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Research

Scientific computing and academic tools.

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bioinformatics
156

jax-modal-analysis

3D tetrahedral FEM modal analysis of a membrane STL. Takes a binary STL (mm units) + material properties JSON, repairs surface mesh, generates tetrahedral volume mesh via TetGen, assembles 3D stiffness/mass matrices with jax-fem, solves the generalised eigenvalue problem, and reports eigenfrequencies + mode shapes. Returns artifact JSON with eigenfrequencies_hz, eigenfrequencies_khz, modes_in_range, target_range_pass, and paths to summary PNG and CSV.

lamm-mit
lamm-mit
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bioinformatics
156

bioreason-pro

Multimodal reasoning LLM for protein function prediction integrating protein embeddings with biological context to generate structured reasoning traces and functional annotations.

lamm-mit
lamm-mit
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bioinformatics
156

anndata

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

lamm-mit
lamm-mit
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bioinformatics
156

cellxgene-census

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.

lamm-mit
lamm-mit
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bioinformatics
156

torchdrug

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

lamm-mit
lamm-mit
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bioinformatics
156

string-database

Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.

lamm-mit
lamm-mit
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bioinformatics
156

uniprot

Protein sequence, function, and annotation lookup. Query MUST be a bare gene symbol or protein name — 1 to 3 words maximum. Valid examples: 'KRAS', 'EGFR', 'BTK', 'TP53', 'Bruton tyrosine kinase', 'P01116'. If the topic is 'sotorasib KRAS G12C', the correct query is 'KRAS'. If the topic is 'imatinib BCR-ABL resistance', the correct query is 'BCR-ABL'. Strip the drug name, mutation label, and all mechanism words — pass only the protein or gene name.

lamm-mit
lamm-mit
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bioinformatics
156

scientific-schematics

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

lamm-mit
lamm-mit
research
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bioinformatics
156

scikit-bio

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

lamm-mit
lamm-mit
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bioinformatics
156

sequence

Analyze biological sequences using Biopython - translate, align, parse FASTA/GenBank

lamm-mit
lamm-mit
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bioinformatics
156

scanpy

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

lamm-mit
lamm-mit
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bioinformatics
156

phylogenetics

ToolUniverse workflow — Phylogenetics

lamm-mit
lamm-mit
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bioinformatics
156

conservation-map

Compute per-position conservation/entropy for an aligned peptide MSA (aligned sequences).

lamm-mit
lamm-mit
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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
lamm-mit
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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
lamm-mit
research
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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.

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lamm-mit
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