Summary of Mac genetics software (vs. GCG)
Tae Bum Shin
tshin at fas.harvard.edu
Sun Sep 3 14:36:17 EST 1995
Thanks to everyone who answered my question about Mac programs
that are comparable to GCG. The recommendations include: GeneWorks,
MacVector, DNAStar, Vector NTI, and the X-windows interface to GCG
(WPI). Some also mentioned that the speed of GCG on a UNIX box cannot be
duplicated on a Mac. To judge for yourself, I've excerpted comments at
the end of this message.
Thanks again to the following people!
Lucien Bachner <bachner at Cassini.genethon.fr>
Gregg Wells <wells at biochem.dental.upenn.edu>
Francois Jeanmougin <jeanmougin at titus.u-strasbg.fr>
Carolyn Blake <csb at aretha.jax.org>
"Daniel B. Oerther" <oerther at students.uiuc.edu>
Jeff Shumaker <informax at access.digex.net>
Dr. JOAO V. COSTA <jcosta at gulbenkian.pt>
David Wang <ddw2 at midway.uchicago.edu>
Shan <duncan at loris.cisab.indiana.edu>
Patrick Martin <martin at microcide.com>
tshin at fas.harvard.edu
I think you can find Mac packages giving more or less GCG features
but you will not have the power you have with GCG-Unix.
I must admit this fact despite the fact that I am
a Mac fanatic lover.
Take a look at GeneWorks from Intelligenetics (800-876-9994). I
currently use MacVector and am stuck with it because of the price of
changing (any such molecular biology software costs >$2500). If I could
buy a new package, I would go with GeneWorks. I cannot compare it to
GCG, but get a demo disk and check it out.
I'd test a package named DNA star, two or three years ago. It gives
some of the most important functions of GCG. in other and, you will never
have the power of a UNIX machine (or DEC) on a mac. This will give headhake
to your system manager to index the databases on a Mac. (big disks with
fast accesses are, for me, not easy to manipulate). More than that, I was
never able to run the equivalent of the gelaseemble programm correctly.
I think that it will be better to buy some 17" screens and install
MacX and then run GCG under the WPI (Wisconsin package interface). It needs
to learn a little bit and waste one or two hours to understand how it
works, but it will take less time than to find and test and learn a new
package, even on a Mac.
Never forget that research needs liberty, that is in informatic
synonyme of complexity, and that GCG is the most open package that will
ALWAYS be in the TOP of the research (in terms of algorithm, matrix AND
a number of our scientists decided on the GeneWorks Mac program.
i don't know how it compares with GCG functionality, however. there
is currently a movement here to get GCG, since that's what postdocs
et al are used to from their university experience...
i think you should check with GCG first, though, and see if they've
got a Mac interface to their package. i know they've got an X-windows
interface that, in the worst case, you could probably run on a Mac
using MacX or eXodus.
I know that Kodac Co. has a package called MacVector which does many of
the same things through a window interface. MacVector relies heavily
upon either CD ROM or Internet connection to access the data from the
NCBI database (GENEMBL, and Medline, and Prosite(?)) Anyway, if you had
a decent server client interface within your department, it might be
worth trying. Best of Luck.
May I respectfully ask you to check out our web site, InforMax, Inc. at
the URL listed in our .sig.
Vector NTI is the best plasmid drawing, construction, design and pcr
software available on the market.
We are currently working on a sequencing/alignment application as well.
If you are interested in contacting us all the information is there.
I have two packages for the Mac: MacVector from IBI/Kodak and GeneWorks from
Intelligenetics. They are comparable in features but most of my students
prefer MacVector because it seems more friendly. Both do database searches
but they take a lot of time. I think they can't compare with GCG.
Both programs are VERY expensive.
I had the same problem with young people used to the Mac OS and unfamiliar
with command line language. However, this has been considerably solved with
the new graphical interface of version 8 of GCG. Since I am used to the old
Unix style, it was not a wonder for me, but some of my students welcomed
the new WPI interface.
I hope this helps.
My name is David Wang and I'm in charge of building a molecular biocomputing
cluster here at the University of Chicago.
As you may have noticed, the UNIX version of GCG isn't exactly the easiest
thing in the universe -- it is not intuitive and there are far too many
commands and options.
This is why, at the UofC, we are providing full support for the Ver8.1 of the
GCG package under the X-window emulation mode. You might want to check it out.
If you aren't aware of the development pathway, GCG just came out with an
X-window interface to GCG.
In real terms what does it mean?
It means that it looks and feels like any other windowed program.
Additionally, if you have X-window emulators running on IBM or Macs, it
can be pseudo-native.
You should check it out.
Doesn't the GCG have a point and click - GUI interface using X
considering that i had to do this same evaluation for our company two
years ago, i'd say that "LaserGene" from DNAstar (somewhere in Wisconsin,
I think) is the clear winner, with a much more extensive set of
general biochem/molbio utilities than any other Mac-based package
available at the time. I looked at many mac apps, including MacVector
and IntelliGenetics' "GeneJockey", and while Genejockey came close
in overall utility and flexibility, LaserGene wins out.
we ended up sticking with GCG partly because the industrial license is
$6,000 (GCG is $12,000, but you get complete source code) and
partly because we need size and speed for some of our applications
(we have a Sun SPARC20+64 MB RAM for this)
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