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Lopez Lab (LoLab-MSM)

Lopez Lab

LoLab-MSM

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Location:United States of America

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Lopez Lab's repositories

PyDREAM

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

Language:PythonLicense:GPL-3.0Stargazers:49Issues:8Issues:19

pyvipr

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

Language:Jupyter NotebookLicense:MITStargazers:27Issues:7Issues:26

PyBILT

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

Language:PythonLicense:MITStargazers:24Issues:6Issues:19

simplePSO

Particle Swarm Optimization algorithm in Python

Language:PythonLicense:NOASSERTIONStargazers:13Issues:12Issues:3

pysb-tutorials

PySB tutorials and examples for IPython (Jupyter) notebook

Language:Jupyter NotebookStargazers:10Issues:20Issues:0

MAGINE

Mechanism of Action Generation involving Network Analysis

Language:Jupyter NotebookLicense:GPL-3.0Stargazers:9Issues:8Issues:10

pydyno

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

Language:Jupyter NotebookLicense:BSD-2-ClauseStargazers:8Issues:16Issues:7

pysb

Python framework for Systems Biology modeling [Lopez Lab Mods]

Language:PythonLicense:BSD-2-ClauseStargazers:6Issues:8Issues:37

Gleipnir

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

Language:PythonLicense:MITStargazers:3Issues:5Issues:14

swarm_it

Utility to help setup PSO runs for PySB models.

Language:PythonLicense:MITStargazers:3Issues:6Issues:2

BioComparator

software toolset to compare biological-models

Language:PythonLicense:GPL-3.0Stargazers:2Issues:6Issues:0

HypBuilder

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

Language:PythonStargazers:2Issues:6Issues:0

JARM

JNK3 activation reaction model

Language:Jupyter NotebookStargazers:2Issues:7Issues:0

earm

EARM V2.0 FILES

Language:PythonStargazers:1Issues:9Issues:0

Opt2Q

Language:PythonStargazers:1Issues:6Issues:0

aEARM_cell_viability_calibration

Language:PythonStargazers:0Issues:0Issues:0

Bayes-MMI

Language:PythonLicense:MITStargazers:0Issues:6Issues:0

Boolean_rules_creator

Unsupervised logic-based mechanism inference for network-driven biological processes

Language:PythonLicense:MITStargazers:0Issues:6Issues:0

COVID-19

Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE

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GPU_SSA_paper2023

Language:Jupyter NotebookStargazers:0Issues:0Issues:0

MAGINE-complete

MAGINE with databases pre-downloaded

Language:DockerfileStargazers:0Issues:6Issues:0

MAGINE_Supplement_notebooks

Supplement notebooks to demonstrate MAGINE

Language:Jupyter NotebookLicense:GPL-3.0Stargazers:0Issues:2Issues:0

NERM

Language:Jupyter NotebookStargazers:0Issues:7Issues:0

pydream_it

Read PySB models and generate a script for PyDREAM calibration

Language:PythonLicense:MITStargazers:0Issues:2Issues:0

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)

Language:MATLABLicense:MITStargazers:0Issues:0Issues:0

SPN

segment polarity network

Language:PythonStargazers:0Issues:0Issues:0

TRuML

Language:PythonLicense:NOASSERTIONStargazers:0Issues:6Issues:0

TruthTable2Rules

Algoritm to convert Boolean Truth Tables to PySB rules. Designed to enable ODE based simulations.

Language:PythonStargazers:0Issues:0Issues:0

tutorials

Docker container for demoing Lopez Lab tools

Language:DockerfileStargazers:0Issues:6Issues:0

zombie-apocalypse

Modeling a Zombie Apocalypse using ODEs and PySB

Language:Jupyter NotebookStargazers:0Issues:0Issues:0