Review of sequencing software in J of NIH Rsrch

Howard Cash cash at geneva.csmil.umich.edu
Tue Dec 21 19:09:49 EST 1993

On 1 Dec 93 15:34:58 GMT, Tim Burcham (timb at apldbio.com) wrote:
> Harry writes:
>>See: The Journal of NIH Research, Vol 5, No 10, p 81-82 for one (not very
>>complementary) view of it.  I saw one at a local meeting but the rep
>>couldn't tell me what the advantages were over BLAST/fasta.  I can't see
>>anyone spending that kind of $ on such a specialized piece of hardware -
>>well I guess I can - they built the B2, the space shuttle, and several
>>billions worth of aircraft carriers.
> I won't comment on most of this (I'm obviously biased ;-), but the article
> cited should be considered an ADVERTISEMENT, not a research article. Look
> for a response in an upcoming issue of Journal of NIH Research. The
> INHERIT system used in the study was PRE-RELEASE TEST VERSION. INHERIT is
> now undergoing it's fourth iteration since that test version was released.
> The current iteration includes a MAJOR HARDWARE CHANGE from the test system
> that was reviewed in Journal of NIH Research.
> I sorry you didn't get a good demo. 
> Look into Journal of NIH Research and their editorial policies. You will 
> probably be as disgusted as I was...
> ---------------------------------------------------------------------------
> Tim Burcham                                                 Data Products R&D
> timb at apldbio.com                                           Applied Biosystems
> (415)570-6667                                           850 Lincoln Centre Dr
> (800)874-9868                                           Foster City, CA 94404

Tim, I feel I must respond to you on the net because your comment was made
in this very public forum.  Though you may not have had all the facts 
when you wrote your message, it was unfair to The Journal of NIH Research
and misrepresents the involvement of my employer, Gene Codes.  (PLEASE READ

The article in the October issue of the Journal of NIH Research clearly
starts out with "Submitted by Gene Codes, Inc.," so I can see where you 
might think that the Application Note was "ghost written" by someone connected
with Gene Codes.  Let me bring you up to speed:  The J. of NIH Research makes
available space for Application Notes only to advertisers.  Fair enough.  Gene
Codes was invited to take more ads and to submit an Application Note on its 
product.  The company decided to buy the advertising space but to invite a 
user to write an  independent article.  Dr. Salser's group at UCLA had been 
doing large scale sequencing and had made heavy demands on the software, so 
he was invited to write something about how the program was used in his own
laboratory.  Speaking for myself, I assumed that he would use the article
to describe his high-volume sequencing work or his comparative sequencing 
of genes related to ataxia telangiectasia.  We did not suggest nor did we 
expect an article describing the department's long-term comparison of 
different sequencing programs.  In point of fact (and I realize you may have 
not been told by your supervisor, Tim) nobody at Gene Codes even saw a DRAFT 
of the article until the day it was submitted to the Journal of NIH Research.

In summary, I would make two points:  First and most important, I do not 
believe that the editorial policies of The Journal of NIH Research deserve 
such derision.  If anything, the article in question was overly cautious 
by stating in large type that the authors were nominated by Gene Codes, even 
though Gene Codes was not involved in any way with either the research or 
the reporting.  Secondly, to say that the article is an advertisement is true, 
but the context of your posting implies that it was written by or with the
influence of Gene Codes.  That happens to be untrue, though you may have been
honestly mistaken.

I will respond to mail or postings from anyone who wants clarification 
or additional details on how the article "DNA Sequence Assembly and Editing 
Products Which Permit Direct Visualization of Raw Data Traces From 
Automated Fluorescent Sequencing Data" was written or selected, or how the
author was chosen.  In deference to Dr. Kristofferson's concerns, I have not 
mentioned the name of our commercial software and I will not respond to 
email asking for information on that product.

Howard Cash

University of Michigan    
Gene Codes Corporation, Ann Arbor, MI
GeneCodes at AOL.com
Phone 313-769-7249
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Disclaimer.  Please Read.
I am an employee of and a stock holder in Gene Codes Corp.  Although 
bionet.software is an UNmoderated newsgroup (yes, that surprised me, too!)
I want to be sensitive to Dave's concern about commercial discussion
on the internet.  This text, as well as postings that have gone before, 
have been reviewed by our systems administrators here at the University of 
Michigan for fairness and appropriateness to the net, as well as by other 
regular contributors to this discussion group.  The text was also reviewed 
and approved by Dave Kristofferson and found to be appropriate in light of 
the negative statements about the Journal of NIH Research and the 
Application Note published in the October, 1993 issue.  Neither my views 
nor the conclusions reached in the cited article are a reflection of any 
official position of the University of Michigan or CSMIL.
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