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53 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.
Memote
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117
memote – the genome-scale metabolic model test suite
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
Biosimulations
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36
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
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.
Sbmlutils
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31
Python utilities for SBML
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
Pysces
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29
The official PySCeS project source code repository.
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
Roadrunner
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25
libRoadRunner: A high-performance SBML simulator
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.
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.
Sbscl
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19
The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.
Libpetab Python
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14
Python package for working with PEtab files
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.
Keggtranslator
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14
A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.
Spatial Model Editor
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14
Spatial bio-chemical reaction model editor and simulator
Biosimulators
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13
Registry of containerized biosimulation tools that support a standard command-line interface
Yaml2sbml
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13
Tool to convert an ODE model specified in the YAML format to SBML.
Cbmpy
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13
CBMPy is a Python based platform for constraint based modelling and analysis.
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.
Dfba
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9
Encoding Dynamic Flux Balance Analysis in SBML
Sbml Org Website
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8
The source code and issue tracker for the SBML.org website.
Simplesbml
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8
Python package for building SBML models without needing to use libSBML.
Cy3sbml
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8
cy3sbml: SBML for Cytoscape 3
Biosimulators_test_suite
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7
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
Copasi Dependencies
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7
Collection of OpenSource libraries to simplify COPASI build
Fbc_curation
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7
FROG analysis in python for the reproducibility of FBC models
Xitosbml
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7
XitoSBML - the spatial SBML plugin for ImageJ
Sbmlme
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7
Encoding ME models in SBML
Moccasin
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7
MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.
Spatial Sbml
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7
libraries & tools for spatial simulation of SBML models
Org.neuroml.export
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7
Export from NeuroML & LEMS
Rust_sbml
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6
SBML parser + bindings to python
Flint
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6
A simulator for biological and physiological models
Sbmlinterface.jl
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5
Interface between the Systems Biology Markup Language and Julia
Sbmlviewer
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5
The collection of transformations from SBML files into human readable formats
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.
Cd2sbgnml
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5
Translation between CellDesigner-flavoured SBML and SBGN-ML
Als_model
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5
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease of the adult, characterized by degeneration of motor neurons in the spinal cord, brain stem and motor cortex. There is no bio-informatic model of ALS.
Mergem
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5
mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models
Sbmlmath
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5
SBML MathML <-> SymPy
1-53 of 53 search results
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