XRambo: a Bayesian Monte Carlo parameter estimation program for NMR data



© 1997 BY MICHAEL ANDREC AND JAMES H. PRESTEGARD
ALL RIGHTS RESERVED.


The authors ask that you read and abide by the conditions stated in the COPYRIGHT file included in the source code distribution.

This software is distributed in the form of a gzip-ed .tar file containing all of the required source code, and may be downloaded from the Prestegard lab WWW page (http://glyco.chem.yale.edu). The code presupposes that you have the X11 and Motif 1.2 libraries installed in the normal search path of the C compiler. If you do have the libraries, but they are not in the standard search path, you will need to modify the Makefile to include the explicit paths. Also, the Makefile uses the F77, I77, and isam libraries, which are necessary for the proper linking of objects generated from fortran code on IRIX systems. This may not be necessary on other systems. Your milage may vary. This can be easily changed by editing the "LIBS = " line of the Makefile.

This software has been compiled sucessfully on SGI INDY workstations running IRIX 5.3 and 6.2, and should be readily compilable on other systems. Some compilation problems have been reported using LINUX, the source of which we have not been able to trace. If you attempt to compile this package on a system other than IRIX, please let us know of your successs (or lack thereof) and what modifications had to be made so that we can get a better idea of the portability of the package and reduce the heartache for future users.

1) Uncompress and un-tar the distribution file

	gzip -d XRambo_source.tar.gz
		(or XRambo_all.tar.gz)

	tar xvf XRambo_source.tar
		(or XRambo_all.tar)

2) Do a simple "make":

	make

3) If there are problems with the lexer or parser generation (i.e. you do not have lex or yacc, and make complains that it doesn't know how to make y.tab.c or lex.yy.c), then "precompiled" versions of y.tab.* and lex.yy.c can be found in the directory "lexyacc". Simply copy those files up one level to the main source code directory, and try "make"-ing again.

4) Upon sucessfull compilation, copy the executable "xrambo" to a convenient location (such as /usr/local/bin), and copy the X resource file "Xrambo" to an appropriate location (either the user's home directory or a global location such as /usr/lib/X11/app-defaults). Note that XRambo WILL NOT WORK without the X resource file.

5) We highly recommend that you obtain a sufficiently powerful data visualization program to plot the resulting Monte Carlo samples. We have had great sucess with the "Xgobi" package from Bellcore. XRambo does not contain any visualization or plotting features (although it probably should).

6) READ THE DOCUMENTATION AND BE CAREFUL!!!!! This is actually very important, because naive use of Bayesian Monte Carlo sampling can lead to absurdly wrong "fits" of the data. Carefully monitor the progress of your burn-in convergence, and use your spectroscopic common sense: if a parameter estimate seems fishy, it probably is. The authors assume no responsibility for mis-use of this software.

Although you may modify the code within the restrictions stated in the COPYRIGHT file, we recommend that you do not (except for your own user.c routines as described in the full documentation), unless you are ready to undertake some challenging electronic archeology. As mentioned in the documentation, this software grew out of research-grade, proof-of-principle code, and is quite sprawling. This is especially true of the Motif GUI code. This software probably ought to be rewritten from the ground up... :-(


Best of luck, and happy parameter estimation!

Michael Andrec (the programmer responsible for this package)
andrec@cabm.rutgers.edu

James H. Prestegard (the principle investigator who supported it)
jpresteg@ccrc.uga.edu