The clojure way seems to be to do as much as possible with functions on raw (immutable) data, rather than building up object systems. The sequence is already one of clojure's primary abstractions, and it may not always *need* to wrapped in something like defrecord. (Though for some applications, I'm sure it will.)
Anyway, I'd be interested in contributing, whatever design decisions are ultimately made. Rob On Jun 28, 11:22 am, 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
