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    67 repositories

    • pydyno

      Public
      Tool that uses tropical algebra concepts to 'decompose' species trajectories in the protein-protein interactions that drive changes of concentration in time
      clusteringsystems-biologydynamic-analysispysb
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•8•6•5•Updated Sep 26, 2024Sep 26, 2024

    • PyDREAM

      Public
      MT-DREAM(ZS) algorithm for model optimization, calibration, selection
      Python
      •
      GNU General Public License v3.0
      •33•50•11•3•Updated Jul 24, 2024Jul 24, 2024

    • Bayes-MMI

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 5, 2024Jun 5, 2024

    • simplePSO

      Public
      Particle Swarm Optimization algorithm in Python
      Python
      •
      Other
      •4•13•1•0•Updated Apr 23, 2024Apr 23, 2024

    • pydream_it

      Public
      Read PySB models and generate a script for PyDREAM calibration
      Python
      •
      MIT License
      •2•0•0•0•Updated Mar 25, 2024Mar 25, 2024

    • pysb

      Public
      Python framework for Systems Biology modeling [Lopez Lab Mods]
      Python
      •
      BSD 2-Clause "Simplified" License
      •71•6•11•0•Updated Mar 8, 2024Mar 8, 2024

    • Opt2Q

      Public
      Python
      •0•1•0•0•Updated Feb 9, 2024Feb 9, 2024

    • SCLC-TF-Network-Analysis

      Public
      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)
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Oct 31, 2023Oct 31, 2023

    • pyvipr

      Public
      Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
      systems-biologynetworkxnetwork-visualizationjupyter-widgetcytoscapejssbmlsbgnjupyterlab-extensionvisualizationpysb
      Jupyter Notebook
      •
      MIT License
      •4•27•6•17•Updated Mar 13, 2023Mar 13, 2023

    • GPU_SSA_paper2023

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 1, 2023Mar 1, 2023

    • aEARM_cell_viability_calibration

      Public
      Python
      •0•0•0•0•Updated Jan 26, 2023Jan 26, 2023

    • MAGINE

      Public
      Mechanism of Action Generation involving Network Analysis
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•9•1•3•Updated Dec 27, 2022Dec 27, 2022

    • zombie-apocalypse

      Public
      Modeling a Zombie Apocalypse using ODEs and PySB
      Jupyter Notebook
      •0•0•0•0•Updated Nov 24, 2022Nov 24, 2022

    • NERM

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Jul 25, 2022Jul 25, 2022

    • HypBuilder

      Public
      HypBuilder is software for the large scale construction of physicochemical models in the format of PySB.
      Python
      •1•2•0•0•Updated Jun 20, 2022Jun 20, 2022

    • MAGINE_Supplement_notebooks

      Public
      Supplement notebooks to demonstrate MAGINE
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 13, 2022Jun 13, 2022

    • pysb-tutorials

      Public
      PySB tutorials and examples for IPython (Jupyter) notebook
      Jupyter Notebook
      •6•10•0•0•Updated Sep 13, 2021Sep 13, 2021

    • PyBILT

      Public
      Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
      molecular-simulationmolecular-dynamics-simulationmolecular-dynamics-trajectorieslipid-bilayersanalyseslipids
      Python
      •
      MIT License
      •10•24•6•0•Updated May 12, 2021May 12, 2021

    • Boolean_rules_creator

      Public
      Unsupervised logic-based mechanism inference for network-driven biological processes
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 11, 2021Apr 11, 2021

    • Gleipnir

      Public
      Python toolkit for Bayesian parameter inference, model calibration, and model selection using Nested Sampling
      pythonsystems-biologybayesian-methodsmodel-selectionparameter-estimationnested-samplingbiological-modeling
      Python
      •
      MIT License
      •2•3•4•0•Updated Jan 8, 2021Jan 8, 2021

    • SPN

      Public
      segment polarity network
      Python
      •1•0•0•0•Updated Oct 16, 2020Oct 16, 2020

    • tutorials

      Public
      Docker container for demoing Lopez Lab tools
      Dockerfile
      •0•0•0•0•Updated Oct 8, 2020Oct 8, 2020

    • MAGINE-complete

      Public
      MAGINE with databases pre-downloaded
      Dockerfile
      •0•0•0•0•Updated Aug 5, 2020Aug 5, 2020

    • COVID-19

      Public
      Novel Coronavirus (COVID-19) Cases, provided by JHU CSSE
      R
      •18k•0•0•0•Updated Jul 2, 2020Jul 2, 2020

    • swarm_it

      Public
      Utility to help setup PSO runs for PySB models.
      Python
      •
      MIT License
      •1•3•2•0•Updated Mar 11, 2020Mar 11, 2020

    • TruthTable2Rules

      Public
      Algoritm to convert Boolean Truth Tables to PySB rules. Designed to enable ODE based simulations.
      Python
      •1•0•0•0•Updated Feb 7, 2020Feb 7, 2020

    • BioComparator

      Public
      software toolset to compare biological-models
      Python
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Jan 1, 2020Jan 1, 2020

    • TRuML

      Public
      Python
      •
      Other
      •4•0•0•0•Updated Dec 10, 2019Dec 10, 2019

    • earm

      Public
      EARM V2.0 FILES
      Python
      •17•1•0•0•Updated Dec 4, 2019Dec 4, 2019

    • JARM

      Public
      JNK3 activation reaction model
      Jupyter Notebook
      •0•2•0•0•Updated Dec 4, 2019Dec 4, 2019