lamm-mit/scienceclaw - Página 3

diagramming

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

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

docx

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

Idioma del texto original: inglés

drug-drug-interaction

ToolUniverse workflow — Drug Drug Interaction

Idioma del texto original: inglés

drug-repurposing

ToolUniverse workflow — Drug Repurposing

Idioma del texto original: inglés

drug-target-validation

ToolUniverse workflow — Drug Target Validation

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

epigenomics

ToolUniverse workflow — Epigenomics

Idioma del texto original: inglés

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,…

Idioma del texto original: inglés

etetoolkit

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

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

expression-data-retrieval

ToolUniverse workflow — Expression Data Retrieval

Idioma del texto original: inglés

fabric

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

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

firecrawl-scraper

Web scraping of JavaScript-rendered scientific websites using Firecrawl API

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

gene-enrichment

ToolUniverse workflow — Gene Enrichment

Idioma del texto original: inglés

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,…

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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,…

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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.

Idioma del texto original: inglés

gwas-drug-discovery

ToolUniverse workflow — Gwas Drug Discovery

Idioma del texto original: inglés

gwas-finemapping

ToolUniverse workflow — Gwas Finemapping

Idioma del texto original: inglés

gwas-snp-interpretation

ToolUniverse workflow — Gwas Snp Interpretation

Idioma del texto original: inglés

gwas-study-explorer

ToolUniverse workflow — Gwas Study Explorer

Idioma del texto original: inglés

gwas-trait-to-gene

ToolUniverse workflow — Gwas Trait To Gene

Idioma del texto original: inglés

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…

Idioma del texto original: inglés

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.

Idioma del texto original: inglés