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Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,578 skills3 installs3,530 views
- Genomics Sv Detection--> --- name: bio-genomics-sv-detection description: 'Structural variant detection (DEL/DUP/INV/TRA): SV VCF parsing with BND notation, size classification (50bp-10Mb), evidence types. Wraps Manta, Lumpy, Delly, Sniffles.' tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Structural variant calling for deletions, duplications, inversions, and translocations. Wr...Votes: 0GitHub stars: 32
- Genomics Variant Annotation--> --- name: bio-genomics-variant-annotation description: 'Variant functional impact prediction: VEP consequence types (HIGH/MODERATE/LOW/MODIFIER), SIFT, PolyPhen-2, and CADD scoring. Rule-based annotation engine for demo, wraps VEP/snpEff/ANNOVAR.' tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Variant annotation and functional effect prediction. Supports...Votes: 0GitHub stars: 32
- Genomics Variant Calling--> --- name: bio-genomics-variant-calling description: Germline and somatic variant calling (SNVs, Indels) using GATK HaplotypeCaller, Mutect2, DeepVariant, or FreeBayes. Includes GVCF workflow, VQSR, and hard filtering. tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Germline and somatic small variant calling (SNVs, Indels). Supports GATK HaplotypeCaller, M...Votes: 0GitHub stars: 32
- Genomics Vcf Operations--> --- name: bio-genomics-vcf-operations description: 'VCF operations: multi-allelic parsing, variant classification (SNP/MNP/INS/DEL/COMPLEX), Ti/Tv ratio, QUAL/DP filtering, INFO field parsing. Mirrors bcftools stats.' tool_type: mixed primary_tool: genomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- VCF manipulation, filtering, merging, and summary statistics. Wraps bcftools and GATK Selec...Votes: 0GitHub stars: 32
- Opencrispr Gene EditorsEvaluate and operate released Profluent OpenCRISPR gene-editing systems, especially OpenCRISPR-1, for controlled research workflows using its published Cas9-like protein, compatible guide RNA designs, protocols, licensing, specificity testing, and experimental validation. Use when comparing OpenCRISPR-1 with SpCas9, planning nonclinical editing studies, or assessing use in nuclease, nickase, deactivated, base, prime, or epigenome-editing contexts.Votes: 0GitHub stars: 32
- Doublet Detection--> --- name: bio-flow-cytometry-doublet-detection description: Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering out cell aggregates before clustering or quantitative analysis. tool_type: r primary_tool: flowCore measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- LLM Research--> --- name: bio-literature description: Parse scholarly articles (PDF, DOI, URL) to extract metadata, GEO accessions, and acquisition links using OpenAlex + GROBID pipelines. tool_type: mixed primary_tool: literature measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- ScientificSpectralVqaBenchmark Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'scientific-spectral-vqa-benchmark' description: 'Evaluate MLLMs on scientific spectral images using SpecVQA-style figure extraction, curve-aware sampling, QA design, and scoring workflows.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 32
- End To End Agentic AI Lab--> --- name: end-to-end-agentic-ai-lab description: Deploy MDalamin5's End-to-End Agentic AI Automation Lab to prototype lab automation swarms that span LangChain/LangGraph agents, MCP servers, and n8n-run experiment control. keywords: - lab-automation - multi-agent - langgraph - n8n - mcp measurable_outcome: Stand up one multi-agent workflow plus an MCP-backed automation pipeline from the lab within a single working day. license: MIT metadata: author: Lab Automation Guild version: "2026.03"...Votes: 0GitHub stars: 32
- BiocontextAiMcpRegistry Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'biocontext-ai-mcp-registry' description: 'Use the BioContextAI Registry to discover, compare, and select biomedical MCP servers for bioinformatics, systems biology, and biomedical AI workflows.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 32
- Biomed Agent--> --- name: biomed-agent-mcp description: A general-purpose biomedical knowledge assistant that connects to MCP biomedical data sources (OpenTargets, Monarch, MyGene, MyChem, MyDisease) and synthesizes answers using LLMs. keywords: - mcp - biomed-agent - general-purpose - knowledge-graph - data-integration measurable_outcome: Successfully query at least three distinct biomedical databases (e.g., Monarch, MyGene, OpenTargets) via MCP and synthesize a comprehensive answer in a single workflow...Votes: 0GitHub stars: 32
- MCP Operations 2026Implement and operate Model Context Protocol systems safely. Use when designing MCP clients or servers, selecting transports, configuring auth, onboarding remote servers, or enforcing approval and egress controls.Votes: 0GitHub stars: 32
- MCPmed--> --- name: bio-mcpmed-bioinformatics-server description: Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Adapts the Model Context Protocol (MCP) to bioinformatics web server backends. This creates a standardized, machine-actionable layer for LLMs to ...Votes: 0GitHub stars: 32
- PubmedNcbiMcpServer Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'pubmed-ncbi-mcp-server' description: 'Use the cyanheads PubMed MCP server to search PubMed, fetch metadata and full text, generate citations, inspect MeSH, and find related research.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 32
