Science Simulation Skills
Browse 98 curated science & simulation skills for AI coding agents. License-verified, MCP-ready, free to start.
Adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
AI Analyzer
AI驱动的综合健康分析系统，整合多维度健康数据、识别异常模式、预测健康风险、提供个性化建议。支持智能问答和AI健康报告生成。
Ansys Simulation
Automate ANSYS Fluent CFD simulations via Python scripting and journal files
Astropy
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
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.
Bom
BOM (Bill of Materials) management for electronics projects — the primary orchestrator skill that coordinates DigiKey, Mouser, LCSC, element14, JLCPCB, PCBWay, and KiCad skills into a unified workflow. Create, update, and maintain BOMs with part numbers, costs, quantities stored as KiCad symbol properties. ALWAYS trigger this skill for any task involving component sourcing, pricing, ordering, distributor searches, BOM export, or fabrication preparation — even if the user names a specific distributor or fab house (e.g. "search DigiKey for...", "generate JLCPCB BOM", "order from Mouser"). This skill decides which distributor/fab skills to invoke and in what order. Also trigger on phrases like "what parts do I need", "order components", "how much will this cost", "export for JLCPCB", "find parts for this board", "cost estimate", "compare pricing", or "check stock".
Cavitation Risk DB
Query vapor pressures and NPSH requirements for cavitation assessment
Cellxgene Census
Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.
Chembl Database
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
Cirq
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
Cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Comsol Multiphysics
Set up coupled fluid-structure interaction for pump vibration analysis
Convergence Study
Perform spatial and temporal convergence analysis for solution verification — compute observed convergence orders from grid or timestep refinement studies, apply Richardson extrapolation to estimate discretization error, and calculate the Grid Convergence Index (GCI) per ASME V&V 20 standards. Use when verifying that a numerical solution converges at the expected rate, estimating the error on the finest mesh, checking whether grids are in the asymptotic range, or preparing formal verification reports, even if the user only asks "is my mesh fine enough" or "how accurate is my solution."
Coolprop DB
Query thermodynamic properties for 100+ fluids from CoolProp database
Datasheets
Extract structured specifications from electronic component datasheet PDFs — pinouts, electrical characteristics, peripherals, topology, and features. Cache extractions per project for consumption by schematic and PCB analyzers. Primary consumer infrastructure for `kicad`, `emc`, `spice`, and `thermal` analyzers. Use this skill whenever the user asks to extract, verify, or read specs from a component datasheet; when analyzers need verified IC knowledge (EN pin thresholds, PG presence, USB peripheral speed); or when a review mentions datasheet coverage, extraction quality, or per-MPN specifications. Also triggers on "extract this datasheet", "what are the specs for MPN X", "verify datasheet extraction", or "check pin functions for part Y".
Diffdock
DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.
Differentiation Schemes
Select and apply numerical differentiation schemes for PDE and ODE discretization — generate finite-difference stencils at arbitrary order and accuracy, choose between central, upwind, compact (Pade), and spectral methods, handle boundary stencils, and estimate truncation error scaling. Use when discretizing spatial derivatives, picking a scheme for advection- or diffusion-dominated problems, building custom stencils for nonstandard operators, or comparing dispersion and dissipation properties of candidate schemes, even if the user just says "how do I approximate this derivative" or "my solution is too diffusive."
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.
Dse Loop
Autonomous design space exploration loop for computer architecture and EDA. Runs a program, analyzes results, tunes parameters, and iterates until objective is met or timeout. Use when user says \"DSE\", \"design space exploration\", \"sweep parameters\", \"optimize\", \"find best config\", or wants iterative parameter tuning.
