Frank Bergmann: Getting Started with LibSedML (on linux)

A couple of days ago I announced the LibSedML sourceforge project, a library for reading / writing SED-ML files. However, what was missing so far is information on how one would start using the library. (If you feel lucky, I provided a binary at the end of this post!)

Preparing the Virtual Machine

In the following, I’ll describe how to set up an OpenSuse 11.2 Virtual Machine, in order to run SED-ML Simulation Experiments:

Actually, we are not setting up the virtual machine, but instead take the one provided by the Mono team. Simply download the VMware image from:

http://mono-project.com/Downloads

unzip and start the Virtual Machine. It will automatically log in as user ‘rupert’
The first thing we might want to do is to get SBW started. While not strictly necessary … it will help us later on, when we just copy the binary libraries for LibSedMLRunner to execute the simulations. The Latest SBW version for linux can be found here:

http://sourceforge.net/projects/jdesigner/files/Systems%20Biology%20Workbench/2.7.10/SBW-2.7.10-linux-installer.bin/download

The file is simply installed by making it executable (chmod +x SBW-*bin) and executing the binary installer.
Next we might want to install a fresh copy of LibSBML, which is easily done by checking out libsbml from SVN:

svn co http://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml libsbml

the virtual machine at this point has no g++ so we get one by going to a root shell (root password is ‘mono’) and installing:

zypper install gcc-c++
zypper install libxml2-devel

(i also installed additional packages like ‘lapack’ but I’m not sure they are necessary)
Next we get the latest SWIG from http://www.swig.org/download.html, I just downloaded the 1.3.40 version, unpacked it with tar zxf, ran:

./configure && make && sudo make install

which installes SWIG into /usr/local
Now we can compile and run libsbml:

./configure --with-libxml=/usr --with-swig=/usr/local --with-csharp --enable-layout=no && make

which will compile libsbml and create the bindings in the src/bindings/csharp folder

Compiling LibSedML

So far for the prerequisites. The remaining could not be simpler. Here the whole session:

