From: samodena@csemail.cropsci.ncsu.edu (S. A. Modena)
Newsgroups: bionet.molbio.genbank
Subject: Re: Author errors and omissions.
Date: 17 Apr 92 06:31:08 GMT
Distribution: bionet
Organization: Dept. of Crop Science, NCSU, Raleigh, NC.

In article <robison1.703430730@husc10> robison1@husc10.harvard.edu (Keith Robison) writes:
.........
.........LOTS deleted.....
>
>If I write a C program, and it contains garbage, my compiler tells me
>so.  Even better, I can run it through lint and get pages of suggestions.
>GenBank needs a lint of its own.  Upon submission to GenBank, GenLint would
>perform a wide array of checks and then report the results to the
>submitting author.  Error messages might look like:
>
>
>	Exon #5:         5' splice site does not agree with consensus 
>	Bases 0-100:     Possible Alu-derived sequences, bases 0-100
>	Bases 1000-1500: Possible vector sequences (pBR322)
>	
>
>Etc.  
>
>The best curator for any sequence is the original author, and the best
>time is when it is submitted!
>
.....alittle deleted....
>
>Keith Robison

This is one point I can't let slip by:

There is no question about the utility of a GenLint program.  The problem is:
writing it.

I'm going to take what you wrote literally: when you write a C program, it
contains garbage and your compiler balks and once your compiler is
syntactically satisfied, C-Lint offers up pages of suggestions.

Well, I struggle with writing decision support software (which is what you
wish GenBank (or whoever) was producing and using), and I think you are
asking for something that is far harder to produce than all of the mol
bio that's going on out there.

There's no glory, money or recognition in being interdisciplinary....and
that's what it will take: being a genius at software design, uncommonly
efficient at code production and frightfully knowlegable at all, ALL of
mol bio and biochem and anything that molecular is infecting currently and
in the future.

Everytime someone says: that's easy; it can be done with a simple little
program.....I know I'm talking to someone who is an UNprofessional programmer.
And the clue is: if you know that C-Lint will produce pages of suggestions,
then I know that you are an unskilled software designer and implementor. 

I don't know the details and current wisdom about the career advancement
vis-a-vis adequate, knowledgeable sequence annotation by the ORIGINAL
authors, but I know this: few of you are seeing the bigger picture. If
these things about GenBank errors and deficiencies are true, I'd suggest
that the quick-fix is to ship about 90% of your current research budgets
over to GenBank so that they can afford to get on with all those things
that you-all want done right-away for free.

I personally do not doubt that databases full of lurking errors will be
the down fall of many a "scientist," because in the end the career push
will lead many to publish garbage and then move to outright fraud when one
can no longer stand to struggle with corrupted resources.

I see no grand investment opportunity in building new software or new
software methodologies to support the genome projects or mol bio in general
because the "beneficiaries" don't sound like they are interested in
making a monetary, high-risk investment in what it's really going to take
to save your asses down the road.

Turn the sequencing machines on and let'er rip.  Produce tons of exciting
"new" DNA sequences as fast as you can and maybe no one will notice that
it's pure hack.  Patent a few of them: they'll be worth a fortune someday
when someone tries to "use" them.

There's the big investment area: patenting software concepts!  If I
patent enough algorithmic approaches to sequence search and alignment
and auto-annotations, I can bring you all to you knees with royalty
demands and patent-infringement injuctions.

:^)

If some of the above sounds rough and rude, I'm just reflecting some of
the tone I've read this evening.  Have a nice day!

P.S.  I was serious about investing 90% of your research budgets in
software R&D.

---
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|     In person:  Steve Modena     AB4EL                           |
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