bionetgen

Here are 9 public repositories matching this topic...

LoLab-MSM / pyvipr

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

visualization systems-biology networkx pysb network-visualization jupyter-widget cytoscapejs sbml sbgn tellurium bionetgen jupyterlab-extension

Updated Mar 13, 2023
Jupyter Notebook

mcellteam / Workshop_2020

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Repository for models, descriptions, and software supporting the 2020 Workshop

simulation mcell cellblender bionetgen mcell-tutorials cellblender-model cellorganizer

Updated Jun 26, 2020
Jupyter Notebook

achattaraj / Ksp_phase_separation

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Tools for data generation and data analysis for the eLife research article - "The solubility product extends the buffering concept to heterotypic biomolecular condensates"

computational-biology biophysics stochastic-simulations bionetgen biomolecular-simulation springsalad

Updated Jul 13, 2021
Python

achattaraj / maximal_Solubility_product

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Python scripts to analyze and visualize the data presented in the research article: "The maximum solubility product marks the threshold for condensation of multivalent biomolecules".

python molecular-simulation data-visualisation langevin-dynamics rule-based-modeling bionetgen phase-transition data-analysis-python llps springsalad multivalent-clustering biomolecular-condensates nfsim molclustpy

Updated Apr 4, 2023
Jupyter Notebook

biosimulators / Biosimulators_BioNetGen

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BioNetGen biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

docker simulation systems-biology stochastic-simulation-algorithm dynamical-modeling rule-based-modeling bionetgen sed-ml biochemical-networks combine-archive network-free-simulation omex-metadata biosimulators

Updated Feb 25, 2022
Python

biosimulations / biosimulations-rulehub

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Repository of rule-based models implemented with the BioNetGen model language (BNGL) and command-line program for publishing RuleHub to BioSimulations

systems-biology computational-biology combine bionetgen sed-ml omex biosimulations rulehub bngl