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Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating transcriptomics with FBA.
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Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing to community workflow registries.
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Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, generating bootstrap consensus, or needing quick exploratory phylogenies before running full ML analysis.
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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.
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Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.
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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.
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End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV, and SHAP interpretation. Use when building and validating diagnostic or prognostic biomarker signatures from omics data.
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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.
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Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use when batch-converting Ensembl IDs to other namespaces (HGNC, RefSeq, UniProt, Entrez), pulling gene coordinate tables for thousands of genes, building ortholog wide-tables across species, or replacing slow Ensembl REST loops with one-shot bulk export. Encodes BioMart's XML query format, R biomaRt vs Python pybiomart trade-off, mart-vs-dataset hierarchy, and the URL endpoint that's BioMart-specific (separate from rest.ensembl.org).
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Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
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Predicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES gold-standard endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.
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Convert any public web page into clean, structured Markdown. Preserves headings, links, images, code blocks, and tables while removing ads, navigation, and clutter. Perfect for content archival, knowledge base building, and research note-taking.
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Track thought leaders and industry voices across LinkedIn, Twitter, and YouTube. Monitor publishing cadence, content themes, engagement patterns, and audience growth for competitive positioning and relationship-building intelligence.
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Research and collect social proof — testimonials, case studies, user reviews, social mentions, and community endorsements across platforms. Useful for marketing teams building trust content, landing pages, and sales collateral from authentic customer voices.
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Prepare personalized email outreach by researching prospects, verifying email addresses, building company context, and generating relevant talking points. End-to-end outreach preparation from prospect identification to send-ready intelligence.
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When the user wants to create SEO-driven pages at scale using templates and data. Also use when the user mentions "programmatic SEO," "template pages," "pages at scale," "directory pages," "location pages," "[keyword] + [city] pages," "comparison pages," "integration pages," "building many pages for SEO," "pSEO," "generate 100 pages," "data-driven pages," or "templated landing pages." Use this whenever someone wants to create many similar pages targeting different keywords or locations. For auditing existing SEO issues, use an available SEO audit capability. For content strategy planning, use an available content strategy capability.
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Calculate TAM/SAM/SOM for market opportunities using top-down, bottom-up, and value theory methodologies. Use this skill when sizing markets, estimating addressable revenue, validating market opportunity for a new venture, or building investor-ready market analysis for a startup pitch or business plan.
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Turn a vague bug report into a VERIFIED minimal reproduction and then a failing regression test, agent-driven end to end. Covers extracting the implicit repro from a thin report (env, build, steps, data), the reproduce-minimize-isolate-capture loop, git bisect to find the introducing commit, building a deterministic minimal repro (fixed seeds, frozen time, stubbed network), writing the failing regression test BEFORE the fix (red) and confirming the fix flips it green, and writing repro evidence back into the ticket. Distinguishes flaky-not-reproducible from environment-specific. Use when: "reproduce this bug," "minimal reproduction," "repro steps," "find the commit that broke it," "git bisect," "make the repro deterministic," "write a failing test for this bug," "regression test for a defect," "can't reproduce this bug." Not for: Classifying/deduplicating/severity-routing existing failures without reproducing them — that is ai-bug-triage. Generating tests from specs rather than from a defect — that is ai-test-generation. Related: ai-bug-triage, ai-test-generation, test-reliability, systematic-debugging, qa-project-context.
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Validate that analytics and marketing tracking fire CORRECTLY: GA4/GTM dataLayer events, Meta/TikTok/LinkedIn pixels, and ad-tech tags. Covers building a tracking plan as the contract, intercepting collect-endpoint beacons and dataLayer.push in Playwright, asserting event name + params + values + timing + de-duplication, Consent Mode v2 gating, CI regression gating, and news-media events (article-view, scroll-depth, paywall). Use when: "test analytics tracking," "GA4 event test," "verify the pixel fires," "dataLayer test," "tracking plan," "Meta Pixel dedup," "scroll-depth tracking test," "gate tracking in CI." Not for: whether tracking is ALLOWED to fire under consent law (GDPR/CMP) — that is compliance-testing; this skill checks the data is CORRECT. SEO meta tags / structured data — out of scope. Related: compliance-testing, playwright-automation, api-testing, qa-project-context.
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Define, track, and act on QA metrics: test coverage percentage, flakiness rate, defect escape rate, MTTR, test execution time trends, automation ROI, quality gates, and SLAs for test suites. Includes metric formulas, realistic targets by company stage, and the action to take when each metric goes red. Use when: "QA metrics," "test metrics," "quality KPIs," "test health," "flakiness rate," "defect escape rate." Not for: building the dashboard UI (Allure/Grafana) — use qa-dashboard; measuring coverage gaps and mutation score — use coverage-analysis. Related: qa-dashboard, coverage-analysis, ci-cd-integration, release-readiness, quality-postmortem.
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Use when building or editing a devopsdays event's schedule - adding talks, ignites, open spaces, breaks, and evening events to the program, or moving time slots around.
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Submit proof requests on the Boundless ZK proof marketplace. Covers wallet setup, CLI configuration, building or discovering guest programs, self-hosting via Cloudflare Quick Tunnels (no Pinata/S3 needed), submitting, and retrieving results. Use when a developer wants to request a ZK proof, submit a proof request, get started with Boundless, try Boundless, or learn the requestor workflow.
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Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
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