bologna, 15/7/2002bixmas workshop nettab 2002 workshop paolo romano 1 & emanuela merelli 2 &...

Bologna, 15/7/2002 BIXMAS Workshop

NETTAB 2002 NETTAB 2002 WorkshopWorkshop

Paolo RomanoPaolo Romano11 & Emanuela Merelli & Emanuela Merelli22

& Paolo Ciancarini& Paolo Ciancarini33 & Luca Toldo & Luca Toldo44

11National Cancer Research Institute, Genova, ItalyNational Cancer Research Institute, Genova, Italy22University of Camerino, ItalyUniversity of Camerino, Italy33University of Bologna, ItalyUniversity of Bologna, Italy

44Merck KGaA, GermanyMerck KGaA, Germany


The acronymThe acronym

NETNETworkwork

TTools and ools and AApplications in pplications in BBiologyiology

A series of workshops focused onA series of workshops focused on

the most the most promising and innovative ICT toolspromising and innovative ICT tools

and to their usefulness in and to their usefulness in BioinformaticsBioinformatics


NETTAB FormulaNETTAB Formula

NETTAB workshops intend to:NETTAB workshops intend to:

• FocusFocus on a well defined, emerging, promising on a well defined, emerging, promising ICT technologyICT technology (not on a specific biological research topic)(not on a specific biological research topic)

• IntroduceIntroduce the basic knowledgethe basic knowledge related to the technology under related to the technology under analysis, in a analysis, in a non trivialnon trivial way way

• OutlineOutline the the promising featurespromising features of the technology of the technology in bioinformaticsin bioinformatics• ShowShow some valuable some valuable examples in bioinformaticsexamples in bioinformatics or different or different

domainsdomains• Allow forAllow for as much as much discussiondiscussion as possible as possible• DemonstrateDemonstrate “how it works” practically “how it works” practically


NETTAB NETTAB WorkshopsWorkshops

““CORBA and XML: towards a bioinformatics integrated network CORBA and XML: towards a bioinformatics integrated network environmentenvironment””

http://www.nettab.org/2001/ http://www.nettab.org/2001/ Genova, 17-19 May 2001Genova, 17-19 May 2001

----------------------------------““Agents in BioinformaticsAgents in Bioinformatics””

http://www.nettab.org/2002/ http://www.nettab.org/2002/ Bologna, 12-14 July 2002Bologna, 12-14 July 2002

----------------------------------2003 workshop topic under definition2003 workshop topic under definition

through an open discussion on an “ad hoc” mailing lists:through an open discussion on an “ad hoc” mailing lists:subscribe to nettab-discussion on bioinformatics.orgsubscribe to nettab-discussion on bioinformatics.org

Naples / Como LakeNaples / Como Lake


About About bioinformaticsbioinformatics

Some aspects of bioinformatics:Some aspects of bioinformatics:

• Huge amount of data (DNA only Huge amount of data (DNA only 73 Gb73 Gb, coming soon microarray , coming soon microarray data, metabolic pathways, …)data, metabolic pathways, …)

• Exponential increase of data (Exponential increase of data (11-15% every 3 months11-15% every 3 months), soon not ), soon not locally manageablelocally 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 Research environment in continuous evolution and with user

specific needsspecific needs• Many hidden or not known information sourcesMany hidden or not known information sources


Desires of AiBDesires of AiB

Desires:Desires:

• Reduce Reduce data transferdata transfer, esp. for download, esp. for download• Avoid the need for frequent (and difficult) Avoid the need for frequent (and difficult) data updatesdata updates• Avoid the need for frequent (and difficult) Avoid the need for frequent (and difficult) software updatessoftware updates• Avoid Avoid local data integrationlocal data integration (warehouses) (warehouses)• Allow automatic Allow automatic detection of changesdetection of changes• Improve Improve data integrationdata integration• Allow Allow semanticsemantic based based data integrationdata integration through through ontologiesontologies• Monitor Monitor evolutionevolution of information sources of information sources


