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SPADE™ is written in the multi-platform language Python, and has dependencies that are also free and multi-platform. These must be downloaded and installed for non-Windows users, as described below. Please report installation problems in the Forums.


Contents

Running SPADE

To launch SPADE from the source package, double-click SPADE.py in the downloaded, unzipped directory. Windows users can run SPADE from the Desktop or Quick-Launch icons. Note that the first time SPADE is loaded it will take 1-2 minutes to compile many .pyc files. The molecular viewer and database manager are immediately available for use. Use the menu command File>>Download a PDB to query the RCSB database by accession name. Try 1otc for instance, the dimeric Telomere End-Binding Protein. Once downloaded, the given project title appears in the 'systems' listings. Select it, and launch its molecular viewer by pressing the button on its right hand side.

To download applications (which typically provide a demo project), use the menu command Downloads>>application, and select from the available listings. Once an application packet has downloaded, the new application and new demo system automatically appear in the Control Panel listings. To open a molecular viewer, click on a Molecular System and then the launch button to its right. Then launch the associated application by clicking its title in the top pane of the SPADE control panel. The application launches into a new tab in the molecular viewer window and you are free to explore its user interface.


Installation

Windows Users

Installers for SPADE and for the stand-alone Molecular Viewer are now available at the SourceForge download site. To run SequencePad, install clustalw to the SPADE main directory (typically C:/Program Files/SPADE). To run RAVE, also install matplotlib and Python Imaging Library, as described below


Linux/Mac Users

Required Core Packages:

 Python Home About Download 2.5. 
 Numpy Home About Download fast math for python.
 Scipy Home About Download Install includes lots of goodies.
 VTK Home About Download a powerful graphics library.
 Note that VTK does not automatically work with Python.
 A fix for this will be available soon. 
 For now please use Enthon, if you are in a degree-granting institution.
 Advice for non-academic Windows installation is available here.
 
 SPADE Download code is hosted by the SourceForge project.
 Decompress the downloaded Zip file with i.e. 7-zip.


Requirements for SequencePad:

 BioPython Home About Download provides Blast functionality and ClustalW access tools.
 Clustalw Home About Download Note that ClustalW may not be free for commercial use. Please read the licence here. 
 Place the executable (clustalw2.exe or clustalw2) into the SPADE directory.


Requirements for RAVE:

 matplotlib Home About Download
 Python Imaging Library Home About Download
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