Directory: /home/rupert/Desktop
Tue Mar  9 02:35:51 UTC 2010
rupert@linux:~/Desktop> cd
rupert@linux:~> cd Development/
rupert@linux:~/Development> l
stotal 12
drwxr-xr-x  3 rupert users 4096 2010-03-08 20:20 ./
drwxr-xr-x 33 rupert users 4096 2010-03-08 22:21 ../
drwxr-xr-x  8 rupert users 4096 2010-03-08 20:21 sbwbuild/
rupert@linux:~/Development> svn co http://libsedml.svn.sourceforge.net/svnroot/libsedml/trunk LibSedML
A    LibSedML/ICON_MIASE.ico
A    LibSedML/SEDML.sln
A    LibSedML/libSedMLScript
A    LibSedML/libSedMLScript/HelperFunctions.py
A    LibSedML/libSedMLScript/libSedMLScript.csproj
A    LibSedML/libSedMLScript/SedMLPythonConverter.cs
A    LibSedML/libSedMLScript/ITextImporter.cs
A    LibSedML/libSedMLScript/ITextExporter.cs
A    LibSedML/libSedMLScript/Properties
A    LibSedML/libSedMLScript/Properties/AssemblyInfo.cs
A    LibSedML/libSedMLScript/Properties/Resources.resx
A    LibSedML/libSedMLScript/Properties/Resources.Designer.cs
A    LibSedML/libSedMLScript/SedMLScript.cs
A    LibSedML/SedMLWeb
A    LibSedML/SedMLWeb/Default.aspx.designer.cs
A    LibSedML/SedMLWeb/MasterASPX.master
A    LibSedML/SedMLWeb/SedMLWeb.csproj
A    LibSedML/SedMLWeb/Web.config
A    LibSedML/SedMLWeb/Default.aspx.cs
A    LibSedML/SedMLWeb/_sysbiostyles.css
A    LibSedML/SedMLWeb/MasterASPX.master.cs
A    LibSedML/SedMLWeb/SysBio_MasterASPX.master
A    LibSedML/SedMLWeb/KGI0717_MasterASPX.master
A    LibSedML/SedMLWeb/Properties
A    LibSedML/SedMLWeb/Properties/AssemblyInfo.cs
A    LibSedML/SedMLWeb/SysBio_MasterASPX.master.cs
A    LibSedML/SedMLWeb/Default.aspx
A    LibSedML/SedMLWeb/KGI0717_MasterASPX.master.cs
A    LibSedML/Samples
A    LibSedML/Samples/model1.xml
A    LibSedML/Samples/sedmltest.txt
A    LibSedML/Samples/curien.xml
A    LibSedML/Samples/EllowitzRepressilator.miase
A    LibSedML/Samples/lorenz.txt
A    LibSedML/Samples/BIOMD0000000021.xml
A    LibSedML/Samples/miaseTest.xml
A    LibSedML/Samples/sedmlCurienJWS.xml
A    LibSedML/Samples/JanaWolf.miase
A    LibSedML/Samples/miaseBioModels21.xml
A    LibSedML/Samples/brusselator.miase
A    LibSedML/Samples/brusselator.xml
A    LibSedML/Samples/lorenz.miase
A    LibSedML/Samples/lorenz.xml
A    LibSedML/Samples/sedMLBIOM21.miase
A    LibSedML/Samples/sedMLBIOM21.xml
A    LibSedML/libSedMLRunner
A    LibSedML/libSedMLRunner/SedMLRunner.cs
A    LibSedML/libSedMLRunner/libSedMLRunner.csproj
A    LibSedML/libSedMLRunner/RunResult.cs
A    LibSedML/libSedMLRunner/SimpleRunner.cs
A    LibSedML/libSedMLRunner/Properties
A    LibSedML/libSedMLRunner/Properties/AssemblyInfo.cs
A    LibSedML/SedMLConsole
A    LibSedML/SedMLConsole/ICON_MIASE.ico
A    LibSedML/SedMLConsole/Web References
A    LibSedML/SedMLConsole/Web References/BioModels
A    LibSedML/SedMLConsole/Web References/BioModels/Reference.cs
A    LibSedML/SedMLConsole/Web References/BioModels/BioModelsWebServices.wsdl
A    LibSedML/SedMLConsole/Web References/BioModels/Reference.map
A    LibSedML/SedMLConsole/Web References/MIRIAM
A    LibSedML/SedMLConsole/Web References/MIRIAM/Reference.cs
A    LibSedML/SedMLConsole/Web References/MIRIAM/MiriamWebServices.wsdl
A    LibSedML/SedMLConsole/Web References/MIRIAM/Reference.map
A    LibSedML/SedMLConsole/SedMLConsole.csproj.user
A    LibSedML/SedMLConsole/app.config
A    LibSedML/SedMLConsole/SedMLConsole.csproj
A    LibSedML/SedMLConsole/Resources
A    LibSedML/SedMLConsole/Resources/ICON_MIASE.ico
A    LibSedML/SedMLConsole/Program.cs
A    LibSedML/SedMLConsole/Properties
A    LibSedML/SedMLConsole/Properties/AssemblyInfo.cs
A    LibSedML/SedMLConsole/Properties/Settings.settings
A    LibSedML/SedMLConsole/Properties/Settings.Designer.cs
A    LibSedML/SedMLConsole/Properties/Resources.resx
A    LibSedML/SedMLConsole/Properties/Resources.Designer.cs
A    LibSedML/3rdParty
A    LibSedML/3rdParty/Microsoft.Scripting.ExtensionAttribute.dll
A    LibSedML/3rdParty/LibRoadRunner.dll
A    LibSedML/3rdParty/Microsoft.Scripting.dll
A    LibSedML/3rdParty/IronPython.dll
A    LibSedML/3rdParty/ICSharpCode.SharpZipLib.dll
A    LibSedML/3rdParty/mathLibrary.dll
A    LibSedML/3rdParty/CompareData.dll
A    LibSedML/3rdParty/IronPython.Modules.dll
A    LibSedML/3rdParty/ZedGraph.Web.dll
A    LibSedML/3rdParty/Microsoft.Dynamic.dll
A    LibSedML/3rdParty/SBMLSupport.dll
A    LibSedML/3rdParty/libsbmlcsP.dll
