[BiO BB] Please guide me

Andrius obj at obj.hopto.org
Fri Jan 30 08:37:59 EST 2004

Michael Gruenberger wrote:

>On Fri, 2004-01-30 at 12:53, Andrius wrote:
>>when i was mentioning common schema i wasn't considering database schema 
>>(structure). such global database
>>schema won't make sense since everyone may have different requirements. 
>>i meant common schema as a common communication
>>protocol. yes, it's not a right word, it came from web services, xml 
>Oh sorry I misunderstood you. A common XML schema would indeed be quite
>interesting, but still different databases would have very different
>needs and I'm not sure if it would be feasible...
i was still talking about using xml derived from common xml schemas for 
communication purposes. anyway, i still
haven't done a concise reasearch of bioinformatics tools and can't say 
if something is already implemented, it may.

>>etc. and yes, new bioinformatics language would make
>>lot more for community. indeed, i see some confusion about why should 
>>every bioinformatician use perl (well, perl comes first when you ask 
>>google)... nor it's designed for it, nor it make learning path easier 
>>(time to come and do research). i think the new language should be
>>developed, language which makes good string processing as perl does and 
>>introduces constructs/objects which are familiar for people with 
>>biological background.
>So you mean something like Mathematica for Bioinformatics. Yes, I guess
>that would be useful, but what would it do that BioPerl or BioJava can't
>do? You have the advantage that programmers already know Perl of Java
>and can just plug in the new API's for bioinformatics. A bioinformatics
>language would have a much steeper learning curve, so it would have to
>offer some considerable advantages.
i'm looking forward for scientists to have research tools such as 
programming languages for their
specific field so everyone could develop their own research routines and 
systems. commercial packets
are too closed for this. we need java for bioinformaticians, but it 
should be independant of java (or any other
general programming language) , because java expresses too much of 
object oriented programming, constructs which confuse researcher without 
computer science background. i want all (at least researchers) to be 
programmers, because full computational potential can be
grasped having a right customizable tool ( such as programming 
language). i just have some intuition and if you have something
to add i'll be happy to hear.


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