Hi, I am using Clojure for bioinformatics, but not the same kind of stuff. I am writing a stochastic simulator.
Would love to discuss more about your idea though. You can have something quite close to what you describe as the OO approach with protocols and data-types. + by using defrecord, you can easily have generic functions. That would the easier approach, I think. I will have a look to bio*. But if you want to start a project, count me in. On Sun, Jun 27, 2010 at 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, 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. > > -- > 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<clojure%2bunsubscr...@googlegroups.com> > For more options, visit this group at > http://groups.google.com/group/clojure?hl=en -- 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
