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Search results for python sbml
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20 search results found
Cobrapy
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414
COBRApy is a package for constraint-based modeling of metabolic networks.
Indra
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154
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.
Amici
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105
Advanced Multilanguage Interface to CVODES and IDAS
Cnapy
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36
An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
Sbmlutils
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31
Python utilities for SBML
Pysces
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29
The official PySCeS project source code repository.
Benchmark Models Petab
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23
A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling
Python Libsbml
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19
Standalone Python package containing libSBML with support for SBML Level 3 Core and accepted SBML Level 3 packages.
Libpetab Python
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14
Python package for working with PEtab files
Cbmpy
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13
CBMPy is a Python based platform for constraint based modelling and analysis.
Yaml2sbml
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13
Tool to convert an ODE model specified in the YAML format to SBML.
Biosimulators
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13
Registry of containerized biosimulation tools that support a standard command-line interface
Simplesbml
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8
Python package for building SBML models without needing to use libSBML.
Biosimulators_test_suite
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7
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
Fbc_curation
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7
FROG analysis in python for the reproducibility of FBC models
Moccasin
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7
MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
Rust_sbml
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6
SBML parser + bindings to python
Sbml2julia
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5
A tool to for optimizing parameters of ordinary differential equation (ODE) models. SBML2Julia translates a model from SBML/PEtab format into Julia for Mathematical Programming (JuMP), performs the optimization task and returns the results.
Sbmlmath
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5
SBML MathML <-> SymPy
Mergem
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5
mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models
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