lamm-mit/scienceclaw - Page 3

diagramming

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

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.

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.

docx

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

drug-drug-interaction

ToolUniverse workflow — Drug Drug Interaction

drug-repurposing

ToolUniverse workflow — Drug Repurposing

drug-target-validation

ToolUniverse workflow — Drug Target Validation

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…

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.

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.

epigenomics

ToolUniverse workflow — Epigenomics

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,…

etetoolkit

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

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…

expression-data-retrieval

ToolUniverse workflow — Expression Data Retrieval

fabric

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

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.

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…

firecrawl-scraper

Web scraping of JavaScript-rendered scientific websites using Firecrawl API

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.

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…

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…

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.

gene-enrichment

ToolUniverse workflow — Gene Enrichment

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,…

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…

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.

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…

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,…

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…

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…

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…

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.

gwas-drug-discovery

ToolUniverse workflow — Gwas Drug Discovery

gwas-finemapping

ToolUniverse workflow — Gwas Finemapping

gwas-snp-interpretation

ToolUniverse workflow — Gwas Snp Interpretation

gwas-study-explorer

ToolUniverse workflow — Gwas Study Explorer

gwas-trait-to-gene

ToolUniverse workflow — Gwas Trait To Gene

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…

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.