Search Results for "sbml"
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Showing 62 open source projects for "sbml"
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Systems Biology Markup Language (SBML)
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. -
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Biological Pathway Exchange Language
A Data Exchange Format for Biological Pathway Information
...In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap. -
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...The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters is highly facilitated. SBFC can be executed in two modes: 1. standalone executable downloading the package provided in this website; 2. web-service at http://www.ebi.ac.uk/biomodels/tools/converters . ...
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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SBW (Systems Biology Workbench)
Framework for Systems Biology
...It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML, SBML and MIRIAM. -
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Antimony
Antimony is a human-readable, human-writable model definition language
Antimony is a human-readable, human-writable model definition language. libAntimony is a library that will read and write Antimony and SBML files and provides an API for other programs to import Antimony models into their own internal formats. -
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Flint
A simulator for biological and physiological models
Flint is a simulator for biological and physiological models written in CellML, PHML and/or SBML. -
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CBMPy
PySCeS Constraint Based Modelling
...It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures. . CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed for the ecosystem modelling. ... -
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phraSED-ML
Paraphrased Human-Readable Adaptation of SED-ML
phraSED-ML is a script-like language for defining simulation experiments that is designed to be human-readable and human-writable, but that can be translated to SED-ML for interpretation by simulators. Inspired by Antimony (which performs the same role for SBML), phraSED-ML is designed to be compact, efficient, and easy to use. -
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The SBMLLayout Project provides libraries and tools for handling layout and render information of SBML Models. Supported are SBML Layout / Render Extension, CellDesigner annotations and JDesigner annotations.
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JSBML
The Java library for working with the SBML format.
JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML. To see and get the source code, please visit the new repository at https://github.com/sbmlteam/jsbml. -
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OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.
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ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML).
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SBML2LaTeX
A documentation and report generator for systems biological models
...The purpose of SBML2LATEX is to provide a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication. -
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SloppyCell is a complete environment for building models of biochemical systems, fitting them to data, and extracting falsifiable predictions via a parameter ensemble. SBML l2v1 compatible.
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libRoadRunner
high performance SBML JIT compiler & simulation engine
A high performance and portable simulation engine for systems and synthetic biology. -
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RoadRunner represents a state-of-the-art simulation library for SBML models. It is fast, portable and accurate. This projects hosts the library and tools using the library.
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Ben(Zai)Ten is a graphical modeling environment for computational and systems biology. It supports the community exchange standards: SBML, SBRML, SED-ML as well as ontologies: MIRIAM, SBO, ChEBI, KEGG, GO
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Octave-SBML
Octave package for SBML models.
A GNU Octave package for performing sensitivity analysis of SBML models. Builds upon the currently available libSBML functionality. -
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pybrn is a Python package for the analysis of biochemical reaction networks. It provides basic model handling capabilities, import from SBML, analysis of conservation relations, steady state computation and model simulation.
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SBNW
A Automated Layout Library for SBML
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cy2sbml
cy2sbml: Cytoscape 2 Plugin for SBML
cy2sbml is a plugin for the import and work with SBML files in Cytoscape 2. Latest releases https://github.com/matthiaskoenig/cy2sbml For Cytoscape 3 use cy3sbml https://github.com/matthiaskoenig/cy3sbml -
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EpidermalERKMAPK
Scripts for Modelling Human Epidermal ERK-MAPK Activation
...This package includes: - MATLAB code containing the model definition, together with a script to perform non-linear least squares optimisation for a subset of parameters - python scripts which use libSBML to create an SBML representation of the model - SED-ML scripts which execute the SBML model under a range of conditions, produce output plots to recapitulate results shown in Cursons et al. (2015). -
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yTOS
Metabolic pathways to Systems Biology standards (SBGN and SBML)
yTOS enables transformation of metabolic pathways generated in yEd graph editor into a computational model defined by Systems Biology standards: SBGN (Systems Biology Graphical Notation) format and SBML (Systems Biology Markup Language) with CellDesigner annotations. yTOS takes as input a graphML file. The example of Glycolysis given with yTOS tool was adopted from http://www.sbgn.org/Documents/PD_L1_Examples . Requirements: Java 1.8 is necessary. -
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libRoadRunner_Coyote
GUI interface to libRoadRunner
Coyote is a GUI interface to SBML based simulator libRoadRunner.