[Dynamite] revised bosc abstract fyi

[Ian Holmes]

---------- 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