Bonjour Nicolas, I've started using clojure for my bioinformatics work, but it is still *very* early days. Will try to become more proficient in it, but slowly building up a toolkit for myself might just be the seed for bioclojure. Have no idea to what extent clojure is used at the moment in the field.
Will have a look at protocols and defrecord. Will keep you informed if/ when I think I can take it further. jan. On Jun 28, 7:22 pm, Nicolas Oury <nicolas.o...@gmail.com> wrote: > 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, 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<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
