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.
diagramming
Generate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows
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.
protein-interactions
ToolUniverse workflow — Protein Interactions
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.
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.
cancer-variant-interpretation
ToolUniverse workflow — Cancer Variant Interpretation
metabolomics-analysis
ToolUniverse workflow — Metabolomics Analysis
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.
biopython
Computational molecular biology library (sequence I/O, alignment, phylogenetics). Input: FASTA/GenBank/PDB files you already have. Output: parsed sequences, alignments, phylogenetic trees, structural analysis. Does NOT search databases — invoking by topic returns only a placeholder stub. For literature use pubmed, for protein lookup use uniprot, for sequence homology use blast.
architect-diagnose-performance
Diagnose latency, saturation, and throughput regressions.
hypothesis-library
Curated repository of experiment hypotheses, assumptions, and historical learnings.
feasibility-study
Feasibility analysis from first principles. Use when: evaluating solutions before tech-spec, comparing approaches, risk assessment. Not for: implementation (use feature-dev), architecture advice (use codex-architect). Output: quantitative comparison + recommendation.
virus-genomics
Virus Genomics Analysis - Analyze virus genomics: NCBI virus dataset, annotation, taxonomy, and literature search. Use this skill for virology tasks involving get virus dataset report get virus annotation report get taxonomy search literature. Combines 4 tools from 2 SCP server(s).
smiles-comprehensive-analysis
SMILES Comprehensive Analysis - Comprehensive SMILES analysis: validate, convert name, compute all molecular descriptors, and predict ADMET. Use this skill for cheminformatics tasks involving is valid smiles ChemicalStructureAnalyzer calculate mol basic info pred molecule admet. Combines 4 tools from 3 SCP server(s).
signal-processing
Signal Processing Analysis - Analyze signals: duty cycle, frequency range, electron wavelength, and measurement error analysis. Use this skill for signal processing tasks involving calculate duty cycle calculate frequency range electron wavelength calculate absolute error. Combines 4 tools from 3 SCP server(s).
thermal-analysis
Thermal & Heat Transfer Analysis - Analyze thermal system: calculate heat released, convert energy units, compute potential energy, and dynamic viscosity. Use this skill for thermal engineering tasks involving calculate heat released convert energy MeV to J calculate potential energy calculate dynamic viscosity. Combines 4 tools from 1 SCP server(s).
drugsda-peptide-sampling
Generate new peptide molecules sampling from the input peptide sequence.
drugsda-mol-properties
Calculate different types of molecular properties based on SMILES strings, covering basic physicochemical properties, hydrophobicity, hydrogen bonding capability, molecular complexity, topological structures, charge distribution, and custom complexity metrics, respectively.