feat(genomic-intelligence-nim): hosted DNA-sequence prediction skill#12
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boldakov wants to merge 1 commit into
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feat(genomic-intelligence-nim): hosted DNA-sequence prediction skill#12boldakov wants to merge 1 commit into
boldakov wants to merge 1 commit into
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Add a nim-skills/ skill wrapping Genomic Intelligence's hosted DNA
language models over the /v1/tasks/{task}/predict contract: promoter,
splice, enhancer, chromatin, expression, and annotation. Bearer-authed
via GI_API_KEY; ships a requests-only runner (sync + async), references,
demo FASTAs, and evals. Context: NVIDIA-BioNeMo#5.
Signed-off-by: Alexander Boldakov <boldakov@gmail.com>
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Summary
Adds a
nim-skills/genomic-intelligence-nimskill that wraps Genomic Intelligence's hosted DNA language models, following the existingnim-skills/pattern (aSKILL.mddriving a bearer-authed REST call). One skill, six tasks over the sharedPOST /v1/tasks/{task}/predictcontract:Inference is hosted — no local weights or GPU; the only dependency is
requests.Third-party hosted endpoint
Unlike the existing
nim-skills/(which target NVIDIA-operated endpoints), this skill calls an endpoint operated by Genomic Intelligence. The interface is identical to the hosted-NIM shape (HTTPS +Authorization: Bearer+ JSON); it is hosted-only. Flagging it explicitly so you can weigh in, happy to adjust naming. Context in #5.Why a
scripts/runner (not inline-only)The published
nim-skills/inline their Python inSKILL.md. This skill instead ships a small, self-contained requests-only runner, because the surface (six tasks, async jobs, and an exact 9,198 bp window for expression task) does not inline cleanly. Shippingscripts/is not prohibited by CONTRIBUTING, and other categories ship scripts too.SKILL.mdstill includes a minimal inline example for the simple sync case.What's included
SKILL.md— frontmatter + task table + runner usage + a minimal inline example.scripts/—gi_predict.py(one CLI, six tasks, sync + async, writes report + JSON),gi_client.py(the/v1client), and optionalgi_fetch.py/gi_ensembl.py(gene/region → FASTA via public Ensembl, incl. TSS-centring).references/{api,tasks,authentication,sequence-acquisition,errors}.md.evals/{evals,trigger_evals}.json— matching the repo's eval schema (promoter, expression-window, and annotation-async cases).assets/demo/*.fa— one real reference FASTA per task (e.g. TP53 promoter, HBB splice, HBB-K562 9,198 bp expression window).Auth
Users set
GI_API_KEY(partner key, request at contact@genomicintelligence.ai). No key is committed; the skill resolves it from the environment.Licensing / DCO
Contribution dual-licensed
Apache-2.0 OR CC-BY-4.0; commits are DCO signed-off.