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Road Runner C # -> C++ ->Delphi Code Conversion Project

Road Runner C # -> C++ ->Delphi Code Conversion Project. Totte Karlsson. Involved Code Libraries. LibSBML. Systems Biology Markup Language Format for computer models of biological processes. Reads SBML files (XML) C++. (Delphi) Interface (wrapper) to libSBML .

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Road Runner C # -> C++ ->Delphi Code Conversion Project

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  1. Road Runner C# -> C++ ->Delphi Code Conversion Project Totte Karlsson

  2. Involved Code Libraries LibSBML • Systems Biology Markup Language • Format for computer models of biological processes. • Reads SBML files (XML) • C++ • (Delphi) Interface (wrapper) to libSBML. • One single .h and .cpp file • One global ‘model’ object: • Model* _oModelCPP = NULL; allocated as • SBMLReaderoReader; • _oSBMLDocCPP = oReader.readSBMLFromString(arg); • _oModelCPP = _oSBMLDocCPP->getModel(); NOMLib libStruct • C/C++ library for analyzing the structural properties of • stoichiometric networks Sundials Collection of C libraries. Sundials stands for SUite of Nonlinear and DIfferential/Algebraic equation Solvers.

  3. Road Runner • Simulation environment for SBML models • Library is written in C# (the one to be converted) • Need previously mentioned libraries at link time Testing SBW Inspector Module application Visual Studio IDE Socket Connection RoadRunner-vs2010 (service) LibRoadRunner-vs2010 Call functions in RoadRunner Lib from inspector. Trigger breakpoints set in Visual Studio IDE, e.g. loadSBML(sbml…)

  4. Data flow

  5. Tools • A subversion repository for this work was created at: https://code.google.com/p/roadrunnerwork/ • Libraries, libSBML, NOM, libstruct, SBW core are brought into the repository as externals • CMake – tool to generate build files for various platforms and compilers. • Visual Studio and CodeGear to compile C#, C++ and Delphi

  6. Progress • Got all external libraries compiling, using Cmake, both with Visual Studio and Codegear • Added a new CMake project for NOMlib, to link against the latest libSBML. • Created initial RoadRunner application that will replicate current data flow. Stuck at reading xml file (feedback.xml).

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