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Search results for systems biology sbml
sbml
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systems-biology
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32 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
Petab
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54
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Newt
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48
A web application to visualize and edit pathway models
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!
Sbmltoolkit.jl
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35
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Jsbml
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34
JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
Libsbml
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31
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.
Smfsb
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29
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
Sbml.jl
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27
Julia interface to the Systems Biology Markup Language (SBML) library
Pyvipr
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25
Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
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
Modelpolisher
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23
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
Sbml Test Suite
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21
The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.
Parpe
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19
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
Escherconverter
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14
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
Libpetab Python
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14
Python package for working with PEtab files
Spatial Model Editor
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14
Spatial bio-chemical reaction model editor and simulator
Cbmpy
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13
CBMPy is a Python based platform for constraint based modelling and analysis.
Biosimulators
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13
Registry of containerized biosimulation tools that support a standard command-line interface
Libsbmlsim
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9
LibSBMLSim: A library for simulating SBML models
Sbtabeditor
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9
Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.
Sbml Org Website
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8
The source code and issue tracker for the SBML.org website.
Sbmlme
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7
Encoding ME models in SBML
Xitosbml
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7
XitoSBML - the spatial SBML plugin for ImageJ
Moccasin
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7
MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
Biosimulators_test_suite
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7
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
Mergem
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5
mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models
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.
Sbmlviewer
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5
The collection of transformations from SBML files into human readable formats
Cd2sbgnml
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5
Translation between CellDesigner-flavoured SBML and SBGN-ML
Sbmlinterface.jl
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5
Interface between the Systems Biology Markup Language and Julia
1-32 of 32 search results
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