Emc
EMC pre-compliance risk analysis for KiCad PCB designs — 18 check categories, 44 rule IDs covering ground planes, decoupling, I/O filtering, switching harmonics, clock routing, differential pair skew, board edge radiation, PDN impedance, return paths, crosstalk, ESD protection, shielding, and magnetic leakage from switching inductors. Produces severity-ranked risk report with pre-compliance test plan. Supports FCC Part 15, CISPR 32, CISPR 25 (automotive), MIL-STD-461G. SPICE-enhanced when available. Use when the user asks about EMC, EMI, radiated/conducted emissions, FCC compliance, CE marking, CISPR, ground plane issues, decoupling strategy, clock routing EMC, switching noise, differential pair skew, or whether their board will pass EMC testing. Also for "will this pass FCC?", "check my EMC", "is my ground plane okay?", "check my decoupling", or "generate an EMC test plan".
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.
Esm
Use when working directly with the `esm` Python SDK, ESM3 or ESMC model IDs, Forge/Biohub inference clients, or ESMFold2 folding workflows.
Etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
Evaluating Cosmos Policy
Evaluates NVIDIA Cosmos Policy on LIBERO and RoboCasa simulation environments. Use when setting up cosmos-policy for robot manipulation evaluation, running headless GPU evaluations with EGL rendering, or profiling inference latency on cluster or local GPU machines.
Fluid Dynamics Workflow
Systematic workflow for fluid dynamics analysis from problem setup to validation
Fluid Property Calculator
Quick fluid property calculations using empirical formulas without database queries
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.
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.
Fluids Package
Pipe flow, pump sizing, friction factor, and compressible flow calculations
Freecad Scripts
Expert skill for writing FreeCAD Python scripts, macros, and automation. Use when asked to create FreeCAD models, parametric objects, Part/Mesh/Sketcher scripts, workbench tools, GUI dialogs with PySide, Coin3D scenegraph manipulation, or any FreeCAD Python API task. Covers FreeCAD scripting basics, geometry creation, FeaturePython objects, interface tools, and macro development.
Glycoengineering
Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design.
Histolab
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Best for simple pipelines, dataset preparation, and quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
Hydraulic Components DB
Query loss coefficients for pipes, valves, fittings in pump systems
Hypothesis Generation
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
Hypothesis Generation
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Also owns explicit HypoGeniC-style or automated LLM-driven hypothesis generation/testing requests inside this single skill. For open-ended ideation use scientific-brainstorming.
Kicad
Analyze KiCad projects and PDF schematics: schematics, PCB layouts, Gerbers, footprints, symbols, netlists, and design rules. Reviews designs for bugs, traces nets, cross-references schematic to PCB, extracts BOM data, checks DRC/ERC, DFM, power trees, and regulator circuits. Every finding carries a confidence label and evidence source with trust_summary rollup. Analyzes PDF schematics from dev boards, reference designs, eval kits, and datasheets. Supports KiCad 5–10. Use whenever the user mentions .kicad_sch, .kicad_pcb, .kicad_pro, PCB design review, schematic analysis, PDF schematics, reference designs, Gerber files, DRC/ERC, netlist issues, BOM extraction, signal tracing, power budget, DFM, or wants to understand, debug, compare, or review any hardware design. Also for "check my board", "review before fab", "what's wrong with my schematic", "is this ready to order", "check my power supply", "verify this circuit", or any electronics/PCB design question.
Lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
Latchbio Integration
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
Lcsc
Search LCSC Electronics for electronic components — find parts by LCSC number (Cxxxxx) or MPN, check stock/pricing, download datasheets, analyze specifications. Sister company to JLCPCB, same parts library. Sync and maintain a local datasheets directory for a KiCad project, or use batch MPN-list seeding (`--mpn-list`) for bulk workflows without a project. No API key needed — uses the free jlcsearch community API. Use this skill when the user mentions LCSC, JLCPCB parts library, JLCPCB assembly parts, production sourcing, Cxxxxx part numbers, needs to find LCSC equivalents for parts, is preparing a BOM for JLCPCB assembly, or wants to download datasheets and LCSC is available. For package cross-reference tables and BOM workflow, see the `bom` skill.
