Search Results for "sbml"

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.

...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 . ...

...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.

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.

...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.

...Also, merlin includes tools for the compartmentation of the model that predict the localisation of the proteins encoded in the genome, and thus the localisation of the metabolites involved in the reactions induced by such proteins. Finally, merlin expedites the transition from genome-scale data to SBML metabolic models, allowing the user to have a preliminary view of the biochemical network.

SBSI (Systems Biology Software Infrastructure) is a suite of tools for systems biology, such as parallelized numerical algorithms, and a Java, Eclipse RCP based client for visualizing results, running simulations, and integrating SBML based plugins.

VANTED - Visualization and Analysis of NeTworks containing Experimental Data At SourceForge the VANTED development history is preserved, only limited amount of development will proceed here. Please head on to the most recent developments, which can be observed at www.vanted.org.

Easily find and extract specific chemical reactions from the BioModels database.

The creation of quantitative SBML models is a time-intensive manual process. Saint, an automated SBML annotation integration tool, aids the modeller and reduces development time by providing information about a model in an easy-to-use interface.

We are developing MIRACH, a Statistical Online Model Checker for Biological Pathway Models, based on the PLTLs formalism for expressing the rules/properties to be checked. MIRACH can currently check pathways models written either in CSML or SBML.

GRaPe - a platform-independent software tool for building integrative gene-reaction-protein (GRP) networks. It generates the kinetic equations for each reaction and outputs a SBML document. It also implements two methods for parameter estimation.

SBMLforge is a tool that enables the user to convert and merge KEGG metabolic and signaling pathways (KGML format) to create a single SBML pathway model.

Discrete Event System Specification (DEVS) combined with System Biology Markup Language (SBML) project: a Java-based tool to solve complex biology processes. Support by RTSync Corporation and Arizona Center for Integrated Modeling & Simulation (ACIMS)

Narrator is a graphical modelling tool for the description of dynamical systems and processes. Narrator is SBML compatible.

Cellontro models and simulates cells, other biological entities, and biochemical networks. Specify your models using XML and Java, or SBML. Cellontro is now completely contained within the Xholon sourceforge project.