Bryson, K.,
Luck, M.,
Joy, M.S.,
Jones, D.T.,
Nicolas, P.,
Bessieres, P.
and Gibrat, J.-F.
(2002)
From GeneWeaver to Agmial.
In: Network Tools and Applications in Biology Workshop on Agents in Bioinformatics (NETTAB 2002), 12-14 Jul 2002, Bologna, Italy.
Abstract
We report on our experiences of developing two multi-agent
systems for bioinformatics called GeneWeaver and Agmial.
The concepts behind these systems are described and the
results of experimenting with di�erent agent communities
are given.
The GeneWeaver system provides one possible view of an
architecture which may be used to deal with organizing and
managing bioinformatics data and methods in a distributed,
dynamic environment. Experiments with the GeneWeaver
system reveal bene�ts both in terms of keeping data up-todate, and also in terms of analysis method accuracy.
However, one clear limitation of the GeneWeaver system
is that it has never actually been deployed as an open system between laboratories. A number of reasons exist for this lack of true open deployment. These include the lack of mechanisms to deal appropriately with security and trust between agents, and the lack of a standard, widely adopted agent communication language for inter-agent communication.
Some of these aspects are considered in the second system,
called Agmial, which is currently under development.
It uses some of the standards and technologies which have
arisen since the development of GeneWeaver to provide a
system which, at least theoretically, could provide the basis for an open community of bioinformatics agents. Its approach is one based on the Web services framework, each
agent being deployed as a Java servlet, using XML Protocol
for inter-agent communication and HTTP for human-agent
communication.
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