Lean4
Use when editing .lean files, debugging Lean 4 builds (type mismatch, sorry, failed to synthesize instance, axiom warnings, lake build errors), searching mathlib for lemmas, formalizing mathematics in Lean, or learning Lean 4 concepts. Also trigger when the user asks for help with Lean 4, mathlib, or lakefile. Do NOT trigger for Coq/Rocq, Agda, Isabelle, HOL4, Mizar, Idris, Megalodon, or other non-Lean theorem provers.
Linear Solvers
Select and configure linear solvers for Ax=b systems arising in numerical simulations — choose between direct (LU, Cholesky) and iterative (CG, GMRES, BiCGSTAB, MINRES) methods, analyze sparsity patterns and matrix conditioning, recommend preconditioners (AMG, ILU, IC), apply row/column scaling, and diagnose convergence stagnation from residual histories. Use when setting up a linear solve for FEM/FVM assembly, debugging slow or stalled Krylov iterations, choosing a preconditioner for SPD or nonsymmetric systems, or investigating ill-conditioning, even if the user only says "my solver is slow" or "GMRES won't converge."
Matchms
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
Matlab
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.
Matlab
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.
Medchem
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
Mesh Generation
Plan and evaluate mesh generation for numerical simulations — estimate grid resolution from physics scales (interface width, boundary layers, wavelengths), check aspect ratios and skewness against quality thresholds, choose between structured, unstructured, and adaptive mesh refinement strategies, and compute grid sizing for 1D/2D/3D domains. Use when setting up a new mesh, diagnosing poor solver convergence caused by mesh quality, deciding how many points to place across a phase-field interface or boundary layer, or preparing a mesh convergence study, even if the user only asks "what resolution do I need" or "why is my solver failing."
Metabolomics Workbench Database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
Molecular Dynamics
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
Mouser
Search Mouser Electronics for electronic components — secondary source for prototype orders. Find parts, check pricing/stock, download datasheets, analyze specifications. Use with KiCad for BOM creation and part selection. Also supports batch MPN-list seeding (`--mpn-list`) for bulk datasheet workflows without a KiCad project. Use this skill when the user specifically mentions Mouser, when DigiKey is out of stock or has worse pricing, when comparing prices across distributors, or when searching for parts that DigiKey doesn't carry. For package cross-reference tables and BOM workflow, see the `bom` skill.
Networkx Flow Networks
Model hydraulic networks and multi-pump systems using graph theory
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.
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.
Nonlinear Solvers
Select and configure nonlinear solvers for root-finding f(x)=0, optimization min F(x), and least-squares problems — choose among Newton, Newton-Krylov, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson acceleration, and Levenberg-Marquardt methods, configure line search or trust-region globalization, diagnose convergence rate (quadratic, linear, stagnated), and assess Jacobian quality and conditioning. Use when a Newton solver converges slowly or diverges, choosing between line search and trust region, debugging nonlinear iteration failures in FEM or phase-field codes, or selecting a solver for large-scale unconstrained optimization, even if the user only says "my Newton iterations aren't converging."
Numerical Integration
Select and configure time integration methods for ODE and PDE simulations — choose among explicit Runge-Kutta, BDF, Rosenbrock, and Adams families, set relative and absolute error tolerances, implement adaptive step-size control with I/PI/PID controllers, plan IMEX operator splitting for mixed stiff and non-stiff terms, and estimate splitting errors. Use when picking an integrator for a new simulation, diagnosing step rejections or tolerance failures, setting up operator splitting for phase-field or reaction-diffusion problems, or deciding between explicit and implicit time marching, even if the user only says "my solver keeps rejecting steps" or "which ODE method should I use."
Numerical Stability
Analyze numerical stability for time-dependent PDE simulations — check CFL and Fourier criteria, perform von Neumann stability analysis, detect stiffness, evaluate matrix conditioning, and recommend explicit vs implicit time-stepping schemes. Use when selecting time steps, diagnosing numerical blow-up or solver divergence, checking convergence criteria, or evaluating scheme stability for advection, diffusion, or reaction problems, even if the user doesn't explicitly mention "stability" or "CFL."
