EBP download

EBP has been implemented as an analysis module that can be integrated into the Sashimi suite of proteomic software tools, developed at the Institute of Systems Biology, Seattle, WA. EBP can be run as an alternative to ProteinProphet as part of the Sashimi Trans-Proteomic Pipeline.

The Trans-Proteomic Pipeline and EBP are available as downloads for the Windows platform. They run using the Unix emulator Cygwin. Before installation your PC will need to be configured to use the IIS webserver. Then you can download the Trans-Proteomic Pipeline using the Cygwin installer. Finally, download and install EBP.

Installation Instructions

1. Make sure the Microsoft webserver application IIS is installed and working properly. For instructions on configuring your PC for the Trans-Proteomic Pipeline click here.
   
   
2. Install the TPP/Cygwin package found at http://tools.proteomecenter.org/TPP.php
   
   
3. Make sure that all the configuration changes are complete, including changes to the PATH and environment variables, tpp-bin virtual directory, and so on. The details are here.
   
   
4. Enable remote writing to the tpp-bin and data directories by opening a cygwin console and typing:
   
   cd ${WEBSERVER_ROOT}
   chmod -R 777 tpp-bin/
   chmod -R 777 isb-bin/data/
   
   You may also have to change the owner of these directories to your local system account name using:
   
   chown IUSR_****
   
   where **** denotes the local system name.
   
   
5. Install ONLY the latest "make" package and "gnuplot" package using the cygwin setp found at http://www.cygwin.com
   
   
6. Check the PATH variable and if necessary change it to ensure that it includes c:\cygwin\bin and c:\cygwin\usr\X11R6\bin
   
   
7. Download, save, and untar the EBP Windows Distribution.
   
   
8. Go to the directory where the EBP Windows Distribution is saved. Open the make file and change the path variables if necessary to tailor the installation to your system configuration.
   
   
9. Run "make install-windows". Check for errors. You may have to make further alterations to the makefile.
   
   
10. RESTART YOUR MACHINE
    
    ==== TESTING ===
    
    
11. You should be able to use the newly installed pipeline to analyze peptides and proteins from the Cygwin console using the xinteract command. A sample datafile is available here. Make a new directory C:\inetpub\wwwroot\isb-bin\data\test. Untar the file in this new directory and then run xinteract by typing:
    
    tar -xzf test.tgz
    xinteract summary*.xml
    
    See the ISB documentation for details on running xinteract.
    
    
12. Once you run xinteract on a sample dataset, use the interact.xml file that it creates as the input to EBP. For details on how to run EBP type
    
    perl ebp.pl
    
    in the Cygwin console. Start by running EBP using the default settings:
    
    perl ebp.pl -r interact.xml -O ebp.xml
    
    Note that large datasets will tend to run slowly due to the computational demands and memory burden.