LoLab-MSM/Opt2Q

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Python
Created over 3 years ago
Updated about 1 year ago

LoLab-MSM/Opt2Q

LoLab-MSM

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PyDREAM

MT-DREAM(ZS) algorithm for model optimization, calibration, selection

pyvipr

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

Jupyter Notebook

PyBILT

Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.

simplePSO

Particle Swarm Optimization algorithm in Python

pysb-tutorials

PySB tutorials and examples for IPython (Jupyter) notebook

Jupyter Notebook

MAGINE

Mechanism of Action Generation involving Network Analysis

Jupyter Notebook

pydyno

Tool that uses tropical algebra concepts to 'decompose' species trajectories in the protein-protein interactions that drive changes of concentration in time

Jupyter Notebook

swarm_it

Utility to help setup PSO runs for PySB models.

varsens

Variance Based Sensitivity Analysis by the method of Saltelli

HypBuilder

HypBuilder is software for the large scale construction of physicochemical models in the format of PySB.

JARM

JNK3 activation reaction model

Jupyter Notebook

NFkB

Gleipnir

Python toolkit for Bayesian parameter inference, model calibration, and model selection using Nested Sampling

BioComparator

software toolset to compare biological-models

Boolean2Mechanism

Builds PySB models from a Boolean model and sets of potential biochemical mechanisms.

LogicalModel

Python code for parallel simulation of Logic models.

DDRXM

Division Death Ratio Crosstalk Model

CORM

COX2 Reaction Model

Jupyter Notebook

PySB_NS

A nested sampling algorithm for PySB model selection.

Myc-displacement

NS_calibration

Nested sampling based PySB model calibration.

NightMare

PSO followed by DREAM

PySB_cupSODA_Bioinfo2017