GCG current version feedback

Dr. Greg Quinn greg at franklin.burnham-inst.org
Wed Feb 28 09:34:32 EST 2001

David Mathog (mathog at seqaxp.bio.caltech.edu) wrote:
: 1.  What's it like dealing with GCG these days?  

I'm guessing you mean the company rather than the package; I've always found the 
people at the GCG to be very helpful and very responsive; It's one of the
few software places I've dealt with a help desk staffed with people who 
really know what they're talking about, even to the extent of dealing
with GCG admin issues.

: 2.  How is the turnaround time on maintenance requests (crucial if we go 
:        this way since wouldn't be able to maintain it ourselves anymore.) 

Answered above.

: 3.  Do "naive" users get along ok with SeqWeb or SeqLab, or are they just
:       as lost with those interfaces as most now are with the command line?  

We're probably about to take the plunge with SeqWeb here (as soon as version
2 is released), after having used W2H for some years. Martin (Senger) has done
a great job with W2H but I have concerns about whether it's still being actively 
developed (last reported W2H release December 17, 1999). SeqLab tends to be seen
still here as an 'advanced' interface here, since it requires XWindows and some
computing savvy; the days of being able to provide a UNIX command line sequence
analysis package for all (or even most) postdocs at a research facility is long 
gone; most postdocs now are increasingly brought up through doctoral training
using desktop packages such as MacVector, LaserGene, etc. Even persuading people 
to use a web interface can be tough, letalone having to learn UNIX.

: 4.  Is SeqMerge any better than phred/phrap/consed?  Is it so much better
:       that it's worth the price?

We checked into it but the pricing was prohibitive for us, as is GCG Link which 
links database searching with the Omega package. 

: 5.  What alternatives to GCG, if any, have you adopted?

EMBOSS is actively being developed by an excellent group of folks in the scientific
community but is still a ways off from being at the GCG level of functionality. The
nice aspect is that it should integrate with the W2H interface

: and just slightly off topic
: 6.  Would you be happier with the product if you had access to the source 
:       code?

Not really; in retrospect it was amazing that GCG continued to distribute source
code until they did (do you know many other sequence software companys doing that...!);
however I do understand it's changed attitudes in some parts of the scientific 
community towards the package.

My gut feeling about GCG is that it's still a bargain at the academic pricing, 
particularly since there's a lot of support available in the form of tutorials
etc, plus any number of users can access it; this is probably the biggest sticking 
point for purchasing desktop software such as MacVector, LaserGene etc in that they're
so damn expensive. 

Hope this helps

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