> Applications
Amber
Version: 7
Description: A program for molecular simulation using
mechanical force fields that were developed for proteins and
nucleic acids.
Path: /nfs_exports/apps/gnu-apps/amber
Max CPUs per job: 16
Comments: Contact John.Obenauer@stjude.org for assistance with Amber.
ClustalW-mpi
Version: 0.13
Description: A general purpose multiple sequence alignment
program for DNA or proteins. It produces biologically meaningful
multiple sequence alignments of divergent sequences. It calculates
the best match for the selected sequences, and lines them up
so that the identities, similarities and differences can be
seen.
Path: /nfs_exports/apps/gnu-apps/clustalw
Max CPUs per job: To be determined
Comments: Contact Perdeep.Mehta@stjude.org for assistance with ClustalW
hmmer
Version: 2.3.1
Description: HMMER is a freely distributable implementation
of profile HMM (hidden Markov models) software for protein
sequence analysis. Profile HMMs can be used to do sensitive
database searching using statistical descriptions of a sequence
family's consensus.
Path: /nfs_exports/apps/gnu-apps/hmmer
Max CPUs per job:
Comments: Contact John.Obenauer@stjude.org for assistance with HMMER.
MeMe
Version: 3.0.4
Description: A tool for discovering conserved motifs
in a group of related DNA or protein sequences.
Path: /nfs_exports/apps/gnu-apps/meme
Max CPUs per job: 24
Comments: Contact Suraj.Mukatira@stjude.org for assistance with MeMe.
mpiBLAST
Version: 1.1.1
Description: A freely available open source parallelization
of NCBI BLAST. mpiBLAST segments the BLAST database and distributes
it across cluster nodes, permitting BLAST queries to be processed
on many nodes simultaneously
Path: /nfs_exports/apps/gnu-apps/mpiBLAST
Max CPUs per job: 28
Comments: Contact Scott.Malone@stjude.org for assistance with mpiBlast.
R
Version: 1.7.1
Description: R is `GNU S' - A language and environment
for statistical computing and graphics. It provides a wide
variety of statistical and graphical techniques linear and
nonlinear modeling, statistical tests, time series analysis,
classification, and clustering.
Path: /nfs_exports/apps/gnu-apps/R
Max CPUs per job: 1
Comments: R is not a parallelized application, meaning
one job submission can not use more than one processor. You
can submit multiple, single cpu jobs to increase the throughput
of R. Check out the Job Array Information from Platform Computing
on how to make repetitive submissions.
http://www.science-computing.de/produkte/lsf/html/5.1/admin_5.1/G_jobarrays.html Contact Xiaoping.Su@stjude.org for assistance with R.
