This is MCPD release 2.0
========================

Markov Chain Pooling Decoder (MCPD) was developed at Los Alamos National Laboratory.

What is it?
-----------

MCPD is a software package for performing decoding of pooling design
experiments necessary in screening of clone libraries. MCPD uses a
Markov chain Monte Carlo method for estimating posterior probability
of a clone being positive given test results for the pools.  The
posterior probability can be used to select ``likely'' clones for
confirmatory testing and thus reduce the total number of tests
necessary.


To use this software you should read: 
E. Knill, David C. Torney and
Alexander Schliep.  Interpretation of Pooling Experiments Using the
Markov Chain Monte Carlo Method. Journal of Computational Biology,
Vol. 3 (3), 1996, pp. 395-406.


Copyright: 
---------- 

Copyright, 1994-1997, The Regents of the University of
California. This software was produced under U.S. Government
contract(DOE W-7405-ENG-35) by Los Alamos National Laboratory, which
is operated by the University of California for the U.S. Department of
Energy. The U.S Government is licensed to use, reproduce, and
distribute this software. Permission is granted to the public to copy
and use this software without charge, provided that this Notice and
any statement of authorship are reproduced on all copies. Neither the
Government nor the University makes any warranty, express or implied,
or assumes any liability or responsibility for the use

This work was performed under the auspices of the U.S. Department of
Energy under Contract No. W-7405-ENG-36.



The Distribution:
-----------------

Files: 

  MCPD.h	Interface definitions for the MCPD
  MCPD.c 	Its implementation
  MCPDMain.c	Command line user interface
  Random.h      Random number generator interfaces
  Random.c      Helper functions


Documentation:
  README	This file
  MCPD.tex	A short user guide for the software (read the paper!)

Sample files:

  sample.dsg	Design file (actually the cla I design described in the paper)
  sample.res    An result file


Building and installing:
------------------------

Unpack and run make. Move the binary whereever you want to move it to.



Bugs:
-----

None known at this time (but I bet there are some). I used quantify
and purify on the code, so I suspect it should be working.



Things to come:
---------------

Callable interface for tcl/python/perl. With some help from SWIG I had
no problems integrating MCPD into any of the scripting languages. I
have to clean things up and decide how I want things to work. I
probably throw in a WWW-Interface with a python CGI-script.


Different random number generator. Something portable and better than
what we are using right now.



Info:
-----

Alexander Schliep
Center for Parallel Computing (ZPR)
University of Cologne
Weyertal 80
50931 Cologne, Germany

Tel: +49-221-470-6011 (w)
FAX: +49-221-470-5160

Email: schliep@zpr.uni-koeln.de
WWW:   http://www.zpr.uni-koeln.de/~schliep/MCPD