lamm-mit/scienceclaw - 3ページ

diagramming

Generate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows

原文の言語: 英語

diffdock

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.

原文の言語: 英語

dnanexus-integration

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.

原文の言語: 英語

docx

Extract text, tables, headings, and metadata from Microsoft Word .docx files

原文の言語: 英語

drug-drug-interaction

ToolUniverse workflow — Drug Drug Interaction

原文の言語: 英語

drug-repurposing

ToolUniverse workflow — Drug Repurposing

原文の言語: 英語

drug-target-validation

ToolUniverse workflow — Drug Target Validation

原文の言語: 英語

drugbank-database

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…

原文の言語: 英語

ena-database

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.

原文の言語: 英語

ensembl-database

Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

原文の言語: 英語

epigenomics

ToolUniverse workflow — Epigenomics

原文の言語: 英語

esm

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,…

原文の言語: 英語

etetoolkit

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

原文の言語: 英語

exploratory-data-analysis

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…

原文の言語: 英語

expression-data-retrieval

ToolUniverse workflow — Expression Data Retrieval

原文の言語: 英語

fabric

Pattern-based analysis using Fabric's 242+ specialized prompts for summarizing papers and extracting insights

原文の言語: 英語

fda-database

Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.

原文の言語: 英語

fem-analysis

Modal analysis of a membrane STL using Kirchhoff plate FEM (scipy eigensolver). Takes a binary STL + material properties JSON, constructs a 2D rectangular FEM mesh, assembles stiffness and mass matrices, extracts the first N eigenfrequencies, and reports…

原文の言語: 英語

firecrawl-scraper

Web scraping of JavaScript-rendered scientific websites using Firecrawl API

原文の言語: 英語

flowio

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.

原文の言語: 英語

fluidsim

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…

原文の言語: 英語

fred-economic-data

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…

原文の言語: 英語

gene-database

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.

原文の言語: 英語

gene-enrichment

ToolUniverse workflow — Gene Enrichment

原文の言語: 英語

generate-image

Generate or edit images using AI models (FLUX, Gemini). 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,…

原文の言語: 英語

geniml

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…

原文の言語: 英語

geo-database

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.

原文の言語: 英語

geometry-generator

Generate parametric bioinspired ribbed membrane STL geometry via LLM-guided design. Takes a spec JSON (from StructureAnalyst/PropertyPredictor upstream artifacts), calls the LLM with a structured CAD prompt to produce design parameters, then builds a…

原文の言語: 英語

geopandas

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,…

原文の言語: 英語

get-available-resources

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…

原文の言語: 英語

gget

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…

原文の言語: 英語

gtars

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…

原文の言語: 英語

gwas-database

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.

原文の言語: 英語

gwas-drug-discovery

ToolUniverse workflow — Gwas Drug Discovery

原文の言語: 英語

gwas-finemapping

ToolUniverse workflow — Gwas Finemapping

原文の言語: 英語

gwas-snp-interpretation

ToolUniverse workflow — Gwas Snp Interpretation

原文の言語: 英語

gwas-study-explorer

ToolUniverse workflow — Gwas Study Explorer

原文の言語: 英語

gwas-trait-to-gene

ToolUniverse workflow — Gwas Trait To Gene

原文の言語: 英語

histolab

Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial…

原文の言語: 英語

hmdb-database

Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

原文の言語: 英語