Results for “genetic-compatibility”

Query the Open Targets Platform GraphQL API for target-disease associations, tractability and safety data, genetics/omics evidence, and known drugs. Use when identifying or prioritizing therapeutic drug targets, assessing target druggability/safety, or gathering target-disease evidence for drug discovery. Part of the AlterLab Academic Skills suite.

Reimplements DnaSP 6 for population genetics analysis of aligned DNA sequences, including nucleotide diversity, haplotype statistics, neutrality tests, linkage disequilibrium, recombination, mismatch distribution, InDel polymorphism, between-population divergence, outgroup-based tests, HKA test, McDonald-Kreitman.

Use to build Science's data, code, and materials availability — mandatory deposition in approved repositories, accession numbers, a compliant data-availability statement, and materials/reagent sharing.

NIH grant research skill for clinical researchers. Grill-me intake (research idea + career stage + preliminary data + environment + submission posture + known institute targets) locks down the funding strategy before any search runs. Runs a 5-facet Consensus positioning analysis (with draft Significance/Innovation language), maps the research to the right NIH institutes and study sections via RePORTER, finds NOSIs and funded overlap, and produces an editable Word document (.docx) with budget/scope-aware mechanism recommendations, submission timelines, and a mandatory program officer recommendation. Use when the user asks about research funding or makes any grant-related request (e.g., 'grants for [topic]', 'find grants for my research idea', 'what grants match my research', 'help me find NIH funding', 'grant opportunities for my research'). NIH-only scope — non-NIH funders (PCORI, DOD CDMRP, VA, foundations) are out of scope and flagged at intake.

Manage feature manifests for code traceability. Use when creating new features, updating existing features, checking feature health, or exploring the feature-to-code relationship. Activates for manifest validation, feature creation, changelog updates, and traceability queries.

Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing, checking PGx drug-safety associations (e.g. HLA-B*57:01 and abacavir), or supporting precision medicine and clinical pharmacogenomics decisions. For star-allele definitions/frequencies see PharmVar; for germline/somatic variant pathogenicity see alterlab-clinvar. Part of the AlterLab Academic Skills suite.

Use when calculating thermodynamics of RNA-RNA interactions, including accessibility and binding energy predictions for RNA duplex formation.

Queries 9 genomic databases in parallel for a given rsID, returning unified GWAS, PheWAS, eQTL, and fine-mapping reports.

Triage mutation testing results by combining survived mutants, unnecessary test statements, and code graph analysis to identify false positives, missing test coverage, and fuzzing targets.

Query the 1000 Genomes Project dataset at the individual participant level to find variants, carriers, and relatedness information.

Combined verification — recite (description quality via cold-read prediction) + validate (schema compliance) + review (health checks). Use as a quality gate after creating notes or as periodic maintenance. Triggers on "/verify", "/verify [note]", "verify note quality", "check note health".

Composite skill — diagnose, repair, and validate a test suite end-to-end. Chains test-health (diagnose) → config-drift-detect (gate compatibility) → test-cleanup (prune + add integration tests) → mutation-test (validate survivors) → adr-write (capture decisions) → docs-sync. Use when "the test suite is bad" or you've hit the test-cleanup-bails-at-the-gate failure mode.

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

Use Geniml for audited local genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibility, and assess consensus universes.

Casting personas: rapid generation from diverse inputs, registry-based persistence and lifecycle, data-driven evolution, inter-agent sync. Not for UI walkthroughs (Echo) or user research (Field).

Discovers and uses scientific datasets, models, blog posts, and interactive demos from a curated catalog for AI/ML work in domains like biology, chemistry, physics, and genomics.

Process and analyze mass spectrometry data: import spectra from MGF, mzML, MSP, and JSON formats; apply 40+ filters for metadata harmonization and peak cleaning; compute spectral similarities (cosine, modified cosine) for compound identification; build reproducible processing pipelines.

Adaptive, resumable Git delivery across repositories and agent runtimes — probe policy, checkpoint coherent work, publish, review, integrate, and verify cleanup

Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities and called sites.

Machine learning on genomic interval data (BED files) with the geniml Python package — region embeddings (Region2Vec), joint region+metadata embeddings (BEDspace/StarSpace), single-cell ATAC-seq embeddings (scEmbed), consensus peak sets / universes (build-universe), tokenization, BEDshift randomization, and BBClient/BEDbase caching. Use when training or using region/cell embeddings, clustering scATAC-seq, building a tokenization universe from BED collections, or any ML/feature-learning task over genomic regions. NOT for plain interval arithmetic (overlap/intersect/merge counts) — that is gtars, not geniml. Part of the AlterLab Academic Skills suite.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.

Access AI-ready drug discovery datasets and benchmarks from Therapeutics Data Commons, covering ADME, toxicity, drug-target interactions, and molecular generation with standardized splits and evaluation metrics.

Reconcile a processkit project’s migrations, health findings, and repository collaboration queue. Use when resolving all migrations, pk-doctor findings, GitHub issues, pull requests, or release blockers.

Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.

Registers an AI agent on inbed.ai as a blob-flexible dating profile, discovers matches, swipes, chats, and manages relationships via the platform's REST API.

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.

Configure Gemini and Codex CLI tools with Cloudflare AI Gateway endpoints and MCP servers.

Audits colour decisions on a screen for contrast ratios, palette coherence, semantic meaning, and accessibility, flagging deviations and recommending specific corrections.

SSOT（Single Source of Truth）と実際のファイル/設定の整合性をチェックし、乖離があれば修正するスキル。 「SSOTチェックして」「SSOT整合性チェックして」「SSOT整理して」「SSOTのズレを直して」 「00_SYSTEM更新して」「乖離を修正して」と言った時にトリガーする。 /ssot-check でも呼び出せる。

Composite skill — take a PR from "I think it's ready" to merged with full gate verification. Chains pr-merge-readiness (verdict) → ci-watch / gh-fix-ci (if blockers) → gh-address-comments (if review needed) → ship (when verdict is MERGE). Use as the one-call answer to "can I merge this?" instead of running 4 skills sequentially.

A git SHA pins the transformation.

Gemini: A Family of Highly Capable Multimodal Models

Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants, returning variants, carriers, and relatedness with allele frequencies and annotations.