Hi Jan,
Perhaps R's excellent bioconductor project could be mapped nicely into
Incanter (Clojure's R) ?
Edmund
On 27 Jun 2010, at 23:15, jandot wrote:
> Hi all,
>
> I have been a ruby user for several years and have contributed to the
> bioruby toolkit for bioinformatics. Lately however I got interested in
> clojure as it's a functional language and should be very good for
> working with the huge datasets we have to handle.
>
> Although there are bioinformatics toolkits for many OO languages
> (biojava, bioperl, biopython and bioruby), nothing similar exists for
> clojure yet. And I'd be interested to start building such toolkit
> while I learn the language. At first for my own use, but maybe
> later... who knows.
>
> Being new to functional languages, I wonder how such a toolkit would
> be best approached. In an OO language you create classes with
> properties and methods that describe one particular entitiy in the
> field. For example: you define a DNASequence class with a "name" and
> "sequence" property, and a method to print it out in an international
> standard text format, and another method for translating the DNA
> sequence in that of the resulting protein. Much of the functionality
> of these toolkits is about retrieving a bit of information,
> manipulating it and ultimately writing it to screen/file.
>
> As functional languages are more about verbs than nouns: how could a
> bioinformatics toolkit be idiomatically set up? Would it still be the
> Right Way (TM) to create some type of classes, a-la OO?
>
> For more information on the OO toolkits, see www.bioperl.org, www.biojava.org,
> bioruby.org and biopython.org.
>
> As clojure (especially combined with incanter) seems to be a very good
> candidate for future work in bioinformatics, I would very much welcome
> a little discussion on this.
>
> Many thanks,
> jan.
>
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Edmund
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