getElementsByTagName($tagName)->item(0); if(!empty($tagValue)) { return $tagValue->nodeValue; } else { return null; } } # EXAMINE A BOUNDARY - DETERMINE IF IT IS GAS OR BULK, AND ADD THE RELEVANT PARAMETERS TO THE PROTOCOL FILE function addBulkAndGasTags($paramDetailsToAppendTo,$domainProcessing,$domainParam,$boundaryNum,$boundaryArrayRef) { if($_SESSION["computationDomains"][$domainProcessing][$domainParam][$boundaryNum][$boundaryArrayRef]=="BoundaryBulk") { $activeForSolute = $paramDetailsToAppendTo->addChild("param",$_SESSION["computationDomains"][$domainProcessing][$domainParam][$boundaryNum][3]); $activeForSolute->AddAttribute("name","activeForSolute"); $bulk = $paramDetailsToAppendTo->addChild("param",$_SESSION["computationDomains"][$domainProcessing][$domainParam][$boundaryNum][4]); $bulk->AddAttribute("name","bulk"); } else if($_SESSION["computationDomains"][$domainProcessing][$domainParam][$boundaryNum][$boundaryArrayRef]=="BoundaryGasMembrane") { $isPermeableTo = $paramDetailsToAppendTo->addChild("param",$_SESSION["computationDomains"][$domainProcessing][$domainParam][$boundaryNum][5]); $isPermeableTo->AddAttribute("name","isPermeableTo"); $isPermeableTo->AddAttribute("detail",$_SESSION["computationDomains"][$domainProcessing][$domainParam][$boundaryNum][3]); $bulk = $paramDetailsToAppendTo->addChild("param",$_SESSION["computationDomains"][$domainProcessing][$domainParam][$boundaryNum][4]); $bulk->AddAttribute("name","bulk"); } } ?> Simulation Experiment Specification

iDynoMiCS Protocol File Maker

iDynoMiCS uses plain-text XML files in order to define the simulation to run; these files are called Protocol Files. In a protocol file, an XML mark-up is used to define the simulation parameters, including details such as run time, simulated solutes, simulated agents, and included reactions. This tool goes through the creation of a protocol file step by step, creating a protocol file that can be downloaded after the final step.

Although this tool makes generating protocol files much easier, it is recommended that you still study the iDynoMiCS tutorial in detail to ensure you understand the role of each parameter in the simulation

Simulation Setup Parameters