## 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

##
1. 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`.

##
2. 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.

##
3. 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.

##
4. 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.

Last updated October 15, 2007; maintained by Nuno Bandeira.