[Bioperl-l] Proposal for AI methods in Bioperl

Michael Seewald mseewald at gmail.com
Wed Oct 12 03:53:53 EDT 2005

Hi Mauricio,

You might want to check out R (r-project.org <http://r-project.org>) and its
biostatistical modules (bioconductor.org <http://bioconductor.org>). As much
as I love perl/bioperl, R is the place to go for OS biostatistics computing.
You will duplicate a lot of functionality, if you start implementing e.g.
neural networking in perl/bioperl. It *may* be worthwile, however, to take
some of the C code from R in order to use it in perl calls. I would consider
this only, if perl code/speed/parsing outweighs the R code you need.


On 10/12/05, Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
> Hi all,
> As far as I know, there aren't any modules in Bioperl providing access
> to Artificial Intelligence (AI) methods such as neural networks, genetic
> algorithms, cellular automata, among others.
> At the moment, I'm interested in developing some interface for using
> genetic algorithms. By using the interface, users could access these
> methods for generating optimized schemes based on sets of homologous
> sequences. I think that the generated results could be a nice
> alternative for motif/pattern searching in diverse novel sequences
> (instead of regular expressions, HMM's and other methods). What do you
> think?
> Any guidance would be really helpful. If you know of any external
> application that you can recomend for using with the interface, a
> suggested location in the code tree, etc., please let me know. I've
> thought of something like a Bio::AI family that can be included in the
> bioperl-live or maybe as a bioperl-ai package. I'm open to all kind of
> thoughts. Thanks in advance.
> Regards,
> Mauricio.
> --
> arareko at campus.iztacala.unam.mx
> Laboratorio de Genética
> Unidad de Morfofisiología y Función
> Facultad de Estudios Superiores Iztacala, UNAM
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