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Installation
The software can be downloaded from the box on the right hand side of the overview webpage. Afterwards add the code folder /arFramework3
to your MATLAB search path.
Further topics:
[TOC]
- MATLAB (best R2010 or newer)
- MATLAB Symbolic Toolbox
- MATLAB Optimization Toolbox
- (optional: MATLAB Statistics Toolbox)
Take care to setup your MATLAB mex compiler correctly.
The parallelization uses the pthread
package. This only work for Unix type operating system, for instance Linux or Mac OS X. On Windows systems parallelization is disabled.
The source code of our community based software is stored on a Mercurial server on BitBucket ssh://[email protected]/d2d-development/d2d-software and can be reached via SSH. We recommend to use the freely available SourceTree (Mac) or TortoiseHG (Linux) software for managing the repository and for contribution to the software.
The initial steps to fetch the D2D software repository are
- Install SourceTree
- Set user name and email
- Click in "add repository" button in the upper left conner of the window
- Source URL: ssh://[email protected]/d2d-development/d2d-software or https://[email protected]/d2d-development/d2d-software without the use of a public key-chain file
- Destination Path: select our local path for the D2D software repository
- SourceTree will fetch the most recent version of the software from the server
To upload changes, open SourceTree, select the respective changes that have been automatically detected, click "commit" and "push". Please also give a informative description what you changed.
To download the most recent updates of the software from the D2D server, select the respective updates that have been automatically detected and click "pull".
##Troubleshooting with installation on Mac
Installation of Matlab and the D2D software on new Mac versions might lead to technical problems. Below, you can find a series of hints that proved helpful:
- Installation of Xcode with "command line tools" component is required.
- (This step might be optional) Link the gcc command in
/usr/bin/gcc
to/usr/bin/gcc-4.2
usingsudo ln -s /usr/bin/gcc /usr/bin/gcc-4.2
- (This step might be optional) For saving plots as PDF and generating reports, link the corresponding commands to
/bin/
, e.g.:sudo ln -s /usr/local/bin/ps2pdf /bin/ps2pdf
. Repeat this for all required files. - Edit
~/.matlab/yourmatlabversion/mexopt.sh
. The default setting forSDKROOT
is wrong for recent versions of MacOS and has to be replaced with:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk
- For R2013a: Download the patch according to your OSX version from http://www.mathworks.de/support/solutions/en/data/1-FR6LXJ/ at the bottom of the page and follow the instructions to install the patch
- Installation and system requirements
- Setting up models
- First steps
- Advanced events and pre-equilibration
- Computation of integration-based prediction bands
- How is the architecture of the code and the most important commands?
- What are the most important fields of the global variable ar?
- What are the most important functions?
- Optimization algorithms available in the d2d-framework
- Objective function, likelhood and chi-square in the d2d framework
- How to set up priors?
- How to set up steady state constraints?
- How do I restart the solver upon a step input?
- How to deal with integrator tolerances?
- How to implement a bolus injection?
- How to implement washing and an injection?
- How to implement a moment ODE model?
- How to run PLE calculations on a Cluster?