Search Results for "sbml"
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Showing 64 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
... 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 Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. 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...
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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. -
PMG is a low-code software platform that allows users to configure automation solutions and business applications to drive digital transformation initiatives. From streamlining business processes through automation, to integrating existing systems and filling in point solution functionality gaps, to delivering a collaborative workspace and unified user experience – PMG’s low-code platform does it all without coding. Business users as well as IT resources are empowered to configure, deploy, and maintain solutions that meet their company’s specific needs.
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SBW (Systems Biology Workbench)
Framework for Systems Biology
..., SBML and MIRIAM. -
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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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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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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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CBMPy
PySCeS Constraint Based Modelling
PySCeS CBMPy is a new platform for constraint based modelling and analysis. 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... -
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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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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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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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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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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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SBML2LaTeX
A documentation and report generator for systems biological models
SBML2LATEX is a tool to convert files in the System Biology Markup Language SBML) format into LATEX files. A convenient online version is available, which allows the user to directly generate report from SBML in form of PDF or TeX, which can be further processed to various file types including DVI, PS, EPS, GIF, JPG, or PNG. SBML2LATEX can also be downloaded and used locally in batch mode or interactively with its Graphical User Interface or several command line options. The purpose... -
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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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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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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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This project hosts the 'Simulation Tool', an extensible, interactive environment for carrying out simulation experiments of SBML models. This project can use RoadRunner or SBW enabled simulators to carry out simulations.
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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
...-0509-4-157]. 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).