Briefings in Bioinformatics Advance Access published online on May 26, 2006
Briefings in Bioinformatics, doi:10.1093/bib/bbl014
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* To whom correspondence should be addressed. 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. Emanuela Merelli is a researcher in Computer Science at the University of Camerino in Italy and member of the COmplex SYstem Research Group. Her main interests lie in applying formal, semiformal and agent-based methods for designing software systems with applications in bioinformatics and systems biology. Giuliano Armano is currently an Associate Professor of computer engineering at the University of Cagliari, leading the IASC (‘Intelligent Agents and Soft-Computing’) group. His educational background ranges over machine learning and software agents. The above research topics are mainly experimented in the field of bioinformatics. Nicola Cannata is a Postdoctoral researcher in the COmplex SYstem Research Group, Department of Mathematics and Computer Science, University of Camerino. His main research interests include bioinformatics, computational and systems biology. Flavio Corradini is a Full Professor in Computer Science at the University of Camerino, Italy. He is the leader of the COmplex SYstem Research Group involved in studying formal methods for modelling complex systems for different application domains. He has published many books and papers on formal methods and concurrent systems. Mark d’Inverno is a Professor in Computer Science at the University of Westminster. His research has been concerned with developing mathematical models of intelligent agent and multi-agent systems, which he is now applying in a number of different contexts including biology, music, art and design. Andreas Doms is a PhD student at the Biotec of TU Dresden and a software architect at Transinsight. His interest are biomedical textmining and semantic web technologies. Phillip Lord is a Lecturer at the School of Computing Science, University of Newcastle-Upon-Tyne. His research interests lie in applying new computing technologies to biology Andrew Martin received his degree and DPhil from the University of Oxford. He is the Senior Lecturer in Bioinformatics at UCL with particular interests in antibody sequence and structure, protein modelling and the effects of mutations on protein structure and function. Luciano Milanesi is a Researcher at the Italian National Research Council (CNR). He is the head of the Bioinformatics Division of CNR-ITB. He has been Principal Investigator of many European Project. He has published more than 140 contributions in books and scientific publications in bioinformatics. Steffen Möller teaches Bioinformatics at the University of Lübeck, Germany. His research interests in agent technology have their roots in the information integration for automated sequence annotation and the collection of evidence for putatively disease-associated genes in statistical genetics. Michael Schroeder is a Professor in Bioinformatics at the Biotec of TU Dresden and CSO of Transinsight. His main interests are structural protein interactions and ontology-based literature search. Michael Luck is a Professor of Computer Science at the University of Southampton in the UK. He has published eight books and over 150 papers on aspects of agents and multi-agent systems, including in relation to the application of agents to bioinformatics.
Original Papers
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
Emanuela Merelli, E-mail: emanuela.merelli{at}unicam.it
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