediction head. `GET /v1/tasks/chromatin/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. 2. **POST** to `/v1/tasks/chromatin/predict`. 3. **Render**: `report.md` (window + total-annotation counts; per-track detail in `result.json`). ## CLI Reference ```bash python skills/gi-chromatin/gi_chromatin.py --demo --output /tmp/gi-chromatin-demo python skills/gi-chromatin/gi_chromatin.py --input my_region.fa --output report_dir python clawbio.py run gi-chromatin --demo ``` ## Authentication The skill requires a Genomic Intelligence partner key in `GI_API_KEY`. Resolution order: 1. `--api-key ` CLI flag (explicit override). 2. `GI_API_KEY` environment variable. 3. Otherwise: the skill raises a `RuntimeError` pointing here. ### Quick start โ€” 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 โ€” 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: ```bash # Repo root (git clone) โ€” or ~/.claude/plugins/cache/clawbio/clawbio// 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: ```bash export GI_API_KEY=gi_yourkeyhere ``` ## Demo ```bash python clawbio.py run gi-chromatin --demo ``` Bundled fixture is an active-promoter region from chr19. Expect dense annotation across active-promoter tracks (H3K4me3, H3K27ac, DNase, etc.) and many called windows. ## Gotchas - **Big response.** 919 tracks ร— N windows โ†’ multi-MB `result.json`. The report.md summarizes; mine `result.json` programmatically for specific tracks. - **Track labels are in the response.** Do not hardcode track indices โ€” read the names from `data.tracks`. - **Length bounds are 200โ€“500,000 bp**, published as `minLength` / `maxLength` on `ChromatinPredictRequest` and counted after whitespace is stripped. Both ends are a `422 validation_failed` (over-max is *not* a 413 โ€” 413 is the separate 16 MiB raw-body cap). The skill rejects either locally before spending a request. - **200 bp is admission control, not regime.** The model's context window is 1,000 bp (`bio_spec.context_window_bp` on `GET /v1/tasks/chromatin/models`), so 200โ€“999 bp is accepted and scored โ€” against a window padded out to 1,000 bp. The skill warns when you are under it. - **Pre-windowing is unnecessary** โ€” the API windows and strides internally. - **Hackathon key is shared** โ€” `GI_API_KEY` for heavier use. ## Output Structure ``` output_dir/ โ”œโ”€โ”€ report.md โ”œโ”€โ”€ result.json โ””โ”€โ”€ reproducibility/ โ”œโ”€โ”€ command.sh โ””โ”€โ”€ environment.json ``` ## Integration with Bio Orchestrator Routes here on: "chromatin", "histone marks", "DNase", "ATAC", "TF binding", "DeepSEA". Chains with: `gi-enhancer` (cross-validate enhancer calls against H3K27ac), `gi-promoter` (active-promoter signature: high H3K4me3 + DNase), `variant-annotation` (variants in accessible chromatin). ## Safety Research and development use. Not for clinical or diagnostic decisions. --- Source attribution: ClawBio Original project: https://github.com/ClawBio/ClawBio License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice MIT License Copyright (c) 2026 Gabriel Moreira Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Mega AI Hub resource metadata Creator / publisher: ClawBio Original project: https://github.com/ClawBio/ClawBio Attribution basis: Upstream repository explicitly recorded in package mirror path Fields of work: Education & Research, Data & Analytics Roles: Researcher, Data Scientist, Business Intelligence Analyst Specialties: API Tools: Genomic Intelligence Api Country applicability: Country not specified Classification basis: Source category, role and specialization labels Instruction SHA-256: 93a858d37a6b4f446bf76c664a7fd547d9b5e72a94303985143ff148b199d622