NETTAB 2002 Workshop

Paolo Romano

1

& Emanuela Merelli

2

& Paolo Ciancarini

3

& Luca Toldo

4 1 National Cancer Research Institute, Genova, Italy 2 University of Camerino, Italy 3 University of Bologna, Italy 4 Merck KGaA, Germany

Bologna, 15/7/2002 BIXMAS Workshop

The acronym NET work T ools and A pplications in B iology A series of workshops focused on the most

promising and innovative ICT tools

and to their usefulness in

Bioinformatics Bologna, 15/7/2002 BIXMAS Workshop

NETTAB Formula

NETTAB workshops intend to: • • • • • • Focus on a well defined, emerging, promising ICT technology (not on a specific biological research topic) Introduce the basic knowledge analysis, in a non trivial way related to the technology under Outline the promising features of the technology in bioinformatics Show some valuable domains examples in bioinformatics or different Allow for as much discussion as possible Demonstrate “how it works” practically Bologna, 15/7/2002 BIXMAS Workshop

NETTAB Workshops

“ CORBA and XML: towards a bioinformatics integrated network environment ” http://www.nettab.org/2001/ Genova, 17-19 May 2001 ---------------- “ Agents in Bioinformatics ” http://www.nettab.org/2002/ Bologna, 12-14 July 2002 ---------------- 2003 workshop topic under definition through an open discussion on an “ad hoc” mailing lists: subscribe to nettab-discussion on bioinformatics.org

Naples / Como Lake Bologna, 15/7/2002 BIXMAS Workshop

About bioinformatics

Some aspects of bioinformatics: • Huge amount of data (DNA only 73 Gb , coming soon microarray data, metabolic pathways, …) • Exponential increase of data ( 11-15% every 3 months ), soon not locally manageable • Largely distributed information and application softwares • Heterogeneous data structures and semantics • Heterogeneous information systems • Research environment in continuous evolution and with user specific needs • Many hidden or not known information sources Bologna, 15/7/2002 BIXMAS Workshop

Desires of AiB

Desires: • Reduce data transfer , esp. for download • Avoid the need for frequent (and difficult) data updates • Avoid the need for frequent (and difficult) software updates • Avoid local data integration (warehouses) • Allow automatic detection of changes • Improve data integration • Allow semantic based data integration through ontologies • Monitor evolution of information sources Bologna, 15/7/2002 BIXMAS Workshop

Known examples

• • • • • • Infosleuth samples (MCC) – annotatation of livestock genetic TAMBIS (University of Manchester) – semantic based databanks integration GeneWeaver (University of Warwick) – MAS for genome analysis and protein structure prediction EDITtoTrEMBL (EBI) – protein sequence annotation DECAF (University of Delaware) – MAS for genomic annotation BioAgent (University of Camerino) – a mobile agent system for bioscientists Bologna, 15/7/2002 BIXMAS Workshop

AiB: Technology

•

The basic technology

The implementation of the Semantic Web , Ian Horrocks, Computer Science Department, University of Manchester , United Kingdom

•

Introduction to agents and to agents architecture and infrastructure

,

Paolo Ciancarini, University of Bologna , Italy

Bologna, 15/7/2002 BIXMAS Workshop

AiB: Perspectives

•

Perspectives

On the Use of Agents in a Bioinformatics Grid , Luc Moreau, University of Southampton , United Kingdom (+31 more authors with 6 affiliations) State: myGrid project Goal : workflow based in-silico experiments Agents uses : user agents for personalisation and negotiation over QoS, agent communication language

Bologna, 15/7/2002 BIXMAS Workshop

AiB: Examples (i)

• • • •

Good examples (i)

BioAgent: A Mobile Agent System for Bioscientists Emanuela Merelli, University of Camerino , Italy From GeneWeaver to Agmial , Kevin Bryson, Institut National de la Recherche Agronomique (INRA) , France A short report on BioMAS, a Multi-Agent System for Genomic Annotation , Keith Decker, University of Delaware , USA Integration of Heterogenous Data Sources for Proteomics and Transcriptomics , Steffen Möller, Proteom-Zentrum Rostock , Germany

Bologna, 15/7/2002 BIXMAS Workshop

Agmial

From GeneWeaver to Agmial Kevin Bryson, INRA, France State: under development Goal : analysis of Lactobacillus genomes Agents uses : development of GeneWeaver, simplified communication between agents via Web services, electronic signature, bio-ontologies

Bologna, 15/7/2002 BIXMAS Workshop

Integration of Data Sources

Integration of Heterogenous Data Sources for Proteomics and Transcriptomics , Steffen Möller, Proteom-Zentrum Rostock, Germany State: ongoing project Goal : analysis of gene expression levels for RNA and proteins Agents uses : implementation of EDITtoTrEMBL and analysis of related pros and cons

Bologna, 15/7/2002 BIXMAS Workshop

AiB: Examples (ii)

• • •

Good examples (ii)

A Knowledge Based Interface for Distributed Biological Databases , Paolo Bresciani, ITC-IRST, Trento, Italy. Web Crawling Agents for Retrieving Biomedical Information , Padmini Srinivasan, National Library of Medicine, USA An Agent Architecture for Predicting Protein Secondary Structures , Giuliano Armano, University of Cagliari, Italy