A    LibSedML/3rdParty/SBWCSharp.dll
A    LibSedML/3rdParty/Microsoft.Scripting.Core.dll
A    LibSedML/3rdParty/LibStructuralCSharp.dll
A    LibSedML/3rdParty/Microsoft.Scripting.Debugging.dll
A    LibSedML/3rdParty/ZedGraph.dll
A    LibSedML/SedMLScript
A    LibSedML/SedMLScript/ICON_MIASE.ico
A    LibSedML/SedMLScript/MainForm.resx
A    LibSedML/SedMLScript/SedMLScriptTest.csproj
A    LibSedML/SedMLScript/MainForm.Designer.cs
A    LibSedML/SedMLScript/Program.cs
A    LibSedML/SedMLScript/icons
A    LibSedML/SedMLScript/icons/run.png
A    LibSedML/SedMLScript/MainForm.cs
A    LibSedML/SedMLScript/Properties
A    LibSedML/SedMLScript/Properties/AssemblyInfo.cs
A    LibSedML/SedMLScript/Properties/Settings.settings
A    LibSedML/SedMLScript/Properties/Settings.Designer.cs
A    LibSedML/SedMLScript/Properties/Resources.resx
A    LibSedML/SedMLScript/Properties/Resources.Designer.cs
A    LibSedML/libSedML
A    LibSedML/libSedML/Report.cs
A    LibSedML/libSedML/Util.cs
A    LibSedML/libSedML/ModelStore.cs
A    LibSedML/libSedML/UniformTimeCourse.cs
A    LibSedML/libSedML/TaskStore.cs
A    LibSedML/libSedML/DataGenerator.cs
A    LibSedML/libSedML/Parameter.cs
A    LibSedML/libSedML/SedMLInfo.cs
A    LibSedML/libSedML/Simulation.cs
A    LibSedML/libSedML/Variable.cs
A    LibSedML/libSedML/Change.cs
A    LibSedML/libSedML/libSedML.csproj
A    LibSedML/libSedML/Properties
A    LibSedML/libSedML/Properties/AssemblyInfo.cs
A    LibSedML/libSedML/DataGeneratorStore.cs
A    LibSedML/libSedML/SedMLBase.cs
A    LibSedML/libSedML/Output.cs
A    LibSedML/libSedML/Model.cs
A    LibSedML/libSedML/SimulationStore.cs
A    LibSedML/libSedML/Task.cs
A    LibSedML/libSedML/Plot2D.cs
A    LibSedML/IronPythonScript
Checked out revision 4.
rupert@linux:~/Development> cd LibSedML/
rupert@linux:~/Development/LibSedML> ls
3rdParty          libSedML        Samples       SEDML.sln
ICON_MIASE.ico    libSedMLRunner  SedMLConsole  SedMLWeb
IronPythonScript  libSedMLScript  SedMLScript
rupert@linux:~/Development/LibSedML> mdtool build -c:Release
MonoDevelop Build Tool
Loading solution: ./SEDML.sln
   Loading solution: ./SEDML.sln
      Loading projects ..
Building: SEDML (Release)
   Building Solution SEDML
      Building: libSedML (Release)
         Performing main compilation...
         /usr/bin/gmcs /noconfig
         "/out:/home/rupert/Development/LibSedML/bin/libSedML.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/CompareData.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/ICSharpCode.SharpZipLib.
         dll" "/r:/home/rupert/Development/LibSedML/3rdParty/libsbmlcsP.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/mathLibrary.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/SBMLSupport.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/SBWCSharp.dll"
         "/r:System.dll" "/r:System.Data.dll" "/r:System.Xml.dll" /nologo
         /warn:4 /optimize+ /codepage:utf8 /platform:x86 "/define:TRACE" 
         /t:library "/home/rupert/Development/LibSedML/libSedML/Change.cs"
         "/home/rupert/Development/LibSedML/libSedML/DataGenerator.cs"
         "/home/rupert/Development/LibSedML/libSedML/DataGeneratorStore.cs"
         "/home/rupert/Development/LibSedML/libSedML/SedMLBase.cs"
         "/home/rupert/Development/LibSedML/libSedML/SedMLInfo.cs"
         "/home/rupert/Development/LibSedML/libSedML/Model.cs"
         "/home/rupert/Development/LibSedML/libSedML/ModelStore.cs"
         "/home/rupert/Development/LibSedML/libSedML/Output.cs"
         "/home/rupert/Development/LibSedML/libSedML/Parameter.cs"
         "/home/rupert/Development/LibSedML/libSedML/Plot2D.cs"
         "/home/rupert/Development/LibSedML/libSedML/Properties/AssemblyInfo.cs"
          "/home/rupert/Development/LibSedML/libSedML/Report.cs"
         "/home/rupert/Development/LibSedML/libSedML/Simulation.cs"
         "/home/rupert/Development/LibSedML/libSedML/SimulationStore.cs"
         "/home/rupert/Development/LibSedML/libSedML/Task.cs"
         "/home/rupert/Development/LibSedML/libSedML/TaskStore.cs"
         "/home/rupert/Development/LibSedML/libSedML/UniformTimeCourse.cs"
         "/home/rupert/Development/LibSedML/libSedML/Util.cs"
         "/home/rupert/Development/LibSedML/libSedML/Variable.cs" 
         Compilation succeeded - 1 warning(s)
         