Omero Integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
Ontology Validator
Validate material sample annotations against ontology constraints — check that class names and property names exist in the ontology, verify domain and range consistency for object property relationships, assess annotation completeness (required, recommended, and optional properties), and flag unknown or misspelled terms. Use when verifying that CMSO or other ontology annotations are correct before publishing, checking whether all required properties are present for a class like Crystal Structure or Unit Cell, auditing relationship triples between instances, or catching annotation errors early in a FAIR data workflow, even if the user only says "is my annotation correct" or "what am I missing."
Opentrons Integration
Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.
Parameter Optimization
Explore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection — generate Latin Hypercube, quasi-random, or factorial sample plans, rank parameter influence with sensitivity scores, recommend Bayesian optimization, CMA-ES, or gradient- based methods based on dimension and budget, and fit surrogate models for expensive evaluations. Use when calibrating material properties against experimental data, planning a parameter sweep, performing uncertainty quantification, or choosing an optimization strategy for a simulation with a limited evaluation budget, even if the user only says "which parameters matter most" or "how do I calibrate my model."
Pcbway
PCBWay PCB fabrication and assembly — turnkey/consigned assembly, design rules, ordering workflow. Alternative to JLCPCB for manufacturing. Use with KiCad. Use this skill when the user mentions PCBWay, needs turnkey assembly (PCBWay sources parts by MPN), has parts not available on LCSC, needs assembled boards with non-LCSC components, wants to compare PCBWay vs JLCPCB, or needs assembly with parts sourced globally rather than from LCSC only. For gerber/CPL export, stencil ordering, and BOM management, see the `bom` skill.
Peer Review
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating claims/evidence quality use scientific-critical-thinking; for quantitative scoring frameworks use scholar-evaluation.
Performance Profiling
Identify computational bottlenecks, analyze parallel scaling, estimate memory requirements, and generate optimization recommendations for materials simulations — parse timing logs to find dominant phases (solver, assembly, I/O), evaluate strong and weak scaling efficiency, profile memory from mesh and field parameters, and detect bottlenecks with actionable fix suggestions. Use when a simulation is running slower than expected, investigating MPI scaling efficiency, planning HPC resource allocation, deciding whether to tune the preconditioner or reduce I/O frequency, or estimating if a problem fits in available RAM, even if the user only says "my simulation is too slow" or "how many nodes do I need."
Phylogenetics
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
Pint Units
Handle engineering units with automatic conversion and dimensional analysis
Polars Bio
High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.
Post Processing
Extract, analyze, and summarize simulation output data — pull spatial fields at specific timesteps, compute time-series trends and detect steady state, extract line profiles through the domain, generate statistical summaries and distributions, calculate derived quantities (gradients, fluxes, volume fractions, interface area), compare results against analytical solutions or experimental data, and produce automated analysis reports. Use when interpreting finished simulation results, checking mass or energy conservation, comparing two runs or meshes, extracting interface profiles from phase-field output, or preparing publication-quality analysis, even if the user only says "what do my results look like" or "did my simulation reach steady state."
Proof Checker
Rigorous mathematical proof verification and fixing workflow. Reads a LaTeX proof, identifies gaps via cross-model review (external reviewer backend, xhigh reasoning), fixes each gap with full derivations, re-reviews, and generates an audit report. Use when user says "检查证明", "verify proof", "proof check", "审证明", "check this proof", or wants rigorous mathematical verification of a theory paper.
Pump Selection Helper
Decision tree for selecting pump type based on flow, head, and fluid properties
Pydicom
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
Pylabrobot
Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation. For Opentrons-only protocols with official API, opentrons-integration may be simpler.
Pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
Pymoo
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
Pymoo
Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.
Pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.
Pyopenms
Complete mass spectrometry analysis platform. Use for proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free and isobaric quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.
Pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
Pyvista Visualization
Create 3D visualizations of velocity fields and pump CFD results
Qutip
Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
Rdkit
Core cheminformatics toolkit for SMILES/SDF/InChI parsing, descriptors (MW, LogP, TPSA), fingerprints, ECFP/Morgan fingerprints, substructure search, 2D/3D generation, similarity, reactions, and datamol-style molecule standardization when no separate wrapper skill is routed.
Rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
Rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.
Scanpy
Single-cell RNA-seq and retained scverse workflow owner. Load .h5ad/10X data, manage AnnData metadata, plan scVI/scANVI batch-correction workflows, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
Scientific Brainstorming
Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
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.
Simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
Simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
Simulation Orchestrator
Orchestrate multi-simulation campaigns — generate parameter sweep configurations (grid, linspace, or Latin Hypercube sampling), initialize and track batch job campaigns, monitor job completion status, and aggregate results with summary statistics across all runs. Use when running a parameter study across dt, kappa, or other simulation inputs, managing dozens or hundreds of simulation configurations, combining outputs from completed batch runs to find the best result, or automating the generate-run-collect workflow for systematic studies, even if the user only says "I need to try many parameter combinations" or "how do I organize a sweep."
Simulation Validator
Validate simulations across three stages — run pre-flight checks on configuration files (parameter ranges, required fields, disk space), monitor runtime logs for residual growth, NaN/Inf, and adaptive dt collapse, and perform post-flight validation of results (physical bounds, mass/energy conservation, convergence). Diagnose failed simulations with probable-cause analysis and recommended fixes. Use when preparing to launch a simulation, checking whether a running job is healthy, verifying that finished results are trustworthy, or debugging a crash or blow-up, even if the user only says "my simulation crashed" or "can I trust these results."
Spice
Run automatic SPICE simulations on subcircuits detected from KiCad schematic analysis — validates filter frequencies, divider ratios, opamp gains, LC resonance, and crystal load capacitance. Supports ngspice, LTspice, and Xyce (auto-detected). Generates testbenches, runs batch mode, produces structured pass/warn/fail report. Use when the user asks to simulate, verify, or validate any analog subcircuit — RC filters, LC filters, voltage dividers, opamp circuits, crystal oscillators. Also for "simulate my circuit", "run spice", "verify with simulation", "check my filter cutoff", "does this divider give the right voltage", "what's the bandwidth of this opamp stage". Consider suggesting simulation during design reviews when the schematic analyzer reports simulatable subcircuits and a SPICE simulator is available.
Structural Analysis Workflow
FEA workflow for pump casings and impellers under fluid loads
Sympy
Use when you need exact symbolic math in Python — algebra, calculus, equation solving, symbolic linear algebra, or code generation via lambdify/LaTeX. Prefer NumPy or SciPy when floating-point approximations are sufficient.
Sympy Symbolic
Derive and solve fluid dynamics and pump equations symbolically
Thermodynamics Workflow
Analyze thermodynamic cycles and heat transfer in pump systems
Thermo Package
Calculate thermodynamic properties and mixture behavior for pump applications
Tiledbvcf
Efficient storage and retrieval of genomic variant data using TileDB. Scalable VCF/BCF ingestion, incremental sample addition, compressed storage, parallel queries, and export capabilities for population genomics.
Time Stepping
Plan and control time-step policies for transient simulations — couple CFL and physics-based stability limits with adaptive stepping, ramp initial transients through sharp gradients or phase changes, schedule output intervals and checkpoint cadence, and plan restart strategies for long-running jobs. Use when choosing dt for a new simulation, diagnosing adaptive time-step oscillations, deciding checkpoint frequency to minimize lost work, or setting up output schedules aligned with physical time scales, even if the user only says "my run is too slow" or "how often should I save."
Treatment Plans
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.
Turbulence Models DB
Select and configure turbulence models (k-epsilon, k-omega SST, LES) for CFD