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<div class="breadcrumb"><a href="/">Home</a> › Interoperability tools</div> <h1 class="title">Interoperability tools</h1>
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<p>Effective interoperability depends on well-crafted standards, but also on the existence of software tools to support them. We gather here information on a few tools developed to facilitate this interoperability. The list is by no mean complete, but will evolve as we get to know other tools. If you think a tool should be listed here, please tell-us at <a rel="nofollow" class="external text" href="https://groups.google.com/d/forum/combine-discuss">combine-discuss</a>. </p> <h1><span class="mw-headline" id="Converters">Converters</span></h1> <p>Although COMBINE standards are meant to be orthogonal, it is sometimes possible to generate one <a class="freelinking external" href="http://old_co.mbine.org/Standards#Core_COMBINE_Standards "> core COMBINE representation</a> from another, for instance using additional information coming from the <a class="freelinking external" href="http://old_co.mbine.org/Standards#Associated_standardization_efforts "> associated standardization efforts</a> </p> <h2><span class="mw-headline" id="System_Biology_Format_Converter_.28SBFC.29">System Biology Format Converter (SBFC)</span></h2> <p>The <a rel="nofollow" class="external text" href="http://sbfc.sf.net">System Biology Format Converter</a> is a generic open framework in Java that can potentially translate any system biology format into another. SBFC currently include several converters from SBML, including SBML to BioPAX. An SBML to SBGN-ML converter is under development. An <a class="freelinking external" href="http://www.ebi.ac.uk/compneur-srv/converters/converters"> online version</a> is available. </p> <h2><span class="mw-headline" id="Biological_Network_Manager_.28BiNoM.29">Biological Network Manager (BiNoM)</span></h2> <p><a class="freelinking external" href="http://bioinfo-out.curie.fr/projects/binom/ "> BiNoM</a> is a software (standalone or used as a <a href="/www.cytoscape.org/" class="freelinking"> Cytoscape</a> plugin) developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment. </p> <h1><span class="mw-headline" id="Tools_supporting_multiple_COMBINE_standards">Tools supporting multiple COMBINE standards</span></h1> <p>One of the goals of COMBINE is to encourage the synergy between the different standard description formats and associated efforts. The following tools help fulfilling this role by integrating information coming from several standards. </p> <h2><span class="mw-headline" id="Cytoscape">Cytoscape</span></h2> <p><a class="freelinking external" href="http://www.cytoscape.org/ "> Cytoscape</a> is an open source platform for network analysis and visualization. A very large number of plugins have been designed to extend the capabilities of the software, including several to support COMBINE standards. One can mention <a class="freelinking external" href="http://www.charite.de/sysbio/people/koenig/software/cysbml/ ">CySBML</a> to support SBML, <a class="freelinking external" href="http://sourceforge.net/p/cysbgn/wiki/Home/">CySBGN</a> to support SBGN, and <a class="freelinking external" href="http://bioinfo-out.curie.fr/projects/binom/ "> BiNoM</a>, that supports BioPAX, SBGN and SBML. </p> <h2><span class="mw-headline" id="The_Virtual_Cell">The Virtual Cell</span></h2> <p><a class="freelinking external" href="http://vcell.org "> The Virtual Cell</a> is a modeling platform that can import and export SBML, and can use BioPAX to build and annotate models. Current versions support querying and downloading pathways in BioPAX from Pathways Commons, a gateway to nine popular pathway databases. Upcoming versions add <a class="freelinking external" href="http://www.sbpax.org "> SBPAX</a> support for quantitative data to build reaction kinetics. </p> <h2><span class="mw-headline" id="Vanted">Vanted</span></h2> <p><a class="freelinking external" href="http://vanted.ipk-gatersleben.de/ "> VANTED</a> (Visualization and Analysis of Networks containing Experimental Data) makes possible to load and edit graphs, which may represent biological pathways or functional hierarchies. It is possible to map experimental datasets onto the graph elements and visualize time series data or data of different genotypes or environmental conditions in the context of a the underlying biological processes. Vanted supports SBML and BioPAX and the extension SBGN-ED provides full support for SBGN. </p> <!-- NewPP limit report Cached time: 20220802172746 Cache expiry: 86400 Dynamic content: false CPU time usage: 0.022 seconds Real time usage: 0.023 seconds Preprocessor visited node count: 129/1000000 Preprocessor generated node count: 272/1000000 Post‐expand include size: 0/2097152 bytes Template argument size: 0/2097152 bytes Highest expansion depth: 2/40 Expensive parser function count: 0/100 --> <!-- Transclusion expansion time report (%,ms,calls,template) 100.00% 0.000 1 - -total --> </div>
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