1. Bologna, 15/7/2002BIXMAS Workshop 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

2. Bologna, 15/7/2002BIXMAS Workshop The acronym NETwork Tools and Applications in Biology A series of workshops focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics

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

4. Bologna, 15/7/2002BIXMAS Workshop NETTAB Workshops CORBA and XML: towards a bioinformatics integrated network environmentCORBA and XML: towards a bioinformatics integrated network environment http://www.nettab.org/2001/ Genova, 17-19 May 2001 ----------------- Agents in BioinformaticsAgents 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

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

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

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

8. Bologna, 15/7/2002BIXMAS Workshop AiB: Technology The basic technology The implementation of the Semantic Web, Ian Horrocks, Computer Science Department, University of Manchester, United KingdomThe implementation of the Semantic Web, Ian Horrocks, Computer Science Department, University of Manchester, United KingdomComputer Science Department, University of ManchesterComputer Science Department, University of Manchester Introduction to agents and to agents architecture and infrastructure, Paolo Ciancarini, University of Bologna, ItalyIntroduction to agents and to agents architecture and infrastructure, Paolo Ciancarini, University of Bologna, ItalyUniversity of BolognaUniversity of Bologna

9. Bologna, 15/7/2002BIXMAS 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)On the Use of Agents in a Bioinformatics Grid, Luc Moreau, University of Southampton, United Kingdom (+31 more authors with 6 affiliations)University of SouthamptonUniversity of Southampton State: myGrid project Goal: workflow based in-silico experiments Agents uses: user agents for personalisation and negotiation over QoS, agent communication language

10. Bologna, 15/7/2002BIXMAS Workshop AiB: Examples (i) Good examples (i) BioAgent: A Mobile Agent System for Bioscientists Emanuela Merelli, University of Camerino, ItalyBioAgent: A Mobile Agent System for Bioscientists Emanuela Merelli, University of Camerino, ItalyUniversity of CamerinoUniversity of Camerino From GeneWeaver to Agmial, Kevin Bryson, Institut National de la Recherche Agronomique (INRA), FranceFrom GeneWeaver to Agmial, Kevin Bryson, Institut National de la Recherche Agronomique (INRA), FranceInstitut National de la Recherche Agronomique (INRA)Institut National de la Recherche Agronomique (INRA) A short report on BioMAS, a Multi-Agent System for Genomic Annotation, Keith Decker, University of Delaware, USAA short report on BioMAS, a Multi-Agent System for Genomic Annotation, Keith Decker, University of Delaware, USAUniversity of DelawareUniversity of Delaware Integration of Heterogenous Data Sources for Proteomics and Transcriptomics, Steffen Möller, Proteom-Zentrum Rostock, GermanyIntegration of Heterogenous Data Sources for Proteomics and Transcriptomics, Steffen Möller, Proteom-Zentrum Rostock, GermanyProteom-Zentrum RostockProteom-Zentrum Rostock

11. Bologna, 15/7/2002BIXMAS 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

12. Bologna, 15/7/2002BIXMAS 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

13. Bologna, 15/7/2002BIXMAS Workshop AiB: Examples (ii) Good examples (ii) A Knowledge Based Interface for Distributed Biological Databases, Paolo Bresciani, ITC-IRST, Trento, Italy.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, USAWeb 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, ItalyAn Agent Architecture for Predicting Protein Secondary Structures, Giuliano Armano, University of Cagliari, Italy + 8 posters

14. Bologna, 15/7/2002BIXMAS Workshop AiB: How-to Three tutorials Theoretical issues on Agents and Multi-agent Systems Michael Luck, University of Southampton, UKTheoretical issues on Agents and Multi-agent Systems Michael Luck, University of Southampton, UK Agents, Middleware, and the Grid Michael Schroeder, City University of London, UKAgents, Middleware, and the Grid Michael Schroeder, City University of London, UK Social issues in Agent systems Andrea Omicini, University of Bologna, ItalySocial issues in Agent systems Andrea Omicini, University of Bologna, Italy