         /home/rupert/Development/LibSedML/libSedML/Util.cs(307,18): warning
         CS0219: The variable `length' is assigned but its value is never used
         
         
         Build complete -- 0 errors, 1 warning
      Building: libSedMLRunner (Release)
         Performing main compilation...
         /usr/bin/gmcs /noconfig
         "/out:/home/rupert/Development/LibSedML/bin/libSedMLRunner.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/CompareData.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/LibRoadRunner.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/LibStructuralCSharp.dll"
          "/r:System.dll" "/r:System.Data.dll" "/r:System.Drawing.dll"
         "/r:System.Windows.Forms.dll" "/r:System.Xml.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/ZedGraph.dll"
         "/r:/home/rupert/Development/LibSedML/bin/libSedML.dll" /nologo
         /warn:4 /optimize+ /codepage:utf8 /platform:x86 "/define:TRACE" 
         /t:library
         "/home/rupert/Development/LibSedML/libSedMLRunner/SedMLRunner.cs"
         "/home/rupert/Development/LibSedML/libSedMLRunner/Properties/AssemblyIn
         fo.cs" "/home/rupert/Development/LibSedML/libSedMLRunner/RunResult.cs"
         "/home/rupert/Development/LibSedML/libSedMLRunner/SimpleRunner.cs" 
         Build complete -- 0 errors, 0 warnings
      Building: SedMLConsole (Release)
         Performing main compilation...
         Compiling resource
         /home/rupert/Development/LibSedML/SedMLConsole/Properties/Resources.res
         x with /usr/bin/resgen2
         /usr/bin/gmcs /noconfig
         "/out:/home/rupert/Development/LibSedML/bin/SedMLConsole.exe"
         "/r:/home/rupert/Development/LibSedML/3rdParty/CompareData.dll"
         "/r:System.dll" "/r:System.Drawing.dll"
         "/r:System.EnterpriseServices.dll" "/r:System.Web.Services.dll"
         "/r:System.Windows.Forms.dll" "/r:System.Data.dll" "/r:System.Xml.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/ZedGraph.dll"
         "/r:/home/rupert/Development/LibSedML/bin/libSedMLRunner.dll"
         "/r:/home/rupert/Development/LibSedML/bin/libSedML.dll" /nologo
         /warn:4 /optimize+
         "/win32icon:/home/rupert/Development/LibSedML/SedMLConsole/ICON_MIASE.i
         co" /codepage:utf8 /platform:x86 "/define:TRACE"  /t:winexe
         "/home/rupert/Development/LibSedML/SedMLConsole/Program.cs"
         "/home/rupert/Development/LibSedML/SedMLConsole/Properties/AssemblyInfo
         .cs"
         "/home/rupert/Development/LibSedML/SedMLConsole/Properties/Resources.De
         signer.cs"
         "/home/rupert/Development/LibSedML/SedMLConsole/Properties/Settings.Des
         igner.cs" "/home/rupert/Development/LibSedML/SedMLConsole/Web
         References/BioModels/Reference.cs"
         "/home/rupert/Development/LibSedML/SedMLConsole/Web
         References/MIRIAM/Reference.cs"
         "/res:/home/rupert/Development/LibSedML/SedMLConsole/Properties/Resourc
         es.resources,SedMLConsole.Properties.Resources.resources" 
         Compilation succeeded - 1 warning(s)
         
         /home/rupert/Development/LibSedML/SedMLConsole/Program.cs(64,29):
         warning CS0169: The private method
         `SedMLConsole.Program.CreateSedMLProgramatically()' is never used
         
