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NEST (Neural Simulation Tool) — high-performance spiking neural network simulator for large-scale networks of point neurons and conductance-based models. Supports iaf_psc_alpha, hh_psc_alpha, aeif_con
Use with AI
Install the MCP server or CLI to instantly fetch NEST documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/nest
Use this skill when building, running, or validating CompuCell3D (CC3D) multicellular simulations. Covers Cellular Potts Model workflows, Python-based steppables, headless execution with `python -m cc
1 shared topic • 2 shared operations
COPASI — COmplex PAthway SImulator for systems biology. Simulates and analyzes biochemical reaction networks using deterministic ODE integration (LSODA, Radau5, CVODE), stochastic simulation (Gibson-B
1 shared topic • 2 shared operations
mrgsolve — R package for simulation from ODE-based PK/PD and systems pharmacology models with C++ model code, NONMEM-style event/data inputs, and high-throughput population simulation workflows. Use w
1 shared topic • 2 shared operations
NEURON — biophysically detailed multi-compartment neural simulation environment for modeling neurons and neural networks. Builds and runs Hodgkin-Huxley style conductance-based neuron models, morpholo
1 shared topic • 2 shared operations
Use when building, running, or validating STEPS (STochastic Engine for Pathway Simulation) models for stochastic reaction-diffusion systems in realistic 3D tetrahedral geometries. Covers source builds
1 shared topic • 2 shared operations