COBRApy is a package for constraint-based modeling of metabolic networks.
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Updated
Apr 8, 2024 - Python
COBRApy is a package for constraint-based modeling of metabolic networks.
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
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.
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
Curated (meta)list of resources for Biology.
Toolbox for including enzyme constraints on a genome-scale model.
python Parameter EStimation TOolbox
The consensus GEM for Saccharomyces cerevisiae
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
Workshop in omics integration and systems biology
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
a modeling environment tailored to parameter estimation in dynamical systems
General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
A Python framework for structural systems biology
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