NetMHC 3.0              INSTALLATION INSTRUCTIONS


   DESCRIPTION

   NetMHC 3.0 software  predicts binding of peptides to a number of different
   HLA alleles  using artificial neural networks (ANNs) and  weight matrices.
   The method is described in detail in the following three articles:
   
   Sensitive quantitative predictions of peptide-MHC binding by a 'Query by
   Committee' artificial neural network approach.
   Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S,
   Fomsgaard A, Hilden J,Holm A, Brunak S.
   Tissue Antigens., 62:378-84, 2003.

   Reliable prediction of T-cell epitopes using neural networks with novel
   sequence representations.
   Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S,
   Brunak S, Lund O.
   Protein Sci., 12:1007-17, 2003.

   Improved prediction of MHC class I and class II epitopes using a novel
   Gibbs sampling approach.
   Nielsen M, Lundegaard C, Worning P, Hvid CS, Lamberth K, Buus S, Brunak S,
   Lund O.
   Bioinformatics, 20(9):1388-97, 2004.

   More information about the method can be found at:
   
      http://www.cbs.dtu.dk/services/NetMHC/


   DOWNLOAD

   The NetMHC 3.0 package  is a  property  of  Center for Biological Sequence
   Analysis.  It may be downloaded  only  by special agreement.  For academic
   users there is a download site at:

        http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC

   Other users are requested to contact software@cbs.dtu.dk.


   PRE-INSTALLATION

   NetMHC 3.0  will run on the most common  UNIX platforms e.g.  Linux, SunOS
   etc. The package consists of two files:
  
      netMHC-3.0.readme         this file
      netMHC-3.0.<unix>.tar.Z   compressed TAR archive

   where 'unix' is the UNIX platform on which you are about to install. After
   installation the software will occupy less than 8 Mb of diskspace.


   INSTALLATION

   0. Make sure that PYTHON (ver. 2.3 or better) is installed on your system.
      Specifically, the module 'datetime' must be installed.

   1. Uncompress and untar the package:

      cat netMHC-3.0.<unix>.tar.Z | uncompress | tar xvf -

      This will produce a directory 'netMHC-3.0'.

   2. In the 'netMHC-3.0' directory edit the script 'netMHC-3.0':
   
      a. On the first line of the script replace the string:
     
         /usr/local/python/bin/python
	 
	 with the full path to the PYTHON executable on your system.
      
      b. At the top of the file  locate the part labelled  "GENERAL SETTINGS:
         CUSTOMIZE TO YOUR SITE"  and set the 'preddir' variable  to the full
	 path to the 'netMHC-3.0' directory on your system.

   3. Still in the 'netMHC-3.0' directory test the software:

      > ./netMHC-3.0 -a A0201 -l 8 -s test/testprot.fsa

      The output should be nearly identical to the file 'test/testprot.out'.

   4. Finish the installation:

      a. Copy or link  the 'netMHC-3.0' script  to a directory  in the users'
         path.

      b. Copy the  'netMHC-3.0/netMHC.1'  file to  a location  in your manual
         system. If you need a compiled version try running:

         man -d netMHC.1 | compress >netMHC.Z

         or:

         neqn netMHC.1 | tbl | nroff -man | col | compress >netMHC.Z

   5. Enjoy ...


   PROBLEMS

   Contact packages@cbs.dtu.dk in case of problems.
   
   Questions on the scientific aspects of the NetMHC method should be sent to
   Claus Lundegaard, lunde@cbs.dtu.dk.

   CBS, 21 May 2008
   K. Rapacki