Known examplesKnown examples

• InfosleuthInfosleuth (MCC) – annotatation of livestock genetic (MCC) – annotatation of livestock genetic samplessamples

• TAMBISTAMBIS (University of Manchester) – semantic based (University of Manchester) – semantic based databanks integrationdatabanks integration

• GeneWeaverGeneWeaver (University of Warwick) – MAS for (University of Warwick) – MAS for genome analysis and protein structure predictiongenome analysis and protein structure prediction

• EDITtoTrEMBLEDITtoTrEMBL (EBI) – protein sequence annotation (EBI) – protein sequence annotation• DECAFDECAF (University of Delaware) – MAS for genomic (University of Delaware) – MAS for genomic

annotationannotation• BioAgentBioAgent (University of Camerino) – a mobile agent (University of Camerino) – a mobile agent

system for bioscientistssystem for bioscientists


AiB: TechnologyAiB: Technology

The basic technologyThe basic technology• The implementation of the Semantic WebThe implementation of the Semantic Web,,

Ian Horrocks, Ian Horrocks, Computer Computer Science DepartmentScience Department, University of Manchester, University of Manchester, United Kingdom , United Kingdom

• Introduction to agents and to agents architecture and Introduction to agents and to agents architecture and infrastructureinfrastructure,,Paolo Ciancarini, Paolo Ciancarini, University of BolognaUniversity of Bologna, Italy , Italy


AiB: PerspectivesAiB: Perspectives

PerspectivesPerspectives• On the Use of Agents in a Bioinformatics GridOn the Use of Agents in a Bioinformatics Grid,,

Luc Moreau, Luc Moreau, University of SouthamptonUniversity of Southampton, United , United Kingdom (+31 more authors with 6 affiliations) Kingdom (+31 more authors with 6 affiliations)

State: State: myGrid projectmyGrid project

GoalGoal: workflow based in-silico experiments: workflow based in-silico experiments

Agents usesAgents uses: user agents for personalisation and negotiation : user agents for personalisation and negotiation over QoS, agent communication languageover QoS, agent communication language


AiB: Examples (i)AiB: Examples (i)

Good examples (i)Good examples (i)• BioAgent: A Mobile Agent System for BioscientistsBioAgent: A Mobile Agent System for Bioscientists

Emanuela Merelli, Emanuela Merelli, University of CamerinoUniversity of Camerino, Italy , Italy • From GeneWeaver to AgmialFrom GeneWeaver to Agmial,,

Kevin Bryson, Kevin Bryson, Institut NationalInstitut National de la de la Recherche AgronomiqueRecherche Agronomique (INRA) (INRA), France , France

• A short report on BioMAS, a Multi-Agent System for Genomic A short report on BioMAS, a Multi-Agent System for Genomic AnnotationAnnotation,,Keith Decker, Keith Decker, University of University of DelawareDelaware, USA , USA

• Integration of Heterogenous Data Sources for Proteomics and Integration of Heterogenous Data Sources for Proteomics and TranscriptomicsTranscriptomics,,Steffen Möller, Steffen Möller, ProteomProteom--Zentrum RostockZentrum Rostock, Germany , Germany


AgmialAgmial

From GeneWeaver to AgmialFrom GeneWeaver to AgmialKevin Bryson, INRA, France Kevin Bryson, INRA, France

State: State: under developmentunder development

GoalGoal: analysis of Lactobacillus genomes: analysis of Lactobacillus genomes

Agents usesAgents uses: development of GeneWeaver, simplified : development of GeneWeaver, simplified communication between agents via Web services, electronic communication between agents via Web services, electronic signature, bio-ontologiessignature, bio-ontologies


Integration of Data SourcesIntegration of Data Sources

Integration of Heterogenous Data Sources for Integration of Heterogenous Data Sources for Proteomics and TranscriptomicsProteomics and Transcriptomics,,

