Hi,
I have been running Linux as my primary OS for about 4 yrs. I have a
strong computer science background, but am a molecular biologist by
training. Recently we got a Pentium II 400 in the lab which I setup
a linux partition on (~8gig). It is running KDE 1.1 with the KDM
login manager (so everything is GUI to the non computer types in the
lab). I have also setup the KDE mime types to atomatically recognize
certain extensions and run the appropriate molecular biology program.
The use of the system is fine for newbies, but setup and administration
are going to require mucking around on the command line. I can't
comment specifically on primer design, but here are some of the apps
we use:
GDE (The Fristensky lab has some nice gde menues available at
http://home.cc.umanitoba.ca/~psgendb/index.html#SOFTWARE)
ClustalX (Great GUI alignment program)
ClustalW
Alscript (For generating publication quality alignments)
DBWatcher (For automatic periodic blast searches, remote or local)
tacg (Great Program for digest maps)
readseq and seqio for sequence file format conversion
Here is an "ls" of my bio directory to give you a hint at what is out there:
Install dotplot2ps predator-2.1.2
Patterns-1.0.3 etc primer-3.0.3
alscript-2.04 fsap-4.0 procheck-3.4.4 bin
gde-2.2 readseq-930201 boxplot97_only_mesa
gde-2.2-old saps-sspa-04111996 boxshade-3.3.1
lib seqio-1.2.2 cleanup-1.8.3
man seqsee-1.3
clustalw-1.7 misc shadybox-2.0.3
clustalx-1.65b naview tacg-2.35
codontree-1.2 ncbi tnimage-2.8.1b
dbwatcher-2.01 ncbi-6.0 treetool-2.0.2
dna-gui-2.0 njplot viennaRNA-1.2.1
dna-tools-1998 phylip-3.5 xylem.1.8.3
On the Non Bio side of software:
Netscape (free)
Star Office (free, can read MS Office 97 stuff)
WordPerfect 8.0 (free)
Acrobat
[ Free may mean for non-commercial use only. ]
If setup right, a linux system can provide you with a great stable
multiuser research workstation; but it is going to take you a log more
time to setup than a MSWindows computer.
I should note that there are several efforts out there to build
free newbie friendly analysis tools. Seqpup, JaMBW, Loci, and
my own GST. JaMBW and Seqpup would be the most mature whereas Loci and GST
are pre pre alpha (ie no usable code yet).
-Alan
Linux and Bio Relevent Links:
SAL.KachinaTech.Com/Z/2/index.shtml
liposome.genebee.msu.su
http://evolution.bmc.uu.se/~thomas/mol_linux/index.htmlhttp://zifi.genetics.utah.edu/~zinc/linux/linux-apps.htmlhttp://alt-www.uia.ac.be/u/pvosta/pcrbioc.htmlhttp://www.gdb.org/Dan/softsearch/softsearch.html
Other Relevent Links:
home.cc.umanitoba.ca/~frist/ (Fristensky Lab)
golgi.harvard.edu/gibert-bi.html (Gilbert Lab)
barton.ebi.ac.uk or geoff.biop.ox.ac.uk
www.genetics.wustl.edu/eddy/software/
www.embl-heidelberg.de/~toldo/JaMBW.html
ftp://area.ba.cnr.it/pub/software/ftp://ftp.bio.indiana.edu/
Jil Tardiff <jtardiff at westnet.com> wrote:
: The sorts of analyses we need to do are mostly centered around primer
: design (this is the *big* issue), restriction maps, protein/nucleotide
: alignment and sequence editing.
: So, my question is this: do you folks think it is worthwhile to add a
: Linux partition to the lab machine and just use Linux for our DNA
: analysis needs? I know that a number of packages exist for Linux, but
: if any end-users could tell me about their experiences and suggestions
: for the most user-friendly programs, I would greatly appreciate it. My
: student is a complete Linux/UNIX newbie, so I would like to make this as
: straightforward as possible for her. I'm also intrigued by GDE, but
: setting it up seems a bit formidable.
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Alan Williams (finger alan at avocado.ucr.edu for pgp public key)
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University of California, Riverside "Where observation is concerned,
Dept. of Botany and Plant Sciences chance favors the prepared mind."
Alan at Avocado.UCR.edu -- Louis Pasteur
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