bioinformatics
156
conservation-map
Compute per-position conservation/entropy for an aligned peptide MSA (aligned sequences).
lamm-mit
research
sorting
stars
current ordering strategy
query
all entries
refine the visible subset
bioinformatics
156
neuropixels-analysis
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
lamm-mit
research
bioinformatics
156
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
lamm-mit
research
bioinformatics
156
brenda-database
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.
lamm-mit
research
bioinformatics
156
clinvar-database
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.
lamm-mit
research
bioinformatics
156
pdb-database
Python API for RCSB PDB 3D structures (search, fetch coordinates, metadata). Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers — pass only the target protein name or PDB accession.
lamm-mit
research
bioinformatics
156
bioservices
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.
lamm-mit
research
bioinformatics
156
arboreto
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.
lamm-mit
research
bioinformatics
156
alphafold-database
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.
lamm-mit
research
bioinformatics
156
peptide-msa
Perform a simple multiple-sequence alignment (MSA) for short peptides and return aligned sequences + consensus.
lamm-mit
research
bioinformatics
156
monarch-database
Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species. Integrates OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use for rare disease gene discovery, phenotype-to-gene mapping, cross-species disease modeling, and HPO term lookup.
lamm-mit
research
bioinformatics
149
r2000-analyze-blocks
Analyzes memory regions of a disassembled binary and converts them to the correct block types (code, bytes, words, text, tables, etc.) using MOS 6502 and the target platform's expertise.
ricardoquesada
research
bioinformatics
149
r2000-analyze-basic
Analyzes a sequence of memory containing Commodore BASIC tokens, formats address/word data types, and constructs side comments representing the plain BASIC commands.
ricardoquesada
research
bioinformatics
148
flydsl-kernel-authoring
Comprehensive reference for authoring FlyDSL GPU kernels on AMD GPUs. Covers the layout algebra, tiled copy/MMA, buffer ops, scf.for loops, SmemAllocator, autotuning, and common patterns. Use when writing, reviewing, or understanding FlyDSL kernel code.
ROCm
research
bioinformatics
129
protein-structure-analysis
Protein Structure Comprehensive Analysis - Comprehensive structure analysis: download PDB, extract chains, calculate geometry, quality metrics, and composition. Use this skill for structural biology tasks involving retrieve protein data by pdbcode extract pdb chains calculate pdb structural geometry calculate pdb quality metrics calculate pdb composition info. Combines 5 tools from 1 SCP server(s).
InternScience
research
bioinformatics
129
protein-interaction-network
Protein Interaction Network Analysis - Build protein interaction network: map identifiers with STRING, get PPI network, compute enrichment, and link to KEGG pathways. Use this skill for systems biology tasks involving mapping identifiers get string network interaction get ppi enrichment kegg link. Combines 4 tools from 2 SCP server(s).
InternScience
research
bioinformatics
129
protein-classification-analysis
Protein Classification Analysis - Classify protein: ChEMBL protein classification, UniProt entry, InterPro domains, and Ensembl biotypes. Use this skill for protein science tasks involving search protein classification get uniprotkb entry by accession query interpro get info biotypes. Combines 4 tools from 4 SCP server(s).
InternScience
research
bioinformatics
129
protein-complex-analysis
Protein Complex Visualization & Analysis - Analyze protein complex: download structure, visualize complex, extract chains, and calculate quality metrics. Use this skill for structural biology tasks involving retrieve protein data by pdbcode visualize complex extract pdb chains calculate pdb basic info. Combines 4 tools from 1 SCP server(s).
InternScience
research
bioinformatics
129
population-genetics
Population Genetics Analysis - Analyze population genetics: Ensembl variation populations, linkage disequilibrium, and variant frequency data. Use this skill for population genetics tasks involving get info variation populations get ld get variation get variant recoder. Combines 4 tools from 1 SCP server(s).
InternScience
research
bioinformatics
129
protein-blast-search
Search for similar protein sequences in UniProt Swiss-Prot database using BLAST to identify homologous proteins and functional relationships.
InternScience
research