[Bioperl-l] Re: Request for advice and pointers on a project to h elp biologists d o simple formatting and analysis

Chris Fields cjfields at uiuc.edu
Thu Mar 10 14:07:21 EST 2005

I completely disagree.  I am a biologist first and a programmer second 
(shock!!!), though I believe that many full-time bioinformaticians would 
agree with my view.  I could spend an enormous amount of time trying to 
accomplish a routine repetitive task in Perl, Java, or whatever your 
language of choice is.  However, the Bioperl (and OpenBio) community has 
made my job much easier.  ANY contribution, whether it is a module, 
package, or a script, is helpful, as long as someone can use 
it.  Furthermore, To make the snap judgement that every biologist entering 
the field already comes equipped with the tools is a bit short-sighted and 
naive.  I do agree that there are many "non-specific" tools (i.e. multiple 
methods for phylogenetic analysis, multiple alignment, etc), but I think 
that any person worth their salt would find that to be a benefit and not a 
problem.  I personally like having multiple methods available.

I could also make the argument that the "experts" in the field, if they 
live up to that title, can actually design the tools for their specific 
(specialist) needs.  Who better knows their specific needs anyway.  In 
other words, why hire a carpenter to do the plumbing?  It doesn't make much 
sense to have somebody with little to no knowledge on RNA structure, for 
example, to design an algorithm ad hoc for another RNA structure expert.

Anyway, I think we're getting a bit off topic here...

My two cents,


At 09:41 AM 3/10/2005, Malay wrote:
>Hello Amir:
>Without going into any arguments, I'll put my two cents into it. The 
>mentality to help out biologists is a fundamental mistake. Most of the 
>biologists who come into this field already knows the tricks of the game, 
>if not they hire someone who knows. But toolmakers in the fields believe 
>they have to help biologists, that's why there are too many 
>non-specialized tools in the field.
>Toolmakers should now concentrate on tools for specialists. There are 
>where the main dearth is and it requires a great effort to actually 
>satisfy experts in the field. Create tools for the experts if you can.


Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer


University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
600 S. Mathews Ave.
Urbana, IL 61801

Phone : (217) 333-7098
Fax : (217) 244-5858 

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