Results for “microbiome”

Analyzes biochemical processes, including enzyme kinetics, metabolic pathways, and biomolecule characterization, with practical techniques and examples.

Searches UK Biobank's 12,000+ data fields and publications by natural language query, returning ranked field IDs and descriptions for research questions.

Biome - Fast all-in-one toolchain for web projects (linter + formatter in Rust, 100x faster than ESLint)

Use when studying cell biology.

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.

Filters and prioritizes compound libraries in drug discovery using drug-likeness rules, structural alerts, complexity metrics, and a query language.

Explains cellular structures, membrane transport, energetics, signaling, and division, connecting molecular events to organismal function.

Audits a research knowledge base for stale profiles, thesis drift, and orphan pages, returning a 0-100 health score with actionable recommendations.

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

Query PubChem via the PUG-REST API and PubChemPy across 110M+ compounds, searching by name, CID, or SMILES and retrieving molecular properties, bioactivity, and similarity/substructure matches. Use when looking up a chemical compound, converting names/SMILES to CIDs, fetching physicochemical properties, or running cheminformatics structure searches. Part of the AlterLab Academic Skills suite.

Access the Human Metabolome Database (HMDB, 220K+ metabolites), searching by name, HMDB ID, or structure to retrieve chemical properties, biomarker data, NMR/MS reference spectra, and associated pathways. Use when identifying a human metabolite, looking up its biomarker or disease associations, matching NMR/MS spectra, or running metabolomics annotation. Part of the AlterLab Academic Skills suite.

Expert guidance for micro — asynchronous HTTP microservices framework by Vercel. Use when building lightweight HTTP servers, API endpoints, or microservices using the micro library.

Assesses genome, transcriptome, and protein completeness with BUSCO v6, automatically resolving the correct lineage from an organism description and generating reproducible reports.

Processes and analyzes multiple physiological signals (ECG, respiration, EDA, EMG, PPG, EOG) together using NeuroKit2, including cross-signal features like RSA and event-related analysis.

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mode multithreading; plus a DIAMOND blastp --ultra-sensitive path for large protein searches. Warns that -max_target_seqs is a heuristic keep-count, not a top-N best-hits filter. Use when the user wants command-line BLAST, makeblastdb, a local BLAST database, blastn/blastp/blastx/tblastn searches, or DIAMOND protein search. For the Bio.Blast web NCBIWWW API prefer alterlab-biopython; for quick one-liner database lookups prefer alterlab-gget. Part of the AlterLab Academic Skills suite.

Esta habilidade deve ser usada ao trabalhar com LaminDB, um framework de dados de código aberto para biologia que torna dados consultáveis, rastreáveis, reproduzíveis e FAIR. Use ao gerenciar datasets biológicos (scRNA-seq, espacial, citometria de fluxo, etc.), rastrear workflows computacionais, curar e validar dados com ontologias biológicas, construir data lakehouses, ou garantir linhagem de dados e reprodutibilidade em pesquisa biológica. Aborda gerenciamento de dados, anotação, ontologias (genes, tipos de célula, doenças, tecidos), validação de esquema, integrações com orquestradores de workflow (Nextflow, Snakemake) e plataformas MLOps (W&B, MLflow), e estratégias de deployment.

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

Complete bedside prescribing reference for Mirago (mirabegron, beta-3 adrenoceptor agonist) for overactive bladder — covering contraindications, safety screening, drug interactions, dose selection in special populations, titration, and administration. Use when a clinician asks how to start mirabegron, what dose to use in renal or hepatic impairment, is mirabegron safe in this patient, mirabegron drug interactions, or Mirago for OAB.

Audit, write, or revise README.md. Use when creating a README, editing one, or noticing smells (missing badges, no install steps, unclear purpose, no engagement guidance). Applies ddbeck's checklist and a shields.io badge principle.

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against ontologies (genes, cell types, diseases, tissues), tracking data lineage and computational workflows, building data lakehouses, or wiring integrations with Nextflow, Snakemake, W&B, or MLflow. Part of the AlterLab Academic Skills suite.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.

Apply medicinal chemistry filters for compound triage: drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and a custom query language for library filtering.

Queries the Metabolomics Workbench REST API to retrieve metabolite, study, and RefMet data in JSON or text formats.

Audits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of previously-passing links; designed for lychee-based GitHub Actions link checkers but generalizes to markdown-link-check and similar tools. Use when the request mentions link audit, dead links, link health, lychee, broken links, link checker, markdown link audit, link-health audit, 404 audit, check-links failing, CI link-check, or 連結健檢, 死鏈, 失效連結, 斷鏈檢查. Part of the AlterLab Academic Skills suite.

Diagnose which organic growth path to pursue by identifying where the growth constraint lives, using a fast triage based on the McKinsey Growth Pyramid.

Provides a framework for proactive health monitoring and optimization, treating the human body as an asset to be maintained through telemetry, diagnostics, and interventions.

Manage Miro boards, sticky notes, and shapes via the Miro API, enabling programmatic creation of collaborative whiteboards.

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Spatial region-aware cell matching for CODEX/scRNAseq integration

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。

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.

Filtros de química medicinal. Aplique regras de similaridade a fármacos (Lipinski, Veber), filtros PAINS, alertas estruturais, métricas de complexidade, para priorização de compostos e filtragem de bibliotecas.

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

Provide direct REST API access to PubMed via the NCBI E-utilities API, supporting advanced Boolean/MeSH queries, batch processing, and citation management. Use when searching biomedical literature by MeSH terms, retrieving abstracts or PMIDs in bulk, or scripting custom PubMed queries over raw HTTP/REST — for Python workflows prefer biopython (Bio.Entrez) instead, use this for direct REST work or custom API implementations. Part of the AlterLab Academic Skills suite.