computational-chemistry
156
peptide-stability
Compute quick peptide stability/solubility heuristics (net charge, GRAVY, cysteines) for candidate sequences.
lamm-mit
research
sorting
stars
current ordering strategy
query
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refine the visible subset
computational-chemistry
156
molfeat
Molecular ML featurization library (100+ featurizers: ECFP, descriptors, ChemBERTa). Input: SMILES strings you already possess. Output: numerical feature vectors for QSAR/ML models. Does NOT retrieve compounds from any database — querying by topic name returns only a metadata stub. Use pubchem or chembl to obtain SMILES first, then featurize here. For ADMET predictions use tdc.
lamm-mit
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lab-tools
156
tooluniverse
Access 1000+ scientific tools from Harvard's ToolUniverse — bioinformatics, drug discovery, genomics, clinical research, and more
lamm-mit
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lab-tools
156
iso-13485-certification
Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.
lamm-mit
research
scientific-computing
156
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 geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
lamm-mit
research
scientific-computing
156
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.
lamm-mit
research
scientific-computing
156
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 type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
lamm-mit
research
scientific-computing
156
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
lamm-mit
research
scientific-computing
156
neurokit2
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
lamm-mit
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scientific-computing
156
diagramming
Generate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows
lamm-mit
research
scientific-computing
156
openmm
OpenMM molecular dynamics engine for protein and ligand simulations. Run NVE/NVT/NPT ensembles, compute free energies, analyze dynamics. Supports AMBER, CHARMM, OPLS force fields and GPU acceleration. For classical MD with periodic systems, use ase. For quick quantum chemistry, use mopac.
lamm-mit
research
scientific-computing
156
protein-interactions
ToolUniverse workflow — Protein Interactions
lamm-mit
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scientific-computing
156
datamol
Python cheminformatics library (RDKit wrapper). Input: SMILES strings you already possess. Output: computed molecular properties, fingerprints, conformers, clustering. Does NOT retrieve compounds from any database — querying by topic name returns only a metadata stub. Use pubchem or chembl to obtain SMILES first, then pass those SMILES here.
lamm-mit
research
scientific-computing
156
cosmic-database
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
lamm-mit
research
scientific-computing
156
cancer-variant-interpretation
ToolUniverse workflow — Cancer Variant Interpretation
lamm-mit
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scientific-computing
156
metabolomics-analysis
ToolUniverse workflow — Metabolomics Analysis
lamm-mit
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scientific-computing
156
ase
Atomic Simulation Environment (ASE) for computational materials science. Perform DFT calculations, geometry optimization, band structure analysis, molecular property prediction, and periodic structure simulations. Supports VASP, MOPAC, Quantum ESPRESSO backends. For quick semi-empirical quantum chemistry, use mopac. For classical molecular dynamics, use openmm.
lamm-mit
research