Steffen Möller, Proteom-Zentrum Rostock, GermanySteffen Möller, Proteom-Zentrum Rostock, Germany

State: State: ongoing projectongoing project

GoalGoal: analysis of gene expression levels for RNA and proteins: analysis of gene expression levels for RNA and proteins

Agents usesAgents uses: implementation of EDITtoTrEMBL and analysis of : implementation of EDITtoTrEMBL and analysis of related pros and cons related pros and cons


AiB: Examples (ii)AiB: Examples (ii)

Good examples (ii)Good examples (ii)• A Knowledge Based Interface for Distributed Biological A Knowledge Based Interface for Distributed Biological

DatabasesDatabases,,Paolo Bresciani, ITC-IRST, Trento, Italy. Paolo Bresciani, ITC-IRST, Trento, Italy.

• Web Crawling Agents for Retrieving Biomedical InformationWeb Crawling Agents for Retrieving Biomedical Information,,Padmini Srinivasan, National Library of Medicine, USAPadmini Srinivasan, National Library of Medicine, USA

• An Agent Architecture for Predicting Protein Secondary An Agent Architecture for Predicting Protein Secondary StructuresStructures,,Giuliano Armano, University of Cagliari, ItalyGiuliano Armano, University of Cagliari, Italy

+ 8 posters+ 8 posters


AiB: How-toAiB: How-to

Three tutorialsThree tutorials

• Theoretical issues on Agents and Multi-agent SystemsTheoretical issues on Agents and Multi-agent SystemsMichael Luck, University of Southampton, UK Michael Luck, University of Southampton, UK

• Agents, Middleware, and the GridAgents, Middleware, and the GridMichael Schroeder, City University of London, UK Michael Schroeder, City University of London, UK

• Social issues in Agent systemsSocial issues in Agent systemsAndrea Omicini, University of Bologna, Italy Andrea Omicini, University of Bologna, Italy


AiB: DiscussionAiB: Discussion

Support to the discussionSupport to the discussion• Bioinformatics applications and the web: today and tomorrowBioinformatics applications and the web: today and tomorrow,,

Michele Finelli, University of Bologna, Italy Michele Finelli, University of Bologna, Italy • Technology innovation in a service environment: HGMP-RCTechnology innovation in a service environment: HGMP-RC,,

Martin Bishop, Human Genome Mapping Project - Resource Martin Bishop, Human Genome Mapping Project - Resource Center, United Kingdom Center, United Kingdom

• The Gene Ontology Project: Content for the Semantic WebThe Gene Ontology Project: Content for the Semantic Web,,Midori Harris, European Bioinformatics Institute, United Kingdom Midori Harris, European Bioinformatics Institute, United Kingdom

• Bio-Agents: an industrial perspectiveBio-Agents: an industrial perspective,,Luca Toldo, Merck KGaA, Germany Luca Toldo, Merck KGaA, Germany

++ Open discussion with all speakersOpen discussion with all speakers


Open discussion (i)Open discussion (i)

• What’sWhat’s an agent for bioinformatics? an agent for bioinformatics?– Consensus: Consensus: design pattern/modeldesign pattern/model (PC, KD, (PC, KD,

LM, ML)LM, ML)

• Are Agents Are Agents usefuluseful for bioinformatics? for bioinformatics?– For query For query personalisationpersonalisation (MB) (MB)– To handle To handle dynamicdynamic environment (ML) environment (ML)– But, But, servicesservices must be available (MS, PS) must be available (MS, PS)


Open discussion (ii)Open discussion (ii)

• Agents need Agents need bio-ontologiesbio-ontologies– because of systems and data heterogeneitybecause of systems and data heterogeneity

• There are There are concernsconcerns about: about:– securitysecurity: agent = virus (electronic signature?): agent = virus (electronic signature?)– IPR, Copyright: how to IPR, Copyright: how to protectprotect rights rights– QoSQoS: agents vs common use: agents vs common use