- Agentomics--> --- name: agentomics-ml description: An autonomous agentic system for supervised machine learning model development, specifically tailored for biomedical data. keywords: - agentomics - automl - biomedical-ml - supervised-learning - autonomous-agents measurable_outcome: Autonomously train, evaluate, and validate a supervised machine learning model on a biomedical dataset (e.g., omics data) with a performance report in under 1 hour. license: MIT metadata: author: BioGeMT source: "https://gi...Votes: 0GitHub stars: 32
- Metabolomics Annotation--> --- name: bio-metabolomics-annotation description: Metabolite annotation and structural identification using SIRIUS, CSI:FingerID, GNPS, or MetFrag. tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Metabolite annotation and structural identification against spectral libraries. Supports SIRIUS/CSI:FingerID, GNPS, and MetFrag.Votes: 0GitHub stars: 32
- Metabolomics De--> --- name: bio-metabolomics-de description: Metabolomics differential analysis using univariate tests (t-test, FDR), multivariate methods (PCA, PLS-DA, OPLS-DA, sPLS-DA), Random Forest, and ROC analysis for biomarker discovery. tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Univariate and multivariate statistical analysis for identifying differentiall...Votes: 0GitHub stars: 32
- Metabolomics Normalization--> --- name: bio-metabolomics-normalization description: Metabolomics data normalization, scaling and transformation. tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Data normalization, scaling, and transformation for metabolomics feature tables.Votes: 0GitHub stars: 32
- Metabolomics Pathway Enrichment--> --- name: bio-metabolomics-pathway-enrichment description: Metabolomics pathway analysis using MetaboAnalystR (KEGG, Reactome), pathview visualization, MSEA, mummichog, and network-based topology analysis. tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Map metabolites to biological pathways and perform enrichment, topology, and network analysis.Votes: 0GitHub stars: 32
- Metabolomics Peak Detection--> --- name: bio-metabolomics-peak-detection description: Peak picking, feature detection, alignment and grouping using XCMS, MZmine 3, or MS-DIAL. tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Peak picking, feature detection, chromatographic alignment and grouping. Supports XCMS, MZmine 3, and MS-DIAL outputs.Votes: 0GitHub stars: 32
- Metabolomics Quantification--> --- name: bio-metabolomics-quantification description: Feature quantification, missing value imputation, and normalization for metabolomics data. tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Feature quantification with missing value imputation (min/median/KNN) and normalization (TIC/median/log).Votes: 0GitHub stars: 32
- Metabolomics Statistics--> --- name: bio-metabolomics-statistics description: "Statistical analysis for metabolomics \u2014 PCA, PLS-DA, clustering,\ \ and univariate tests." tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Statistical analysis module for metabolomics data. PCA, PLS-DA, hierarchical clustering, and univariate tests.Votes: 0GitHub stars: 32
- Metabolomics Xcms Preprocessing--> --- name: bio-metabolomics-xcms-preprocessing description: XCMS3 workflow for LC-MS/GC-MS metabolomics preprocessing. Peak detection (CentWave/MatchedFilter), RT alignment (Obiwarp), correspondence, gap filling, and CAMERA adduct/isotope annotation. tool_type: mixed primary_tool: metabolomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- XCMS3 workflow for untargeted LC-MS/GC-MS metabolomics....Votes: 0GitHub stars: 32
- Connected Multiomics--> --- name: illumina-connected-multiomics description: Operate Illumina's Connected Multiomics SaaS to orchestrate tertiary analysis across single-cell, spatial, proteomic, methylation, and bulk omics with DRAGEN integration. keywords: - multi-omics - illumina - spatial-transcriptomics - methylation - tertiary-analysis measurable_outcome: Build a study, ingest DRAGEN outputs, and publish a multi-layer dashboard (cells + spatial + methylation) for collaborators within one day. license: Propr...Votes: 0GitHub stars: 32
- OncologyConsultSurvivalLlm Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'oncology-consult-survival-llm' description: 'Predict cancer survival from initial oncology consultation documents using zero-shot or fine-tuned LLM workflows with leakage control and calibrated reporting.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 32
- OncologyNeurosymbolicTrialMatching Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'oncology-neurosymbolic-trial-matching' description: 'Match oncology patients to clinical trials using knowledge-graph context, symbolic eligibility reasoning, specialized agents, conflict resolution, and clinician review.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 32
- DmmrCrcHistopathologyAgent Agent--> <!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE --> --- name: 'dmmr-crc-histopathology-agent' description: 'Predict and validate colorectal cancer dMMR signals from H&E histopathology, including non-tumor and low-magnification WSI regions.' measurable_outcome: 'Execute skill workflow successfully with valid output within 15 minutes.' allowed-tools: - read_file - run_shell_command - web_fetch ---Votes: 0GitHub stars: 32
- Differential Abundance--> --- name: bio-proteomics-differential-abundance description: Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes between experimental groups. tool_type: mixed primary_tool: MSstats measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Proteomics Data Import--> --- name: bio-proteomics-data-import description: Import and convert proteomics data formats between MaxQuant, DIA-NN, Spectronaut, and standard CSV. tool_type: mixed primary_tool: proteomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Import and convert proteomics data from various formats (MaxQuant, DIA-NN, Spectronaut output) into standardised tables.Votes: 0GitHub stars: 32
