Sniping on the new (was: what software do biologists need?)

khofmann at biomed.biolan.uni-koeln.de khofmann at biomed.biolan.uni-koeln.de
Wed Mar 24 05:29:13 EST 1993

In article <9303232146.AA04558 at net.bio.net>, 
CLARK at SALK-SC2.SDSC.EDU (Steve Clark) writes:

- some interesting points ommitted -

>A major problem that a lot of biologists have is that they don't want to 
>pay a lot of money for software. I can understand that - the way the 
>granting agencies are these days, not many people can afford to buy several 
>packages at a few thousand dollars each until they find one they like. At 

One addition here: I work in a lab (and I know of several others) where the
head of the department sees absolutely no need to pay any amount of money
for sequence analysis software (this 'computers are good for games only'
while the people who need to have their sequences analysed have to restrict
themselves to free or home-written software.

- more omitted -

>	So there are three choices. Use public-domain, freeware or 
>inexpensive shareware programs and put up with the little bugs, lack of 
>support and upgrades, maddening inconsistancies, etc, or spend a lot of 
>money for commercial software and put up with smarmy salespeople, little 
>bugs, lack of support and upgrades, maddening inconsistancies, etc. The 
>third choice is to write your own code, or hire someone to do it for you. 
>That can be a very expensive proposition in terms of time and/or salary.
>(Of course, in truth there are some excellent programs that are 
>freely available that are supported and maintained by the author(s), and a 
>few commercial programs that aren't a total waste of money.)

I totally agree with Steve in his evaluation of the benefits and drawbacks
of commercial vs. PD software. 
I clearly prefer PD software and like to make some comments on PD, freeware
and shareware:

- I disapprove shareware, at least in science. In my opinion, the typical
  situation of a non-professional program author in science is that he/she
  writes the particular program for his/her own needs and in many cases
  is paid for it anyway by the employer. Why does the programmer try to
  earn money with the product and not share it with his/her fellow researchers?

- more generally, I don't see the point in writing copyright-protected small
  pieces of software in science, unless you are forced to do so by some
  Putting a copyright on the program prevents others from modifying the 
  program for their own needs. There is hardly any source code with copyrighted
  software and what is so unfavourable in letting others improving your

- A major drawback in almost all PD/freeware/shareware programs dedicated to
  SEQUENCE ANALYSIS is the restriction to a particular sequence format.
  I thought that using Don Gilbert's READSEQ and similar routines, it should
  be possible to write format-independent software, this would enlargen the
  group of people able to apply the program substantially.
  (since most of these programs have no sources available, it is not possible
   to include routines for dealing with different sequence formats later)

- I think that far more software is written by researches all over the world
  that could be used by others. Why are such relatively few programmers
  willing to let others use their programs, too? 

Phew, I feeling much better now.
Any comments?

Kay O. Hofmann                            Tel.: +49 221 478-6980
Institut fuer Biochemie (med. Fak.)       Fax.: +49 221 478-6979
Universitaet Koeln
Joseph Stelzmann Str. 52          Internet: khofmann at biomed.biolan.uni-koeln.de
D-5000 Koeln 41                             khofmann at gen1.genetik.uni-koeln.de

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