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SBW - Systems Biology Workbench 2.8.0 is a useful and professional software framework that allows heterogeneous application components-written in diverse programming languages. It runs on different platforms-to communicate and use each others' capabilities via a fast binary encoded-message system.The goal was to create a simple, high performance, open-source software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that the developers provide for different programming languages.Enhancements:JDesignerUpdated to work with Windows 7Fixed a copy compartment bug when pasting modelsAdded Vertical gradient style for nodesFixed when when selecting metatool response: "No Conservation Cycles" Fixed use of assignment rules so that constants can be defined, egk1 = 5.6Xo = Sin (time * k1)Fixed Problem where Modifier arcs would be added, even though an alias node was set.Update color scheme, now uses different default molecule and line color stylesSBML Support: Previously roadRunner, jarnacLite and autoLayout would use their own custom SBML readers with this release these utility functions have been bundled into SBMLSupport.dll and is used by all Modules. Now using libsbml 4, with major rewrites to most modules.Also supports the Parameterset Extension (with import of JD2 parameter sets)Simulation Tool: Allow to create new models (starts JarnacLite via FileNew)Allow to save model with changed Parameters / Boundary Conditions (via FileSaveAs)Change naming scheme to: Simulation Tool: in SBW Menu and Title bar, for example: Simulation Tool: RoadRunner or if registered Simulation Tool: Jarnac ...Steady State Panel: also display (reduced) jacobian ... Read / write settingsChanged display of coordinates in status barSave PGF plot (FileExport Data) select output .tex (and have a file extension .tex)Updated pgfplots export, to include color, line styles, symbols and labels as given with CustomizePlotintroduced PlugIn API with first plugins for running SED-ML files and displaying structural matrices. Jarnac Lite / JarnacLite SBML ConverterBugFix: a default compartment 'compartment' was created in all cases ... Now writing out L2V4 by defaultSBML Layout Toollibrary had problems with some invalid JD1 layout elements (such as BM13)bugfix: now subcompartments as created with CD or JD can be displayed againBugFix: comparison operatorsSBW C# Bindingsadded SBW menu class, that any .NET winforms app can use: just have an instance of the SBWMenu in your form, and initialize it in the constructor with a givenMenuItem / ToolStripMenuItem, module name and a delegate that returns a current SBML model: SBWMenu = new SBWMenu(oSBWMenu, ModuleName, delegate { return _sSBML; });in the load method of the form call SBWMenu.UpdateSBWMenu();and the SBW Menu will be populated with all SBW analyzers.Gillespie DMUpdated Gillespie Simulator to use SBML Support module for performance increasesupdated simulator to .NET 2.0Jarnacp.sim.eval () now excepts the simpler syntax, p.sim.eval (0, 10, 100). This will simulate from 0 to 10 in 100 steps and generate a matrix of all species levels incuding the independent variable time as the first columnRoadRunner: BugFix: RR now correctly distinguishes between events with useValuesFromTriggerTime=true and useValuesFromTriggerTime=falseBugFix: time dependent assignment rules had previously a slight errorBugFix: raterules now correctly handle hOSU flag ...ReImplementation of delayed events, now the delayed time will be reached exactly ... ReImplementation of events, now validates against test suite ... Matlab Translator: BugFix for assignment rulesnow also handles most SBML allowed functions, such as piecewise and the likeBugFix: boundary species are now correctly handledimproved performance Requirements:Win32 (Windows 2000, Windows XP, Windows 2003, Vista)
