Hi, There has been some interest towards Clojure from the cheminformatics community as well (e.g. http://blog.rguha.net/?tag=clojure ) in relation to the Chemistry Development Toolkit (CDK, http://sourceforge.net/projects/cdk) and the approach seems to be to use the CDK java classes directly in clojure or write simple wrapper functions around them and build further abstractions on top. A similar approach here would be to build bioclojure on top of biojava. Best Nik
On Jun 27, 11:15 pm, jandot <jan.ae...@gmail.com> 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, seewww.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. -- You received this message because you are subscribed to the Google Groups "Clojure" group. To post to this group, send email to clojure@googlegroups.com Note that posts from new members are moderated - please be patient with your first post. To unsubscribe from this group, send email to clojure+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/clojure?hl=en
