Installation

Installation is platform dependent. Please find your platform below and follow the directions there.

Windows

Windows is currently the easiest platform on which to install SynBioSS DS. There is an all-in-one installer that includes the necessary runtime files and the SynBioSS DS executable. Installation has no options and just installs into the default programs directory (Administrator access is required).

  1. Download the SynBioSS DS installer. [download]
  2. Double-click the downloaded file to install.
  3. If your are running Windows Vista, click “Continue” to allow the installer access to your programs directory.
  4. SynBioSS DS is installed. Find the entry in your Start Menu under “SynBioSS DS”

Linux

For two distributions, the linux install is easy. Unfortunately, because of library issues it seems impossible to release a binary version that just runs on all distributions. Of course, the source code will still run on your system, even if it’s not SLED or Ubuntu, it’ll just take a little more work on your part (See the Run from Source option).

SLED

  1. Download the SynBioSS DS for SLED tarball. [download]
  2. Extract the tarball (Using Ark or File Roller or the following command)
    tar zxf SynBioSS-1.0-x86-SLED.tgz
  3. If a terminal is not already open, open one.
  4. Change directories until you are in the SynBioSS-DS-1.0 directory.
  5. Type:
    ./run-synbioss

Ubuntu

  1. Download the SynBioSS DS for Ubuntu tarball. [download]
  2. Extract the tarball (Using Ark or File Roller or the following command)
    tar zxf SynBioSS-1.0-x86-Ubuntu.tgz
  3. If a terminal is not already open, open one.
  4. Change directories until you are in the SynBioSS-DS-1.0 directory.
  5. Type:
    ./run-synbioss

Mac OS X

  1. Install native GTK+ for Mac OS X (click here for instructions)
  2. Install PyGTK. Type the following command:
    jhbuild pygtk
  3. Open a jhbuild shell
    jhbuild shell
  4. Continue with the “Run from Source” directions below.

Run from Source

For all of these steps, if your distribution has the package in its package management system you should use it. Otherwise use the installation instructions in that step.

  1. Download and install Numpy. [download]

    cd numpy-1.1.1
    tar zxf numpy-1.1.1.tar.gz
    python setup.py build
    sudo python setup.py install
  2. Download and install NetCDF. [download]
    tar zxf netcdf-4.0.tar.gz
    cd netcdf-4.0
    ./configure
    make
    sudo make install
  3. Download and install PyCDF. [download]
    tar zxf pycdf-0.6-3c.tgz
    cd pycdf-0.6-3c
    python setup.py build
    sudo python setup.py install
  4. Download and install libSBML with Python bindings. [download]
    unzip libsbml-3.2.0-src.zip
    cd libsbml-3.2.0
    ./configure --with-python
    make
    sudo make install
  5. Download and install Sympy. [download]
    tar zxf sympy-0.6.2.tar.gz
    cd sympy-0.6.2
    python setup.py build
    sudo python setup.py install
  6. Download and install Unum. [download]
    tar zxf Unum-4.0.tar.gz
    cd Unum-4.0
    python setup.py build
    sudo python setup.py install
  7. If PyGTK is not installed, perform steps 8 and 9, otherwise skip to step 10.
  8. Download and install PyGObject. [download]
    tar zxf pygobject-2.15.2.tar.gz
    cd pygobject-2.15.2
    ./configure
    make
    sudo make install
  9. Download and install PyGTK. [download]
    tar zxf pygtk-2.12.1.tar.gz
    cd pygtk-2.12.1
    ./configure
    make
    sudo make install
  10. Download Hy3S and put the binaries on the system PATH. [download x86 Linux]

    cd /usr/local/bin
    sudo tar zxf Hy3S-1.1.5-x86-Linux.tgz
  11. Download, extract and run SynBioSS DS. [download]
    tar zxf synbioss-1.0.tar.gz
    cd synbioss-1.0
    python synbioss.py

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