Results for “bio”

Analyzes firmware images for embedded malware, backdoors, and unauthorized modifications targeting routers, IoT devices, UEFI/BIOS, and embedded systems. Covers firmware extraction, filesystem analysis, binary reverse engineering, and bootkit detection.

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.

Assess platform firmware security using Intel CHIPSEC: verify SPI flash write protection, BIOS lock, SMM/SMRR, Secure Boot variables, dump SPI flash, and triage UEFI variables for firmware-level threats.

Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus structured JSON for downstream chaining.

ESLint - pluggable JavaScript/TypeScript linter USE WHEN: user mentions "ESLint", "JavaScript linting", ".eslintrc", asks about "eslint config", "linting rules", "eslint plugins", "flat config" DO NOT USE FOR: Biome - use `eslint-biome` skill, TypeScript-specific - use `typescript-eslint` skill, code quality principles - use `quality-common`

Teleological physiology analysis framework for understanding biological systems through multi-constraint optimization. Use when analyzing physiological mechanisms, explaining apparent biological "inefficiencies", preparing for medical examinations (CICM/ANZCA Primary), understanding why biological systems are designed the way they are, or when seeking deeper mechanistic understanding beyond descriptive knowledge. Triggers on questions like "why is X designed this way", "what purpose does Y serve", "how is Z optimized", analysis of physiological trade-offs, or exploration of evolutionary/design constraints.

AI-powered career biographer that conducts empathetic interviews, extracts structured career narratives, and transforms professional stories into portfolios, CVs, and personal brand assets. This skill should be used when users want to document their career journey, create professional portfolios, generate CVs, or craft compelling career narratives.

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterlab-bindingdb instead. Part of the AlterLab Academic Skills suite.

Use when converting GenBank format files to table format as part of the Entrez Direct toolkit from bioconda.

Use when you need to aggregate quality control reports from multiple bioinformatics tools into a single HTML report

Generate professional clinical decision support documents for pharmaceutical and clinical research, including biomarker-stratified cohort analyses and evidence-based treatment recommendation reports with GRADE grading, statistical analysis, and publication-ready LaTeX/PDF output.

Deploy FIDO2/WebAuthn passwordless authentication using security keys and platform authenticators, covering WebAuthn API integration, FIDO2 server configuration, passkey enrollment, biometric authentication, and migration from password-based systems aligned with NIST SP 800-63B AAL3.

Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs, diseases, phenotypes, pathways, and biological processes. Use when exploring drug-disease or gene-disease links, building disease-centric knowledge subgraphs, or sourcing relations for drug repurposing and precision-medicine analyses. Part of the AlterLab Academic Skills suite.

Query the Reactome REST API for pathway analysis, over-representation/enrichment, gene-to-pathway mapping, disease pathways, molecular interactions, and expression analysis. Use when running pathway enrichment on a gene list, mapping genes to curated biological pathways, or exploring disease pathways for systems biology studies. 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.

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

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

Use when filtering Entrez search results by date, organism, publication type, sequence features, or other database-specific criteria in bioinformatics pipelines.

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.

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

Compile SOUL.md character profiles into synthetic diploid genomes (.genome.json) via trait-to-allele mapping.

Modelagem metabólica baseada em restrições (COBRA). FBA, FVA, knockouts de genes, amostragem de fluxo, modelos SBML, para análise de biologia de sistemas e engenharia metabólica.

Secure iOS apps with secure storage, biometrics, and data protection. Use when implementing secure storage, Face ID/Touch ID, or data protection in iOS.

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

Process and analyze physiological signals including ECG, EEG, EDA, RSP, PPG, EMG, and EOG using Python.

Generates and analyzes protein sequences and structures using ESM3, ESMC, and ESMFold2, with support for local and cloud inference.

Downloads genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

Organize, query, validate, and convert neuroscience and biomedical data using the Brain Imaging Data Structure (BIDS) standard.

Search 10 academic literature APIs for papers, preprints, citations, and open-access full text with reproducible provenance.

Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.

Use when you need to compress or decompress files using BGZF (Blocked GNU Zip Format), create BGZF indexes for random access, or prepare bioinformatics files for tabix indexing.

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.

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

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

Performs HLA allele genotyping from WGS/WES VCF data, producing a structured markdown report and machine-readable JSON results.

Annotates VCF variants using Ensembl VEP, ClinVar, and gnomAD, ranks them by predicted impact, and generates a reproducible report.