[BiO BB] Please guide me

Andrius obj at obj.hopto.org
Fri Jan 30 10:20:36 EST 2004

Michael Gruenberger wrote:

>On Fri, 2004-01-30 at 13:37, Andrius wrote:
>>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.
>So was I. My point was that different databases have very different data
>sets and it would be difficult to find a common xml schema. SOAP seems
>to be a much better way forward (than plain XML + XML Schema), because
>you can customise it much more towards different needs and you don't
>have to agree on a common schema. It also seems to be what most
>databases are implementing at the moment (see BioMoby).... 
>>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.
>Well... in an ideal world... but in my experience there are two kinds of
>researchers: The one's who are really into computers and know a couple
>of programming languages and wouldn't mind learning Java. The other kind
>(the majority) is those who can use web interfaces, but don't really
>want to know anything more about computers and wouldn't want to learn
>even a really simple language. So it's a good idea, but is there a
>'market' for it?
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).



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