         
         Build complete -- 0 errors, 1 warning
      Building: libSedMLScript (Release)
         Performing main compilation...
         Compiling resource
         /home/rupert/Development/LibSedML/libSedMLScript/Properties/Resources.r
         esx with /usr/bin/resgen2
         /usr/bin/gmcs /noconfig
         "/out:/home/rupert/Development/LibSedML/bin/libSedMLScript.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/IronPython.dll"
         "/r:/home/rupert/Development/LibSedML/3rdParty/Microsoft.Scripting.dll"
         
         "/r:/home/rupert/Development/LibSedML/3rdParty/Microsoft.Scripting.Core
         .dll" "/r:System.dll" "/r:System.Core.dll" "/r:System.Xml.Linq.dll"
         "/r:System.Data.DataSetExtensions.dll" "/r:System.Data.dll"
         "/r:System.Xml.dll"
         "/r:/home/rupert/Development/LibSedML/bin/libSedML.dll" /nologo
         /warn:4 /optimize+ /codepage:utf8 "/define:TRACE"  /t:library
         "/home/rupert/Development/LibSedML/libSedMLScript/ITextExporter.cs"
         "/home/rupert/Development/LibSedML/libSedMLScript/ITextImporter.cs"
         "/home/rupert/Development/LibSedML/libSedMLScript/Properties/Resources.
         Designer.cs"
         "/home/rupert/Development/LibSedML/libSedMLScript/SedMLPythonConverter.
         cs" "/home/rupert/Development/LibSedML/libSedMLScript/SedMLScript.cs"
         "/home/rupert/Development/LibSedML/libSedMLScript/Properties/AssemblyIn
         fo.cs"
         "/res:/home/rupert/Development/LibSedML/libSedMLScript/Properties/Resou
         rces.resources,libSedMLScript.Properties.Resources.resources" 
         Build complete -- 0 errors, 0 warnings
      Building: SedMLScriptTest (Release)
         Performing main compilation...
         WARNING: Assembly 'System.Deployment' not found. Make sure that the
         assembly exists in disk. If the reference is required to build the
         project you may get compilation errors.
         Compiling resource
         /home/rupert/Development/LibSedML/SedMLScript/MainForm.resx with
         /usr/bin/resgen2
         Compiling resource
         /home/rupert/Development/LibSedML/SedMLScript/Properties/Resources.resx
          with /usr/bin/resgen2
         /usr/bin/gmcs /noconfig
         "/out:/home/rupert/Development/LibSedML/bin/SedMLScriptTest.exe"
         "/r:System.dll" "/r:System.Core.dll" "/r:System.Xml.Linq.dll"
         "/r:System.Data.DataSetExtensions.dll" "/r:System.Data.dll"
         "/r:System.Drawing.dll" "/r:System.Windows.Forms.dll"
         "/r:System.Xml.dll"
         "/r:/home/rupert/Development/LibSedML/bin/libSedMLRunner.dll"
         "/r:/home/rupert/Development/LibSedML/bin/libSedMLScript.dll"
         "/r:/home/rupert/Development/LibSedML/bin/libSedML.dll" /nologo
         /warn:4 /optimize+
         "/win32icon:/home/rupert/Development/LibSedML/SedMLScript/ICON_MIASE.ic
         o" /codepage:utf8 /platform:x86 "/define:TRACE" 
         /main:SedMLScriptTest.Program /t:winexe
         "/home/rupert/Development/LibSedML/SedMLScript/MainForm.cs"
         "/home/rupert/Development/LibSedML/SedMLScript/MainForm.Designer.cs"
         "/home/rupert/Development/LibSedML/SedMLScript/Program.cs"
         "/home/rupert/Development/LibSedML/SedMLScript/Properties/AssemblyInfo.
         cs"
         "/res:/home/rupert/Development/LibSedML/SedMLScript/MainForm.resources,
         SedMLScriptTest.MainForm.resources"
         "/res:/home/rupert/Development/LibSedML/SedMLScript/Properties/Resource
         s.resources,SedMLScriptTest.Properties.Resources.resources"
         "/home/rupert/Development/LibSedML/SedMLScript/Properties/Resources.Des
         igner.cs"
         "/home/rupert/Development/LibSedML/SedMLScript/Properties/Settings.Desi
