Mac plasmid programs?

Harry Mangalam mangalam at SALK-SC2.SDSC.EDU
Wed Jan 6 15:04:19 EST 1993


Scott Monsma writes:
>Is anyone aware of Mac programs for keeping records of plasmid constructs?
>Such program would hopefully also draw graphic maps of the plasmids,
>and keep sequence information.  Thanks!

   As a matter of fact, yes....  Check out the program Gene Construction
Kit - an excerpt a critically disclaimed review follows (also check Peter
Markiewicz's reviews on the same (but older version of the) program.

Gene Construction Kit by Textco (vox/fax: 603 643 1471) is also a
relatively new entry but it is an extremely interesting cloning tool.  All
of the previously mentioned programs allow you to 'clone electronically',
but GCK is optimized for it (and does nothing else).  It is made only for
the Mac and while it may run on B+W Macs, it really requires a color
monitor to show its stuff.  It combines elements of a drawing program and
sequence editor to allow you to cut and paste elements of a number of
sequences together to form new constructs.  It remembers the history (even
multiple histories) of the sequences you use to clone, what enzymes you
used to clip the sequences, what you did to the ends to allow ligation (and
prevents you from performing biologically impossible operations); whatever
you create, you have a detailed construction history.  It now also allows
boolean searches of the associated text boxes in which you store any
comments.  In this way you could for instance, search all your "electronic
freezer" for any constructs that had a luciferase reporter gene AND amp AND
tet but NOT kan resistance genes.  
   Besides being a great idea, it is also extraordinarily easy to use.  The
last program that attempted this trick was a piece of work from
Intelligenetics called Stratagene (A great idea, if only they hadn't made
it for _only_ a $30,000 Xerox LISP workstation and demanded about $50,000
for the software).  Despite my aforementioned rage at demos, there is an
excellent demo-tutorial of GCK available at the usual archives
(ftp.bio.indiana.bio, in the IUBIO Software+Data/molbio/mac folder by
gopher).  
   There is also a new demo available direct from the company.  From my
experience with the new demo and its very reasonable cost (especially
compared to the amount of aggro and wasted time that a questionable
contruct can bring to a lab) there is no reason why any cloning lab should
be without this bit of software.  Surprisingly enough, it is also available
as a networked version, one of the few that is - however, Textco has taken
a somewhat contrary approach in pricing - they base their pricing not only
on the number of copies you buy (the more, the cheaper, as usual), but also
on the number of Macs that can be served (the larger the number, the more
expensive).  There is a logic to it, but it is not the usual logic 8). 
And, unlike the DNASTAR network license, GCK uses Keyserver, which allows
you find out how many keys are checked out, who has them and for how long. 
For a largish institution, this allows (evil word follows) recharging for
use, if anyone cares. 

   Later today, I'll upload the demo mentioned within to the Indiana (if
there's still room) and U Houston archives.  You can also get it direct
from our anonymous FTP server - FTP to salk-sc2.sdsc.edu, login as
anonymous, any password, get the 890K(!), binhexed, self extracting archive
named GCK_DEMO.SEA_HQX (it's a VAX, he said apologetically) in the
directory [anonymous.mac].

Cheers
Harry

Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                        1'   mangalam at salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                   2'        hjm at salk-sgi.sdsc.edu
La Jolla CA 92037                         3'         mangalam at salk.bitnet






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