[BiO BB] Please guide me

Austin Tanney Austin.Tanney at arragen.com
Mon Feb 2 04:22:04 EST 2004

I have to say I am very much with Dan on this one. Java and Perl work for bioinformatics applications. If someone is going to learn a programming language, why not learn one that will be more generally applicable. Bioperl and Biojava have already made a lot of headway into creating a lot of shortcuts for bioinformatics applications anyway. If a specific language was developed purely for bioinformatics, people would still need to learn that language.. if you are going to take the time to learn a language why not learn one that you can use for more than just bioinformatics?


> 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.

sounds like the tower of babel gone wrong - java, perl, c, all are good for
bioinformatics, laying the concepts on top is the tricky part, and the more you ask
a language to do for you, the more 'locked in' to a particular mind set you get.
Traditional programing languages are good because of the freedom of they give -
beyond that it is a matter of taste. I do not think each dicipline of science should
have its own language. subroutines yes, dialect no.

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