Projects in Awesome Lists by LoLab-MSM
A curated list of projects in awesome lists by LoLab-MSM .
https://github.com/lolab-msm/pydream
MT-DREAM(ZS) algorithm for model optimization, calibration, selection
Last synced: 31 Aug 2025
https://github.com/lolab-msm/pyvipr
Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
bionetgen cytoscapejs jupyter-widget jupyterlab-extension network-visualization networkx pysb sbgn sbml systems-biology tellurium visualization
Last synced: 10 Apr 2025
https://github.com/LoLab-MSM/pyvipr
Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
bionetgen cytoscapejs jupyter-widget jupyterlab-extension network-visualization networkx pysb sbgn sbml systems-biology tellurium visualization
Last synced: 28 Oct 2025
https://github.com/lolab-msm/pybilt
Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
analyses lipid-bilayers lipids molecular-dynamics-simulation molecular-dynamics-trajectories molecular-simulation
Last synced: 19 Jul 2025
https://github.com/lolab-msm/simplepso
Particle Swarm Optimization algorithm in Python
Last synced: 09 May 2025
https://github.com/lolab-msm/pysb-tutorials
PySB tutorials and examples for IPython (Jupyter) notebook
Last synced: 11 Sep 2025
https://github.com/lolab-msm/magine
Mechanism of Action Generation involving Network Analysis
Last synced: 09 May 2025
https://github.com/lolab-msm/pydyno
Tool that uses tropical algebra concepts to 'decompose' species trajectories in the protein-protein interactions that drive changes of concentration in time
clustering dynamic-analysis pysb systems-biology
Last synced: 24 Oct 2025
https://github.com/lolab-msm/gleipnir
Python toolkit for Bayesian parameter inference, model calibration, and model selection using Nested Sampling
bayesian-methods biological-modeling model-selection nested-sampling parameter-estimation python systems-biology
Last synced: 09 May 2025
https://github.com/lolab-msm/varsens
Variance Based Sensitivity Analysis by the method of Saltelli
Last synced: 04 Sep 2025
https://github.com/lolab-msm/swarm_it
Utility to help setup PSO runs for PySB models.
Last synced: 09 Sep 2025
https://github.com/lolab-msm/hypbuilder
HypBuilder is software for the large scale construction of physicochemical models in the format of PySB.
Last synced: 28 Jul 2025
https://github.com/lolab-msm/biocomparator
software toolset to compare biological-models
Last synced: 23 Feb 2025
https://github.com/lolab-msm/pysb_ns
A nested sampling algorithm for PySB model selection.
Last synced: 23 Feb 2025
https://github.com/lolab-msm/logicalmodel
Python code for parallel simulation of Logic models.
Last synced: 03 Oct 2025
https://github.com/lolab-msm/sclc-tf-network-analysis
This repository provides source MATLAB codes for the structural analysis of Small Cell Lung Cancer Transcription Factor network using Dense Spanning Trees (DST) and Minimum Dense Spanning Trees (MDST)
Last synced: 15 Jul 2025
https://github.com/lolab-msm/boolean2mechanism
Builds PySB models from a Boolean model and sets of potential biochemical mechanisms.
Last synced: 28 Jun 2025
https://github.com/lolab-msm/ns_calibration
Nested sampling based PySB model calibration.
Last synced: 23 Feb 2025
https://github.com/lolab-msm/pydrone_earm_analysis
analysis of earm using pydrone
Last synced: 23 Feb 2025
https://github.com/lolab-msm/zombie-apocalypse
Modeling a Zombie Apocalypse using ODEs and PySB
Last synced: 16 Oct 2025
https://github.com/lolab-msm/g2_m
G2/M Cell Cycle Transition from Iwamoto et al. (2011)
Last synced: 23 Feb 2025
https://github.com/lolab-msm/magine-complete
MAGINE with databases pre-downloaded
Last synced: 23 Feb 2025
https://github.com/lolab-msm/tutorials
Docker container for demoing Lopez Lab tools
Last synced: 23 Feb 2025
https://github.com/lolab-msm/mt1_mmp
Binding reactions of MMP2, TIMP2, and MT1-MMP
Last synced: 23 Feb 2025
https://github.com/lolab-msm/cellcycle
Repository for the S/G2 and M/G1 cell cycle phase transitions.
Last synced: 23 Feb 2025
https://github.com/lolab-msm/pydream_it
Read PySB models and generate a script for PyDREAM calibration
Last synced: 23 Feb 2025
https://github.com/lolab-msm/pysb-stochkit_pyurdme
Interfaces between PySB and GillesPy (StochKit) and pyURDME
Last synced: 09 Jul 2025
https://github.com/lolab-msm/magine_supplement_notebooks
Supplement notebooks to demonstrate MAGINE
Last synced: 22 Aug 2025
https://github.com/lolab-msm/boolean_rules_creator
Unsupervised logic-based mechanism inference for network-driven biological processes
Last synced: 23 Feb 2025
https://github.com/lolab-msm/bngl2pysb
A BioNetGen to PySB converter. Currently in development
Last synced: 23 Feb 2025
https://github.com/lolab-msm/truthtable2rules
Algoritm to convert Boolean Truth Tables to PySB rules. Designed to enable ODE based simulations.
Last synced: 23 Feb 2025