[BiO BB] Please guide me

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Mon Feb 2 07:43:09 EST 2004

++ Austin Tanney--
> 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?
> Austin

Although having said that, some friends of mine are working on a 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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