[BiO BB] Please guide me

Andrius obj at obj.hopto.org
Fri Jan 30 11:47:37 EST 2004

Michael Gruenberger wrote:

>On Fri, 2004-01-30 at 15:20, Andrius wrote:
>>i'm sure real world will demand it. it's kind of a feeling when you 
>>doing research with such tools..it
>>reminds me open source climate a lot. the thing is... sometimes even 
>>programmers do not think in a real way.
>>they tend to follow 'practices' and there's little few who follows their 
>>brain. you may disagree and of course i can ask:
>>does our today 'market' demand thinking? same for research i think. as 
>>long as researchers demand tools which
>>allow them to think free ( and gain better results this way ) there's a 
>>market for such tools. of course it may not be mainstream,
>>but there's nothing wrong with that. i'm not much familiar with research 
>>routines (i'm still graduating for bachelor) and people in it, but i 
>>have few friends there. they tend to say that even in academic world 
>>there's a lot of serial writing (i mean writing papers just to increase 
>>curriculum) and there's no surprise such people do not demand open 
>>thinking tools. and there's nothing wrong with that again:) as long as 
>>there's bunch of people who care about a quality of their work (research).
>Yes, you are right, researchers need (computer) tools, but they need to
>be very easy to use and a new programming language would also have to be
>very easy to use. What would your bio-language look like? What would
>make it easier to use than existing BioJava or BioPerl? Bioinformatics
>is a very wide field (I work on two projects at the moment, one is
>mainly database stuff, the other one 3D images). What would your
>language focus on? 
it may be pluggable, but i don't want to speculate. i just have an idea 
for a future. in short
we can build language for JVM for example which uses all what Java ( 
notice 3d here too) can provide but completely hiddens  it from
bioinformatics programmer. i'm sure i'll find problems with existing 
solutions (bioperl and biojava) when i put my hands on it. and yes,
ease of use is a main reason for such custom language. and i guess it 
means how language is presented for a researcher. i doubt
plain java is applicable.


More information about the BBB mailing list