         gner.cs" 
         Build complete -- 0 errors, 1 warning
      Building: SedMLWeb (Release)
         Generating CodeBehind members...
         Waiting for project type database to finish updating...
Object reference not set to an instance of an object
rupert@linux:~/Development/LibSedML> cd bin
rupert@linux:~/Development/LibSedML/bin> ls
CompareData.dll              Microsoft.Dynamic.dll
ICSharpCode.SharpZipLib.dll  Microsoft.Scripting.Core.dll
IronPython.dll               Microsoft.Scripting.Debugging.dll
LibRoadRunner.dll            Microsoft.Scripting.dll
libsbmlcsP.dll               Microsoft.Scripting.ExtensionAttribute.dll
libSedML.dll                 SBMLSupport.dll
libSedMLRunner.dll           SBWCSharp.dll
libSedMLScript.dll           SedMLConsole.exe
LibStructuralCSharp.dll      SedMLScriptTest.exe
mathLibrary.dll              ZedGraph.dll
rupert@linux:~/Development/LibSedML/bin> cp ~/Development/sbwbuild/cvs-dl/libsbml/src/bindings/csharp/libsbmlcs* . 
rupert@linux:~/Development/LibSedML/bin> ls
CompareData.dll              mathLibrary.dll
ICSharpCode.SharpZipLib.dll  Microsoft.Dynamic.dll
IronPython.dll               Microsoft.Scripting.Core.dll
LibRoadRunner.dll            Microsoft.Scripting.Debugging.dll
libsbmlcs.la                 Microsoft.Scripting.dll
libsbmlcsP.dll               Microsoft.Scripting.ExtensionAttribute.dll
libsbmlcs.snk                SBMLSupport.dll
libsbmlcs.so                 SBWCSharp.dll
libSedML.dll                 SedMLConsole.exe
libSedMLRunner.dll           SedMLScriptTest.exe
libSedMLScript.dll           ZedGraph.dll
LibStructuralCSharp.dll
rupert@linux:~/Development/LibSedML/bin> cp ~/SBW-2.7.10/CSharp/libcvode*.so . 
rupert@linux:~/Development/LibSedML/bin> cp ~/SBW-2.7.10/CSharp/libNleqLib.so . 
rupert@linux:~/Development/LibSedML/bin> cp ~/SBW-2.7.10/CSharp/lib
libblas.so           libcvode.so          libLibLA.so
libblas.so.3         libg2c.so            libLibStructural.so
libblas.so.3.0       libg2c.so.0          libNleqLib.so
libblas.so.3.0.3     libg2c.so.0.0.0      libsbl2SBML.dll
libbz2.so            liblapack.so         libsbmlcsP.dll
libbz2.so.1          liblapack.so.3       libsbmlcs.so
libbz2.so.1.0.2      liblapack.so.3.0     libsbml.so
libcvodedll.so       liblapack.so.3.0.3   libSBW.so
rupert@linux:~/Development/LibSedML/bin> cp ~/SBW-2.7.10/CSharp/libLib*.so . 
rupert@linux:~/Development/LibSedML/bin> ls
CompareData.dll              libSedMLRunner.dll
ICSharpCode.SharpZipLib.dll  libSedMLScript.dll
IronPython.dll               LibStructuralCSharp.dll
libcvodedll.so               mathLibrary.dll
libcvode.so                  Microsoft.Dynamic.dll
libLibLA.so                  Microsoft.Scripting.Core.dll
libLibStructural.so          Microsoft.Scripting.Debugging.dll
libNleqLib.so                Microsoft.Scripting.dll
LibRoadRunner.dll            Microsoft.Scripting.ExtensionAttribute.dll
libsbmlcs.la                 SBMLSupport.dll
libsbmlcsP.dll               SBWCSharp.dll
libsbmlcs.snk                SedMLConsole.exe
libsbmlcs.so                 SedMLScriptTest.exe
libSedML.dll                 ZedGraph.dll
rupert@linux:~/Development/LibSedML/bin> mono ./SedMLConsole.exe ../Samples/lorenz.miase

The Results

This will result in the Lorenz Attractor simulated, and you should see:

I hope this gave a little over view in how to compile the library at this stage. I’ve archived the resulting binary and uploaded it to SF:

http://sourceforge.net/projects/libsedml/files/test

Frank Bergmann

Download Links

Monday, March 8, 2010

Getting Started with LibSedML (on linux)

Preparing the Virtual Machine

Compiling LibSedML

The Results

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