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analysis_tools_tutorial

Analysis tool workshop tutorial files

atomizer_analysis

A set of tools for atomizer analysis

bionetgen

Rule-based modeling framework

bng_biosimdocker

bng_vscode_extension

bngl-to-westpa

A tool to convert a BNGL file (BioNetGen) to a WESTPA simulation

bnglib

BioNetGen library

bngsim

A simple python front-end for BioNetGen simulations.

cellblender

Create, Simulate, Visualize, and Analyze Realistic 3D Cell Models

chess

Chess Engine/AI

cov19_sens

A set of sensitivity analysis scripts for a COVID19 tissue simulator

covid19

Rapid prototyping coalition for SARS-CoV-2 tissue infection dynamics. (integrated model)

dom5_map_ext

Dominions 5 map scripting extension

gh_cloning_stats

Simple script to parse and store GitHub cloning statistics

graph_algs

learningswig

Some test cases for learning SWIG to use C functions in Python

livecoms_tut

Tutorial files for livecoms

mcell

MCell Monte Carlo Simulator of Cellular Microphysiology

nfsim

A general-purpose, stochastic, biochemical reaction simulator for large reaction networks

nfsim_vis

Basic visualization helper library for nfsim trajectories

py_conway_gol

A very simple implementation of Conways Game of Life that runs in a terminal

pybionetgen

A simple CLI for BioNetGen

pysb

Python framework for Systems Biology modeling

python_bio_2022

Repo for 2022 python class

rulebender

Rule-Based Modeling and Simulation Gui

screeps

Some code for the game Screeps

simanalyzer

Simulation analysis runner

user_submitted_scripts

Example scripts for WESTPA submitted by users

webng

A set of tools to simplify the weighted ensemble sampling of BioNetGen rule-based simulations.

webng---preprint