+ 8 posters Bologna, 15/7/2002 BIXMAS Workshop

AiB: How-to Three tutorials

• • •

Theoretical issues on Agents and Multi-agent Systems Michael Luck, University of Southampton, UK Agents, Middleware, and the Grid Michael Schroeder, City University of London, UK Social issues in Agent systems Andrea Omicini, University of Bologna, Italy

Bologna, 15/7/2002 BIXMAS Workshop

AiB: Discussion

• • • •

Support to the discussion

Bioinformatics applications and the web: today and tomorrow , Michele Finelli, University of Bologna , Italy Technology innovation in a service environment: HGMP-RC , Martin Bishop, Human Genome Mapping Project - Resource Center , United Kingdom The Gene Ontology Project: Content for the Semantic Web , Midori Harris, European Bioinformatics Institute , United Kingdom Bio-Agents: an industrial perspective , Luca Toldo, Merck KGaA , Germany + Open discussion with all speakers

Bologna, 15/7/2002 BIXMAS Workshop

Open discussion (i) • What’s an agent for bioinformatics?

– Consensus:

design pattern/model

(PC, KD, LM, ML) • Are Agents useful for bioinformatics?

– For query

personalisation

(MB) – To handle

dynamic

environment (ML) – But,

services

must be available (MS, PS)

Bologna, 15/7/2002 BIXMAS Workshop

Open discussion (ii) • Agents need

bio-ontologies – because of systems and data heterogeneity

• There are

concerns

about:

– security : agent = virus (electronic signature?) – IPR, Copyright: how to protect rights – QoS : agents vs common use

• A chance:

open source – develop a bio* on agents for de facto standardization and quick services development Bologna, 15/7/2002 BIXMAS Workshop

Scientific Committee

Chairman : Paolo Romano ( National Cancer Research Institute ) Co-chairs : Emanuela Merelli ( University of Camerino ), Luca Toldo ( Merck KGaA ), Paolo Ciancarini ( University of Bologna ) Members : Giuliano Armano ( University of Cagliari ), Patrizio Arrigo ( ICE/CNR ), Ana Lucia Cetertich Bazzan ( Federal University of Rio Grande do Sul ), Kevin Bryson (INRA) , Keith Decker (University of Delaware ), Angelo Facchiano ( ISA/CNR ), Vasant Honavar ( Iowa State University ), Michael Luck ( University of Southampton ), Robin McEntire ( GlaxoSmithKline ), Luciano Milanesi ( ITB/CNR ), Steffen Möller ( Proteom-Zentrum Rostock ), Luc Moreau ( University of Southampton ), Andrea Omicini ( University of Bologna ), V. S. Subrahmanian ( University of Maryland )

Bologna, 15/7/2002 BIXMAS Workshop

Organizing Committee

Chairman : Paolo Romano ( National Cancer Research Institute ) Co-chairs : Emanuela Merelli ( University of Camerino ), Luca Toldo ( Merck KGaA ), Paolo Ciancarini ( University of Bologna ) Members : Patrizio Arrigo ( ICE/CNR ), Angelo Facchiano ( ISA/CNR ), Luciano Milanesi ( ITB/CNR ), Andrea Omicini ( University of Bologna ), Rita Casadio ( University of Bologna ), Assunta Manniello ( National Cancer Research Institute ) Collaborators : Domenico Marra, Federico Malusa, Beatrice Iannotta ( National Cancer Research Institute ), Laura Bocchi, Biancamaria Gentiloni ( University of Bologna ), Gloria Rossi ( University of Camerino )

Bologna, 15/7/2002 BIXMAS Workshop

Support from

• • • •

Biotechnology Department, National Cancer Research Institute – Genova, Italy Department of Mathematics and Computer Sciences, University of Camerino, Italy Department of Computer Sciences, University of Bologna, Italy Merck KGaA, Germany

• • • •

ISCB GCB AI*IA TABOO

Bologna, 15/7/2002 BIXMAS Workshop

Thanks!

Many thanks to all participants!

Giuliano Armano, Martin Bishop, Laura Bocchi, Diego Bonura, Paolo Bresciani, Tony Brooks, Thomas Bruce, Kevin Bryson, Greg Butler, Paolo Ciancarini, Mick Correl, Rosario Culmone, Keith Decker, Angelo Facchiano, Michele Finelli, Paolo Fontana, Phil Gardner, Alfredo Garro, Robin Gras, Karlheinz Gro ß, Alessandro Guffanti, Frederic Guinand, François Guissart, Midori Harris, Patricia Hernandez, Ian Horrocks, Beatrice Iannotta, Cosimo Laneve, Davide Lorenzoli, Michael Luck, Federico Malusa, Gianmaria Mancosu, Assunta Manniello, Leonardo Mariani, Domenico Marra, Andreas Matern, Daniel McShan, Emanuela Merelli, Audrius Meskauskas, Luciano Milanesi, Michel Millot, Steffen M öller, Luc Moreau, Christine Nardini, Tom Oinn, Andrea Omicini, Francesca Piersigilli, Joke Reumers, Paolo Romano, Elda Rossi, Edith Schlagenhauf, Daniel Schober, Michael Schroeder, Cinzia Segala, Martin Senger, Padmini Srinivasan, V. S. Subrahmanian, Carsten Tham, Luca Toldo, Nadine Zangger This presentation will soon be available in the NETTAB 2002 web site: http://www.nettab.org/2002/

Bologna, 15/7/2002 BIXMAS Workshop