15. Bologna, 15/7/2002BIXMAS Workshop AiB: Discussion Support to the discussion Bioinformatics applications and the web: today and tomorrow, Michele Finelli, University of Bologna, ItalyBioinformatics applications and the web: today and tomorrow, Michele Finelli, University of Bologna, ItalyUniversity of BolognaUniversity of Bologna Technology innovation in a service environment: HGMP-RC, Martin Bishop, Human Genome Mapping Project - Resource Center, United KingdomTechnology innovation in a service environment: HGMP-RC, Martin Bishop, Human Genome Mapping Project - Resource Center, United KingdomHuman Genome Mapping Project - Resource CenterHuman Genome Mapping Project - Resource Center The Gene Ontology Project: Content for the Semantic Web, Midori Harris, European Bioinformatics Institute, United KingdomThe Gene Ontology Project: Content for the Semantic Web, Midori Harris, European Bioinformatics Institute, United KingdomEuropean Bioinformatics InstituteEuropean Bioinformatics Institute Bio-Agents: an industrial perspective, Luca Toldo, Merck KGaA, GermanyBio-Agents: an industrial perspective, Luca Toldo, Merck KGaA, GermanyMerck KGaAMerck KGaA + Open discussion with all speakers

16. Bologna, 15/7/2002BIXMAS Workshop Open discussion (i) Whats an agent for bioinformatics?Whats an agent for bioinformatics? –Consensus: design pattern/model (PC, KD, LM, ML) Are Agents useful for bioinformatics?Are Agents useful for bioinformatics? –For query personalisation (MB) –To handle dynamic environment (ML) –But, services must be available (MS, PS)

17. Bologna, 15/7/2002BIXMAS Workshop Open discussion (ii) Agents need bio-ontologiesAgents need bio-ontologies –because of systems and data heterogeneity There are concerns about:There are concerns about: –security: agent = virus (electronic signature?) –IPR, Copyright: how to protect rights –QoS: agents vs common use A chance: open sourceA chance: open source –develop a bio* on agents for de facto standardization and quick services development

18. Bologna, 15/7/2002BIXMAS Workshop Scientific Committee Chairman: Paolo Romano ( National Cancer Research Institute ) National Cancer Research Institute National Cancer Research Institute Co-chairs: Emanuela Merelli (University of Camerino), Luca Toldo (Merck KGaA), Paolo Ciancarini (University of Bologna) University of CamerinoMerck KGaAUniversity of BolognaUniversity of CamerinoMerck KGaAUniversity 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) University of CagliariICE/CNRFederal University of Rio Grande do Sul(INRA) (University of DelawareISA/CNRIowa State University of SouthamptonGlaxoSmithKlineITB/CNRProteom-Zentrum RostockUniversity of SouthamptonUniversity of BolognaUniversity of MarylandUniversity of CagliariICE/CNRFederal University of Rio Grande do Sul(INRA) (University of DelawareISA/CNRIowa State University of SouthamptonGlaxoSmithKlineITB/CNRProteom-Zentrum RostockUniversity of SouthamptonUniversity of BolognaUniversity of Maryland

19. Bologna, 15/7/2002BIXMAS Workshop Organizing Committee Chairman: Paolo Romano (National Cancer Research Institute) National Cancer Research InstituteNational Cancer Research Institute Co-chairs: Emanuela Merelli (University of Camerino), Luca Toldo (Merck KGaA), Paolo Ciancarini (University of Bologna) University of CamerinoMerck KGaAUniversity of BolognaUniversity of CamerinoMerck KGaAUniversity 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) ICE/CNRISA/CNRITB/CNRUniversity of BolognaUniversity of BolognaNational Cancer Research InstituteICE/CNRISA/CNRITB/CNRUniversity of BolognaUniversity of BolognaNational 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) National Cancer Research InstituteUniversity of BolognaUniversity of CamerinoNational Cancer Research InstituteUniversity of BolognaUniversity of Camerino

20. Bologna, 15/7/2002BIXMAS Workshop Support from Biotechnology Department, National Cancer Research Institute – Genova, ItalyBiotechnology Department, National Cancer Research Institute – Genova, Italy Department of Mathematics and Computer Sciences, University of Camerino, ItalyDepartment of Mathematics and Computer Sciences, University of Camerino, Italy Department of Computer Sciences, University of Bologna, ItalyDepartment of Computer Sciences, University of Bologna, Italy Merck KGaA, GermanyMerck KGaA, Germany ISCBISCB GCBGCB AI*IAAI*IA TABOOTABOO

21. Bologna, 15/7/2002BIXMAS Workshop 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 Groß, Groß, 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 Möller, Möller, 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 Many thanks to all participants! This presentation will soon be available in the NETTAB 2002 web site: http://www.nettab.org/2002/ Thanks!