[Bioperl-l] Proposal for AI methods in Bioperl
palmeida at igc.gulbenkian.pt
Wed Oct 12 12:59:57 EDT 2005
I have used GALib in the past, a C++ library for Genetic Algorithms, which
could give you some ideas.
It is located here: http://lancet.mit.edu/ga/
There is an overview here: http://lancet.mit.edu/galib-2.4/Overview.html
On Wednesday 12 October 2005 17:09, Hilmar Lapp wrote:
> You might want to look at the WEKA project for some design guidance and
> inspiration. The home page is at http://www.cs.waikato.ac.nz/ml/weka/
> and the API is documented at http://weka.sourceforge.net/doc/
> Something that's equally well structured I think could be a generally
> useful contribution. I'd expect that to use a lot of compiled code
> though, number crunching just isn't what perl is best at.
> Also, it may be worth checking out the dp package in Biojava for
> dynamic programming algorithms.
> On Oct 12, 2005, at 12:05 AM, Mauricio Herrera Cuadra wrote:
> > 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.
> > --
> > MAURICIO HERRERA CUADRA
> > arareko at campus.iztacala.unam.mx
> > Laboratorio de Genética
> > Unidad de Morfofisiología y Función
> > Facultad de Estudios Superiores Iztacala, UNAM
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
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