Table of contents

1. Installation instructions for the Windows binaries distribution
2. Installation instructions for the open-source distribution
3. Optional third-party software
4. Testing the installation

Installation instructions for the Windows binaries distribution

1. Unzip the Spectral Networks package to c:\specnets (or another directory of your choice).
2. Execute mglinstaller.exe (just press Enter when asked where to install).
3. Add "c:\specnets;c:\specnets\bin\win32" to Window's PATH environment variable.
4. If necessary, restart your computer for Windows to refresh the environment variables.
5. Test the installation by opening a DOS window and running specnets example.params from c:\specnets\example.

Installation instructions for the open-source distribution

Before installing Spectral Networks:

• Matlab must be installed before using this package; details on the installation of Matlab can be found on Mathworks website.
• Compiling this package requires a standard C++ compiler - a Makefile is provided for GNU gcc.
• Support for mzXML files requires the Xerces-C library. Runtime binaries can be downloaded from the Xerces stable distribution.

Installing Spectral Networks

1. Edit the Makefile and change XERCES_ROOT to the directory where you installed the runtime binaries for Xerces-C. Also change CC if you're using a different compiler.
2. Run make
3. Add the Spectral Networks directory to Matlab's search path:
   • In Windows, choose the menu item "Set Path..." from the "File" menu.
   • In Unix, edit (or create) your startup.m file and use addpath.
4. In Unix, you may also need change the environment variable LD_LIBRARY_PATH to include the path to Xerces-C library files.

Optional third-party software

Spectral networks can be visualized using Graphviz, an open-source visualization tool available here. See the Results section for details on where to find the spectral networks graph files.

Testing the installation

1. cd to the directory containing the example data and parameters file (default is "cd c:\specnets\example")
2. run "specnets example.params"
3. see Results and Analysis for an explanation of how to interpret the results and parameterize the spectral networks analysis.