Results for “ancestry”

Computes HEIM diversity and equity metrics from VCF or ancestry data, generating heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.

Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree, with visualization via ETE3 or FigTree for evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.

Nested Sets

Closure Table

Generates APEXlang artifacts for Oracle APEX applications using deterministic local-context discovery and compact machine-readable contracts.

Query the Ensembl genome database REST API across 250+ species for gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, and Variant Effect Predictor (VEP) annotations. Use when mapping gene IDs or coordinates, fetching genomic sequence, finding orthologs across species, or predicting variant consequences for genomic research. Part of the AlterLab Academic Skills suite.

Mines SpecStory coding histories from any agent into a persistent corpus, surfaces reproducible workflows with corroborated evidence, and interactively forges chosen ones into skills installed across agent harnesses.

Access USPTO APIs for patent and trademark searches, examination history (PEDS), assignments, citations, office actions, and trademark status (TSDR). Use when searching patents or trademarks, conducting prior art searches, retrieving patent examination or assignment records, or doing intellectual property (IP) analysis. Part of the AlterLab Academic Skills suite.

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.

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).

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.

Quickly query genomic reference databases for Ensembl IDs, gene metadata, sequences, BLAST searches, and enrichment analysis using the gget CLI or Python package.

Manage biological datasets and models with LaminDB, an open-source lineage-native lakehouse. Covers setup, artifact registration, query/search, lineage tracking, validation, ontology-backed annotation, collections, branches, storage, and workflow integrations.

Botany Design Advanced Skill

Long-running design anthropologist that builds comprehensive visual databases from 500-1000 real-world examples, extracting color palettes, typography patterns, layout systems, and interaction design across any domain (portfolios, e-commerce, SaaS, adult content, technical showcases). This skill should be used when users need exhaustive design research, pattern recognition across large example sets, or systematic visual analysis for competitive positioning.

Builds a local RAG memory system that indexes session logs and notes into ChromaDB for semantic recall across agent restarts.

Provide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments.

Operate and extend barretlee/agent-pulse, the evidence-backed AI industry intelligence system: inspect source catalog and lifecycle, collect and normalize signals, bind evidence, cluster Events, evaluate system health, generate Scout hypotheses, export the privacy-safe public site, and verify release gates. Use when the user asks to run, configure, debug, extend, or explain Agent Pulse, its collectors, Control Room, narratives, Scout, or GitHub Pages output. Triggers on: agent-pulse, Agent Pulse, evidence-backed intelligence, source catalog, signal collection, Event clustering, source audit, Scout opportunity, public export, weekly brief, or AI industry intelligence pipeline.

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.

Adjacency List

Reference for Benchling REST API v2 endpoints, covering authentication, pagination, error handling, and CRUD operations for sequences, entities, containers, and notebook entries.

绘制研究领域或技术主题的谱系脉络与历史演进图，可视化思想的演化路径，展示早期工作中的技术难题如何被后续研究逐步解决。当用户想了解某个主题的发展轨迹、某个模型或技术的"家族树"（family tree）、某条研究线索在多年间的演进路线、技术迭代脉络、论文/模型谱系，或询问"X 是如何一步步发展来的""X 解决了前人的什么问题""梳理 X 的发展历史"时触发。产出为嵌入 Mermaid 图表的 Markdown 文件（演进图 + 节点明细表 + 阶段叙事），可直接粘贴至 Mermaid 查看器或提交至代码仓库。

Computes phylogenetic distance matrices and trees from genomic VCF or FASTA data using the fastreeR hybrid Java/Python toolkit.

Scores genetic compatibility between all male-female pairings in a Genomebook generation, ranking optimal mating pairs based on heterozygosity, trait complementarity, and disease risk.

Use for writing, reviewing, debugging, or testing Python analysis of Bayesian inference results with ArviZ, including 1.x DataTree groups, legacy InferenceData inputs, xarray dimensions and coordinates, conversion, summaries, R-hat/ESS/MCSE diagnostics, posterior predictive checks, PSIS-LOO, Pareto-k, and model comparison. Trigger on chain/draw shape errors, mislabeled groups, flattened samples, missing log likelihood, or misleading diagnostic claims. Do not use to construct or sample PyMC, NumPyro, or Bambi models, for generic plotting, or for deterministic statistics without Bayesian draws.

Explains syntax differences for common SQL operations across PostgreSQL, MySQL, SQL Server, and Oracle, including auto-increment keys, string concatenation, date functions, pagination, booleans, JSON, case sensitivity, and recursive CTEs.

Populate databases with realistic, reproducible test data for development, testing, and staging environments. Use when the user requests database seeding or provides relevant inputs for this workflow.

八字四柱命理分析工具，属于 fortune-telling-skills 运势测算套件。基于子平真诠体系， 通过出生年月日时推算四柱八字、十神关系、五行旺衰、大运流年，揭示命局格局和人生走向。 排盘为确定性计算 + LLM 综合解读，无外部 API 依赖。 触发词：八字、四柱、命理、生辰八字、bazi、八字排盘、五行、命局分析。 不适用于：星座运势、塔罗占卜、紫微斗数 → 建议使用 fortune-hub。

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use when identifying cancer-specific genetic vulnerabilities, finding synthetic lethal interactions, checking whether a gene is essential in given cell lines, or validating oncology drug targets. Part of the AlterLab Academic Skills suite.

Expert in cultural systems, rituals, kinship, belief systems, and ethnographic method — builds culturally coherent societies that feel lived-in rather than invented

Discover public GitHub repositories that import defineTask from @a5c-ai/babysitter-sdk and maintain a deduplicated catalog of those repositories in docs/repo-with-babysitter-processes.md. Excludes any repo named "babysitter" (to filter out forks of this monorepo). Invoke when asked to find, discover, catalog, or refresh "repos using babysitter", "babysitter in the wild", or "who else is using babysitter".

基于 anchor 论文、topic 关键词或当前 wiki 状态，产出一份排好序的候选论文 shortlist，供用户或上游 skill 决定是否进一步 `/ingest`。当用户问 "接下来该读什么"、"找和这篇相似的论文"、"推荐相关工作"、"这个方向周围有什么" 时触发；`/ingest --discover` 也会内部调用本 skill。本身不 ingest，只提出候选。

Access AWS Bedrock foundation models for generative AI, including text generation, embeddings, and image generation, with CLI and Python examples.