[387] in Software_Announce
for biological software, `add seven'
daemon@ATHENA.MIT.EDU (Matthew Belmonte)
Thu Jan 18 15:30:45 2001
Date: Thu, 18 Jan 2001 15:29:44 -0500 (EST)
Message-Id: <200101182029.PAA24347@mattababy.mit.edu>
From: belmonte@MIT.EDU (Matthew Belmonte)
To: sofa@MIT.EDU
Reply-To: seven@MIT.EDU
Cc: seven@MIT.EDU
The `seven' locker, a project of the Student Information Processing Board
(SIPB), is a collection of biological (i.e., Course 7) software. The locker is
debuting with three packages: AFNI, Genscan, and Biopython.
AFNI (Analysis of Functional NeuroImages) is a collection of programs for
viewing and analysing functional magnetic resonance images of the brain. Our
AFNI installation includes all of the programs and plug-ins in the standard
AFNI distribution, as well as statistical plug-ins developed at SIPB.
Documentation on AFNI is at "/mit/seven/doc/AFNI98/"; please read the README
file in that directory in order to find the specific file that contains the
documentation that you're looking for. A formal description of AFNI appeared
in the June 1996 issue of _Computers and Biomedical Research_, and a reprint of
that article is at "http://varda.biophysics.mcw.edu/~cox/afni_paper1.ps". A
formal description of the SIPB statistical plug-in will appear in the March
2001 issue of _IEEE Transactions on Medical Imaging_, and a preprint is at
"http://www.mattababy.org/~belmonte/Publications/Papers/01_PermutationTest/".
AFNI is installed for Solaris, IRIX, Linux, and Digital UNIX.
Genscan, written by Chris Burge of the Biology Department, is a tool for
predicting the locations and exon-intron structures of genes in genomic
sequences. It's invoked with organism-specific parameter files using one of
three commands: genscana (for arabidopsis), genscanm (for maize), or genscanv
(for vertebrates). Documentation is at "/mit/seven/doc/genscan/genscan.txt".
Genscan is installed for Solaris, IRIX, Linux, and Digital UNIX.
The Biopython package can be used to process common biological sequence
formats and databases in python. The modules are in
"/mit/seven/lib/python2.0/site-packages/Bio/", and can be used by attaching
the seven locker and adding that path to sys.path in your python programs. A
description of the package is at
"http://www.bioinformatics.org/bradstuff/bp/api/". Biopython is installed for
Solaris, IRIX, and Linux.
Bug reports and comments should be addressed to seven@mit.edu. If you have
ideas as to software that you'd like to see installed in the seven locker,
please consider joining us as one of the seven maintainers.
