All authors
Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,578 skills3 installs3,530 views
- Brenda Database--> --- name: bio-brenda-database description: Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis. 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
- Cbioportal Database--> --- name: bio-cbioportal-database description: Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_sh...Votes: 0GitHub stars: 32
- Cellxgene Census--> --- name: bio-cellxgene-census description: Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_f...Votes: 0GitHub stars: 32
- Chembl Database--> --- name: bio-chembl-database description: Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry. 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
- Cirq--> --- name: bio-cirq description: Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output with...Votes: 0GitHub stars: 32
- Citation Management--> --- name: bio-citation-management description: Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow succes...Votes: 0GitHub stars: 32
- Clinical Decision Support--> --- name: bio-clinical-decision-support description: Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs ...Votes: 0GitHub stars: 32
- Clinical Reports--> --- name: bio-clinical-reports description: Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 mi...Votes: 0GitHub stars: 32
- Clinicaltrials Database--> --- name: bio-clinicaltrials-database description: Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching. 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
- Clinpgx Database--> --- name: bio-clinpgx-database description: Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions. 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
- Clinvar Database--> --- name: bio-clinvar-database description: Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine. 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
- Cobrapy--> --- name: bio-cobrapy description: Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis. 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
- Consciousness Council--> --- name: bio-consciousness-council description: Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks for a council/panel/board discussion, wants to explore a problem from multiple angles, requests devil's advocate analysis, or says things like "what would different experts think about this", "help me think through this from all sides", "counci...Votes: 0GitHub stars: 32
- Cosmic Database--> --- name: bio-cosmic-database description: Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication. 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
- Dask--> --- name: bio-dask description: Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes....Votes: 0GitHub stars: 32
- Datacommons Client--> --- name: bio-datacommons-client description: Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between st...Votes: 0GitHub stars: 32
- Datamol--> --- name: bio-datamol description: Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 1...Votes: 0GitHub stars: 32
- Deepchem--> --- name: bio-deepchem description: Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill work...Votes: 0GitHub stars: 32
- Deeptools--> --- name: bio-deeptools description: NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization. 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
- Denario--> --- name: bio-denario description: Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration. tool_type: mixed primar...Votes: 0GitHub stars: 32
- Depmap--> --- name: bio-depmap description: Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets. 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
- Dhdna Profiler--> --- name: bio-dhdna-profiler description: Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, asks "what's my thinking style", "analyze how this person reasons", "cognitive profile", "thinking pattern", "DHDNA", "digital DNA", or wants to understand the mind behind any text. Also trigger when the user prov...Votes: 0GitHub stars: 32
- Diffdock--> --- name: bio-diffdock description: Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction. 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
- Dnanexus Integration--> --- name: bio-dnanexus-integration description: DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution. 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
- Docx--> --- name: bio-docx description: 'Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers include: any mention of ''Word doc'', ''word document'', ''.docx'', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx files, inserting or replacing images in documents, performing find-and-replace in Word fil...Votes: 0GitHub stars: 32
- Drugbank Database--> --- name: bio-drugbank-database description: Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target...Votes: 0GitHub stars: 32
- Edgartools--> --- name: bio-edgartools description: Python library for accessing, analyzing, and extracting data from SEC EDGAR filings. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly reports (10-K, 10-Q), proxy statements (DEF 14A), 8-K current events, company screening by ticker/CIK/industry, multi-period financial analysis, or any SE...Votes: 0GitHub stars: 32
- Ena Database--> --- name: bio-ena-database description: Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats. 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
- Ensembl Database--> --- name: bio-ensembl-database description: Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research. 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
- Esm--> --- name: bio-esm description: Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud...Votes: 0GitHub stars: 32
- Etetoolkit--> --- name: bio-etetoolkit description: Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics. 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
- Exploratory Data Analysis--> --- name: bio-exploratory-data-analysis description: Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, ...Votes: 0GitHub stars: 32
- Fda Database--> --- name: bio-fda-database description: Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research. 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
- Flowio--> --- name: bio-flowio description: Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing. 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
- Fluidsim--> --- name: bio-fluidsim description: Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with...Votes: 0GitHub stars: 32
- Fred Economic Data--> --- name: bio-fred-economic-data description: Query FRED (Federal Reserve Economic Data) API for 800,000+ economic time series from 100+ sources. Access GDP, unemployment, inflation, interest rates, exchange rates, housing, and regional data. Use for macroeconomic analysis, financial research, policy studies, economic forecasting, and academic research requiring U.S. and international economic indicators. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow su...Votes: 0GitHub stars: 32
- Gene Database--> --- name: bio-gene-database description: Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis. 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
- Generate Image--> --- name: bio-generate-image description: Generate or edit images using AI models (FLUX, Nano Banana 2). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a technical diagram or schematic. For flowcharts, circuits, pathways, and technical diagrams, use the scientific-schematics skill instead. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output...Votes: 0GitHub stars: 32
- Geniml--> --- name: bio-geniml description: This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning. tool_type: mixed primary_tool: Unknown meas...Votes: 0GitHub stars: 32
- Geo Database--> --- name: bio-geo-database description: Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis. 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
- Geomaster--> --- name: bio-geomaster description: Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentinel, Landsat, MODIS, SAR, hyperspectral), vector and raster data operations, spatial statistics, point cloud processing, network analysis, cloud-native workflows (STAC, COG, Planetary Computer), and 8 programming languages (Python, R, Julia, JavaScript, C++...Votes: 0GitHub stars: 32
- Geopandas--> --- name: bio-geopandas description: Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks lik...Votes: 0GitHub stars: 32
- Get Available Resources--> --- name: bio-get-available-resources description: This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or m...Votes: 0GitHub stars: 32
- Gget--> --- name: bio-gget description: 'Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.' tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - rea...Votes: 0GitHub stars: 32
- Ginkgo Cloud Lab--> --- name: bio-ginkgo-cloud-lab description: Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run cell-free protein expression (validation or optimization), generate fluorescent pixel art, or interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows. tool_type: mixed primary_tool: Un...Votes: 0GitHub stars: 32
- Glycoengineering--> --- name: bio-glycoengineering description: Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - ...Votes: 0GitHub stars: 32
- Gnomad Database--> --- name: bio-gnomad-database description: Query gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_c...Votes: 0GitHub stars: 32
- Gtars--> --- name: bio-gtars description: High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications. 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
- Gtex Database--> --- name: bio-gtex-database description: Query GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative trait loci), and sQTLs. Essential for linking GWAS variants to gene regulation, understanding tissue-specific expression, and interpreting non-coding variant effects. 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
- Gwas Database--> --- name: bio-gwas-database description: Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores. 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