PottersWheel Documentation

• Overview
• Introduction
• Terminology
• Installation
• Update
• Videos
• First steps
• Configuration
• Function reference
• Important functions
• Fitting
• Glossary
• FAQ

Installation

Part 1: Platform-specific steps

Microsoft® Windows®

1. Install Matlab 7.1 or higher (www.mathworks.com) on MS Windows 32 or 64 bit. PottersWheel is prepared for the 32 bit version of Matlab (independent on MS Windows being 32 or 64 bit). If you intend to use PottersWheel with Matlab 64 bit, please use the CVODES integrator.
2. Configuration of the mex compiler
   Start MATLAB and type mex –setup. At the question prompt, type y to allow MATLAB to locate installed C compilers. With 32 bit Matlab 32 bit select the ‘lcc’ C compiler which is already included in Matlab. For 64 bit Matlab, you have to install a C compiler, e.g. the freely available Microsoft® Visual C++ 2008 Express Edition. A list of compatible compilers can be found here.
3. Continue with the platform-independent steps.

Linux

Usually a C and Fortran compiler and the latex program are already installed.

Macintosh®

Though the core of Mac OS X is a POSIX compliant operating system, usually no C or Fortran compiler is included. While a Fortran compiler is required by PottersWheel only to use the fast integration approach, a C compiler must be available. It is recommended to use the C compiler available together with XCode. Concerning Fortran, the free g95 can be used.

Part 2: Platform-independent steps

1. Download and unzip the PottersWheel toolbox e.g. into
   C:\Program Files\PottersWheel\PottersWheelToolbox.
2. Open Matlab and change the Matlab working directory by clicking the triple dot icon on the MATLAB toolbar. Map your working directory to the folder that you have extracted the PottersWheel zip file. Click OK to continue.
3. Type pwInstall at the Matlab command prompt and press the enter key to install PottersWheel. Essentially, the Matlab path is configured and the PottersWheel C MEX files are compiled for your system.
4. Now PottersWheel has been installed. It is recommended to create a project folder at a location of your choice using e.g. the Windows file explorer, for example C:\Modeling\Project01. Create subfolders Data, Models, WorkingFolder. Set the Matlab working folder to WorkingFolder:
   
   
   
5. Type pw to start PottersWheel. Follow the tutorials and the videos in the documentation section, e.g. First Steps.
6. If PottersWheel is not working correctly, please check the installation by typing pwCheckSystem. If you cannot resolve the problem, send the output of pwCheckSystem and the error message to support at potterswheel de.

Part 3: Optional tools

1. SSm GO Toolbox
   Go to http://www.iim.csic.es/~gingproc/ssmGO.html and download the scatter search for global optimization toolbox, which is required to use all ssm based optimization strategies in PottersWheel. Before installation, request the password to unzip the toolbox by emailing the authors as described on the SSm GO download page.
2. Latex
   Install a Latex distribution like MikTex (http://www.miktex.org/) for Latex based pdf documentation.
3. R
   Install the statistics program R (www.r-project.org), if you do not have the splines toolbox from MATLAB and want to use splined driving inputs or spline based error bar estimation.
4. Graphviz
   Install Graphviz from http://www.graphviz.org. Graphviz is used for automatic species positioning in the PottersWheel Model Designer.
5. SBML toolbox
   Install the SBML toolbox from http://sbml.org/software/sbmltoolbox if you often import SBML models. PottersWheel is compatible with SBML toolbox versions 2 and 3. Follow the installation instructions given in the software documentation. Alternatively, use the PottersWheel web service to convert SBML files within your user account, since the SBML toolbox installation might not be straightforward on your system, especially for Matlab R2006b and below due to incompatible mex libraries.
6. CVODES
   Install the Sundials Matlab toolbox in order to apply the CVODES integrator. Please follow the description given in pwInstallSundialsTB.
7. Fast integration for Windows 32 bit users
   In order to use fast numerical integration, platform-dependent external C and Fortran compiler are required. For MS Windows 32 bit, please download lcc-win32.exe from http://www.cs.virginia.edu/~lcc-win32/ and install it in C:\lcc if possible. Download fortran.exe from http://www.filewatcher.com/m/fortran.exe.453574.0.0.html and install it into the same folder C:\lcc. The folder C:\lcc\bin has to be added to the Windows PATH variable: Select Start > My Computer, then right click and select Properties > Advanced > Environmental Variables > System Variables > PATH. Here you will see a list of program folders separated by semicolon (;). Just append ';C:\lcc\bin'. (Matlab has to be restarted after changing the Windows path variable.)

Troubleshooting (Windows only)

If pwCheckSystem cannot find one of the installed external programs Graphviz, R or Latex, open a Windows command window (in Windows XP, select Start and then Run. Type cmd to call the DOS prompt).

1. Type ‘dot –V’, ‘R’, or ‘latex –version’, respectively.
2. If the program is not available, you must change the system PATH variable.
3. To access the PATH variable, select Start > My Computer, then right click and select Properties > Advanced > Environmental Variables > System Variables > PATH. Here you will see a list of program folders separated by semicolon (;).
4. Just append the missing program, e.g. ‘;C:\Program Files\R\R-2.2.0\bin’ for R, or ‘;C:\Program Files\ATT\Graphviz\bin’ for Graphviz.
5. Close and reopen the Windows command window and check whether Windows finds the programs now.
6. If Rterm, instead of R is available, go to the R installation folder and copy Rterm.exe to R.exe.
7. Restart MATLAB after a change to the PATH variable is instituted.