[Dynamite] revised bosc abstract fyi

[Guy Slater]

Cool.  I like this abstract a lot now.

Guy.
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On Mon, 10 Jul 2000, Ian Holmes wrote:

> ---------- Forwarded message ----------
> 
> Hidden Markov Models (HMMs) have been used successfully for a wide
> range of applications in bioinformatics including protein domain
> classification, signal peptide recognition and gene prediction, among
> others.  New developments such as Fisher kernels suggest that HMMs
> have plenty more to offer and that many ideas remain unexplored.
> 
> Many computational biologists express interest in trying out new kinds
> of HMM architecture for novel problems. In practise, this means
> writing or otherwise leveraging code to handle:
> 
>  (a) arbitrarily structured HMMs
>  (b) mathematical manipulation of likelihood derivatives and calculus
>  (c) training algorithms
>  (d) very fast dynamic programming routines for database searching
> 
> Several free software packages exist that can do some of these things, but
> the absence of a free package with all these capabilities means that
> experimenting with HMMs often necessitates writing a lot of specialised
> code.
> 
> Telegraph picks up where one previous Open Source project -- Dynamite
> -- left off.  Begun as a collaboration between the EnsEMBL group in
> Cambridge and the Berkeley Drosophila Genome Project, Telegraph's
> primary goal was to formalise the functionality of Dynamite while
> adding capabilities essential for machine learning.
> 
> Enrichments of Telegraph over Dynamite include a supportive
> infrastructure for working with likelihood calculus (including
> training, priors, sampling, posterior probabilities and Fisher
> kernels) as well as a modular design with an XML exchange format
> linking the higher-level Perl object model to a fast C engine.
> 
> The BOSC and ISMB 2000 conferences coincide with Telegraph's "going
> public", and we strongly hope that potential developers, users and
> testers will contact us during or after the meetings.  As an
> incentive, there will be a repeat of Dynamite's now-legendary offer of
> a bottle of champagne for the best bugfinder at each release.
> 
> As the number of biologists interested in experimenting with HMMs
> rises, while the computational demands of the latest algorithms exceed
> the capabilities of any one centre, the potential for a "lingua
> franca" in which sequence analysis tools can be described and
> exchanged is high.  We very much hope that you will be interested in
> becoming involved in any capacity, be it as a user or a developer, and
> that you'll contact one of the following Telegraph co-ordinators:
> 
>   Ian Holmes  -- ihh@fruitfly.org
>   Guy Slater  -- guy@ebi.ac.uk
>   Ewan Birney -- birney@ebi.ac.uk
> 
> 
> _______________________________________________
> Dynamite mailing list  -  Dynamite@bioperl.org
> http://www.bioperl.org/mailman/listinfo/dynamite
> 

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%!PS % <------ Guy St.C. Slater ------> http://www.ebi.ac.uk/~guy/  <------
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