Installation

  1. Toolbox download
  2. Installation procedure
  3. Toolbox requirements

Toolbox download
The toolbox can be downloaded from this web page, in the section Home. The name of the toolbox is as follows: 'DOTcvpSB_RXXXX_YN.zip'. The letters mean:
Installation procedure
The installation procedure consists of several steps listed below:
  1. If you have an older installation of DOTcvp, please remove it. This helps to avoid possible compatibility problems.
  2. Unzip the packed file into any directory. To unzip the toolbox the user needs a password which is free to receive. The unziped file contains the name and date when the 'zip' package was created. This helps to recognize a new package of the toolbox. It is recommended to use the latest version of the toolbox.
  3. You can try to download and use some demonstrative examples from this web page and extract them into a 'dotcvp_examples' directory. Of course any different directory can be used.
  4. The next step is the toolbox installation. First, you should start MATLAB and change to the directory where DOTcvp was unpacked, and then run 'dotcvp_install.m' install file. If everything is all right the user will see the following output procedure:
    Installation in progress .................................
    Checking the previous version of DOTcvp .................. not found - OK!
    Setting paths for DOTcvp into a MATLAB environment ....... done!
    Generation of a MATLAB file with path settings ........... done!
    Getting MATLAB version ................................... done!
    The right mex file of SUNDIALS is preparing .............. done!
    Creating f77.bat file needed for the FORTRAN compilation . done!
    
    You can freely modify the following file with the toolbox path settings:
    D:/ your directory /DOTcvp/DOTcvp_paths.m
    
    The installation passed without any problems, enjoy this toolbox!
    This procedure inserts all necessary paths into a MATLAB environment. If you use a different directory for illustrative examples you should specify a proper path into the 'dotcvp_paths.m' file which is generated during the installation procedure. In this file, it is possible to set all necessary paths for saving results from the optimization, simulations, etc. Note, if you quit MATLAB environment, all paths will be deleted, so you need to run the 'dotcvp_install.m' file with the new start of MATLAB again. This time, the 'dotcvp_paths.m' file stays unmodified.
  5. From this moment, everything should work correctly. Enjoy this toolbox!
Toolbox requirements
The toolbox distribution includes most of the needed external solvers: IVP solver CVODE (part of SUNDIALS suite), and (MI)NLP solvers ACOmi, DE, IPOPT, MISQP, MITS and SRES. The Optimization Toolbox is needed if the user wants to use FMINCON as a NLP solver. FORTRAN compilation to speed-up computations is secured by a combination of gnumex and MinGW, packages which are distributed with the toolbox as well. On the other hand, the Symbolic Math Toolbox is needed if automatic generation of sensitivities and Jacobian are desired (recommended). Users must install the SBML and libSMBL toolboxes in order to be able to import SBML models.

In case the user chooses FORTRAN as compiler, the GCC compiler distributed by MinGW will be used. This compiler is directly implemented into the extended toolbox package. For more information about the MATLAB mex files, please have a look on the following web link from the Mathworks web page.

The toolbox is stated and successfully tested on MATLAB versions 7.0-7.7 [2008b] under WINDOWS operating systems. The newest MATLAB versions do not support precompiled libraries for MITS, ACOmi, and MISQP.

If you find any problems, or you have only comments, questions, please do not hesitate to contact us via email!