Projects in Awesome Lists tagged with pysb
A curated list of projects in awesome lists tagged with pysb .
https://github.com/sorgerlab/indra
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
bioinformatics biology computational-biology indra modeling nlp pysb sbml systems-biology
Last synced: 15 May 2025
https://github.com/AMICI-dev/AMICI
Advanced Multilanguage Interface to CVODES and IDAS
adjoint-sensitivities cvode cvodes differentialequations forward-sensitivities hacktoberfest idas kinetic-modeling mechanistic-models modeling ode parameter-estimation petab pysb python sbml sensitivities sensitivity-analysis simulation systemsbiology
Last synced: 04 May 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: 13 Feb 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/blakeaw/galibrate
Parameter estimation and model calibration using Genetic Algorithm optimization in Python.
genetic-algorithm model-calibration optimization optimizer parameter-estimation pysb python3 systems-biology
Last synced: 15 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: 09 May 2025