- Proteomics De--> --- name: bio-proteomics-de description: Differential protein abundance testing using MSstats, limma, proDA, and scipy/statsmodels for Python. Multiple testing correction with BH FDR. tool_type: mixed primary_tool: proteomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Statistical testing for differentially abundant proteins between experimental conditions.Votes: 0GitHub stars: 32
- Proteomics Enrichment--> --- name: bio-proteomics-enrichment description: Pathway, network, and functional enrichment for proteomics using STRING, DAVID, or g:Profiler. tool_type: mixed primary_tool: proteomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Pathway, network, and Gene Ontology enrichment analysis for proteomics data.Votes: 0GitHub stars: 32
- Proteomics Identification--> --- name: bio-proteomics-identification description: Database search for peptide/protein identification using MaxQuant, MS-GF+, Comet, or Mascot. tool_type: mixed primary_tool: proteomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Peptide and protein identification from MS/MS spectra. Wraps MaxQuant/Andromeda, MS-GF+, and Comet.Votes: 0GitHub stars: 32
- Proteomics Ms Qc--> --- name: bio-proteomics-ms-qc description: Mass spectrometry raw data quality control using PTXQC, rawTools, or MSstatsQC. tool_type: mixed primary_tool: proteomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Mass spectrometry data quality control. Computes basic QC statistics for protein/peptide abundance tables.Votes: 0GitHub stars: 32
- Proteomics Ptm--> --- name: bio-proteomics-ptm description: Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Site localization, motif analysis, and quantitative PTM analysis with MSstatsPTM. tool_type: mixed primary_tool: proteomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Identify, quantify, and analyze post-translational modifications from mass spectro...Votes: 0GitHub stars: 32
- Proteomics Quantification--> --- name: bio-proteomics-quantification description: Protein/peptide quantification (LFQ, TMT, DIA) using MaxQuant LFQ, DIA-NN, or Skyline. tool_type: mixed primary_tool: proteomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Protein and peptide quantification for label-free (LFQ), isobaric labelling (TMT), and DIA workflows.Votes: 0GitHub stars: 32
- Proteomics Structural--> --- name: bio-proteomics-structural description: Structural proteomics and cross-linking MS analysis using XlinkX, pLink, or xiSEARCH. tool_type: mixed primary_tool: proteomics measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Cross-linking mass spectrometry (XL-MS) analysis. Identifies protein-protein interaction interfaces and distance constraints.Votes: 0GitHub stars: 32
- Adaptyv--> --- name: bio-adaptyv description: Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluPro...Votes: 0GitHub stars: 32
- Aeon--> --- name: bio-aeon description: This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs. tool_type: mixed p...Votes: 0GitHub stars: 32
- Alpha Vantage--> --- name: bio-alpha-vantage description: Access real-time and historical stock market data, forex rates, cryptocurrency prices, commodities, economic indicators, and 50+ technical indicators via the Alpha Vantage API. Use when fetching stock prices (OHLCV), company fundamentals (income statement, balance sheet, cash flow), earnings, options data, market news/sentiment, insider transactions, GDP, CPI, treasury yields, gold/silver/oil prices, Bitcoin/crypto prices, forex exchange rates, or ...Votes: 0GitHub stars: 32
- Alphafold Database--> --- name: bio-alphafold-database description: Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Anndata--> --- name: bio-anndata description: "Data structure for annotated matrices in single-cell analysis. Use when\ \ working with .h5ad files or integrating with the scverse ecosystem. This is the\ \ data format skill\u2014for analysis workflows use scanpy; for probabilistic models\ \ use scvi-tools; for population-scale queries use cellxgene-census." tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools...Votes: 0GitHub stars: 32
- Arboreto--> --- name: bio-arboreto description: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 ...Votes: 0GitHub stars: 32
- Arxiv Database--> --- name: bio-arxiv-database description: Search and retrieve preprints from arXiv via the Atom API. Use this skill when searching for papers in physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, or economics by keywords, authors, arXiv IDs, date ranges, or categories. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_...Votes: 0GitHub stars: 32
- Astropy--> --- name: bio-astropy description: Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astro...Votes: 0GitHub stars: 32
- Benchling Integration--> --- name: bio-benchling-integration description: Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Bgpt Paper Search--> --- name: bio-bgpt-paper-search description: Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with vali...Votes: 0GitHub stars: 32
- Bindingdb Database--> --- name: bio-bindingdb-database description: Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell...Votes: 0GitHub stars: 32
- Biopython--> --- name: bio-biopython description: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. ...Votes: 0GitHub stars: 32
- Biorxiv Database--> --- name: bio-biorxiv-database description: Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 32
- Bioservices--> --- name: bio-bioservices description: Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. ...Votes: 0GitHub stars: 32