[Bioperl-l] Proposal for AI methods in Bioperl

[Hilmar Lapp]

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.

	-hilmar

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
>
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>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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