dnsim

Dynamic Neural Simulator - a modular modeling tool for large ODE models.

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Setup as Matlab Toolbox (Linux)

1. Download DNSim
   1. Method 1 -- Download zip:
      1. web: http://infinitebrain.org/setup
      2. Click "Download DNSim toolbox"
      3. Unzip DNSim (dnjsim-toolbox_vXX.zip)
   2. Method 2 -- Use Git to download https://github.com/jsherfey/dnsim :
      • enter on the shell: git clone https://github.com/jsherfey/dnsim.git
   3. Either way, once done, make an environment variable for where you unzipped it
      • e.g. by entering on the shell echo "export DNSIM=/path/to/dnsim/here" >> $HOME/.bashrc ; source $HOME/.bashrc
2. Run DNSim
   • from the shell: matlab -r "dnsim"
   • from the MATLAB Command Window: dnsim
   • Tips:
     • if Server Portal is slow, increase MATLAB MAX_JAVA_HEAP (Preferences --> ...)
     • create alias to launch DNSim GUI
       • e.g. add to file ~/.bashrc: alias dnsim='cd ~/dnsim; matlab -r "dnsim;"'
     • make sure you are in the $DNSIM directory to load/run the toolbox in MATLAB

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Setup as Standalone Application (Linux)

1. Download DNSim
   1. web: http://infinitebrain.org/setup
   2. Click "Download DNSim application"
   3. Unzip DNSim (dnsim-application_vXX.zip)
   4. Make an environment variable where you unzipped it
      • e.g. by entering on the shell echo "export DNSIM=/path/to/dnsim/here" >> $HOME/.bashrc ; source $HOME/.bashrc
2. Download MCR Installer
   1. web: http://www.mathworks.com/products/compiler/mcr/index.html
   2. Click the MCR download for Matlab R2013a and your operating system
   3. Install MCR
      1. Unzip MCR Installer (MCR_R2013a_XXX_installer.zip) into $DNSIM/MCRinstaller
      2. Run Installer commands:
         • Linux: run $DNSIM/MCRinstaller/install
         • PCs: run $DNSIM/MCRinstaller/setup.exe
         • Mac: run $DNSIM/MCRinstaller/InstallForMacOSX
      3. See readme.txt for more info
3. Copy paths/environment variables given for $LD_LIBRARY_PATH and $XAPPLRESDIR to file: $DNSIM/run_dnsim.sh
   • to see what these environment variables' values are, enter echo $LD_LIBRARY_PATH into the shell
4. Run DNSim from the shell via $DNSIM/run_dnsim.sh or cd $DNSIM ; ./run_dnsim.sh
   • Tip: don't forget to replace $DNSIM = /path/to/dnsim/here with your own directory in your ~/.bashrc.