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jsherfey / dnsim

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

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

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

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.