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Briefings in Bioinformatics Advance Access originally published online on May 26, 2006
Briefings in Bioinformatics 2007 8(1):45-59; doi:10.1093/bib/bbl014
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Agents in bioinformatics, computational and systems biology

Emanuela Merelli, Giuliano Armano, Nicola Cannata, Flavio Corradini, Mark d'Inverno, Andreas Doms, Phillip Lord, Andrew Martin, Luciano Milanesi, Steffen Möller, Michael Schroeder and Michael Luck

Corresponding author. Emanuela Merelli, Dipartimento di Matematica e Informatica Via Madonna delle Carceri 9 62032 Camerino, Italy, Tel: +39 0737 402567; Fax: +39 0737 402565; E-mail: emanuela.merelli{at}unicam.it

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology. The collaborations gave rise to applications and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grids.

Keywords: agents, multi-agent systems, data analysis and management, biological systems modelling and simulation, grid computing, semantic web, web services, LIMS, bioinformatics, computational biology, systems biology


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