NCBI needs help

Tom Schneider toms at fcs260c2.ncifcrf.gov
Fri Jul 3 12:11:55 EST 1992

In article <1992Jul2.153711.26151 at ccu.umanitoba.ca> frist at ccu.umanitoba.ca writes:

>However, there is only  a very limited amount of money to pay for those
>products. In my opinion, the availability of tools such as those from NCBI
>is potentially a great boon to science, as well as a very economical
>step. It costs the taxpayer a lot less if an agency like NCBI produces
>tools that everyone can use. Shouldn't that be a consideration?

I do not agree with the cost argument, since a contract can specify that
software becomes public domain.

The issue, as I see it, is whether NCBI should be in the software business or not.

First, we now all agree that it is absolutely essential to have a centralized
sequence database.  This is spread over three physical locations, Japan, EMBL
and USA, but they now work (pretty) closely with each other.  (The fact that
there are still comments in GenBank which have not been translated indicates
that this task has not yet been completed.)  This is essential to avoid
redundant sequence entry.

Second, it is impossible to create, maintain and distribute a large database
without software.

Third, database software should be smartly written.  ASN.1 is a great first
step in this direction.

Fourth, only the database people can write the tools to access the software.
This task cannot be separated from their day-to-day work.

Fifth, database access software must be in the public domain.  It makes no sense
to have hundreds of programs with different methods of accessing the data.
If the database is changed, the asn1toolkit gets changed and this will save
a huge number of programs from being broken.

Sixth, there is still plenty to do that software companies could contribute.
  1.  A tool, written in OpenWindows PostScript which would let me "fly"
      around the database and see what is there, with colored symbols.
      (Unfortunately, this depends on objects in the database having
      types and names, which the company cannot do.)
  2.  A service to scientists to help them create the best entries possible
      (Based on the Definition of GenBank, written by GenBank!!)

Seventh:  Search software, such as BLAST, is a continuation of David Lipman's
research.  By doing this research NCBI keeps in touch with current problems in
molecular biology.  This is very important because it makes them sensitive to
what people need.  As with the asn1tools, this has to be placed into the public
domain, having been done at a government institution.  Note that commercial
groups could not take over the BLAST project, because they don't have the
people who wrote BLAST.  Of course they are free to do their own competing
research if they want.

This line of thinking seems quite clear to me.  It leads me to conclude
that NCBI should be producing and distributing software.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms at ncifcrf.gov

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