• A chance: A chance: open sourceopen source– develop a bio* on agents for de facto develop a bio* on agents for de facto

standardization and quick services developmentstandardization and quick services development


Scientific Scientific CommitteeCommittee

ChairmanChairman: Paolo Romano (: Paolo Romano (National Cancer Research InstituteNational Cancer Research Institute))Co-chairsCo-chairs: Emanuela Merelli (: Emanuela Merelli (University of CamerinoUniversity of Camerino), Luca Toldo (), Luca Toldo (

Merck KGaAMerck KGaA), Paolo Ciancarini (), Paolo Ciancarini (University of BolognaUniversity of Bologna))MembersMembers: Giuliano Armano (: Giuliano Armano (University of CagliariUniversity of Cagliari), Patrizio Arrigo (), Patrizio Arrigo (

ICE/CNRICE/CNR), Ana Lucia Cetertich Bazzan (), Ana Lucia Cetertich Bazzan (FederalFederal University of Rio Grande do Sul University of Rio Grande do Sul), Kevin Bryson ), Kevin Bryson (INRA)(INRA), Keith , Keith Decker Decker (University of (University of DelawareDelaware), Angelo Facchiano (), Angelo Facchiano (ISA/CNRISA/CNR), ), Vasant Honavar (Vasant Honavar (IowaIowa State University State University), Michael Luck (), Michael Luck (University of SouthamptonUniversity of Southampton), Robin McEntire (), Robin McEntire (GlaxoSmithKlineGlaxoSmithKline), ), Luciano Milanesi (Luciano Milanesi (ITB/CNRITB/CNR), Steffen Möller (), Steffen Möller (ProteomProteom--Zentrum RostockZentrum Rostock), Luc Moreau (), Luc Moreau (University of SouthamptonUniversity of Southampton), ), Andrea Omicini (Andrea Omicini (University of BolognaUniversity of Bologna), V. S. Subrahmanian (), V. S. Subrahmanian (University of MarylandUniversity of Maryland))


Organizing Organizing CommitteeCommittee

ChairmanChairman: Paolo Romano (: Paolo Romano (National Cancer Research InstituteNational Cancer Research Institute))

Co-chairsCo-chairs: Emanuela Merelli (: Emanuela Merelli (University of CamerinoUniversity of Camerino), Luca Toldo (), Luca Toldo (Merck KGaAMerck KGaA), Paolo Ciancarini (), Paolo Ciancarini (University of BolognaUniversity of Bologna))

MembersMembers: Patrizio Arrigo (: Patrizio Arrigo (ICE/CNRICE/CNR), Angelo Facchiano (), Angelo Facchiano (ISA/CNRISA/CNR), ), Luciano Milanesi (Luciano Milanesi (ITB/CNRITB/CNR), Andrea Omicini (), Andrea Omicini (University of BolognaUniversity of Bologna), Rita Casadio (), Rita Casadio (University of BolognaUniversity of Bologna), ), Assunta Manniello (Assunta Manniello (National Cancer Research InstituteNational Cancer Research Institute))

CollaboratorsCollaborators: Domenico Marra, Federico Malusa, Beatrice Iannotta : Domenico Marra, Federico Malusa, Beatrice Iannotta ((National Cancer Research InstituteNational Cancer Research Institute), Laura Bocchi, Biancamaria ), Laura Bocchi, Biancamaria Gentiloni (Gentiloni (University of BolognaUniversity of Bologna), Gloria Rossi (), Gloria Rossi (University of CamerinoUniversity of Camerino))


Support fromSupport 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, Department of Mathematics and Computer Sciences, University of Camerino,

ItalyItaly• 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


Giuliano Armano, Martin Bishop, Laura Bocchi, Diego Bonura, Paolo Bresciani, Tony Giuliano Armano, Martin Bishop, Laura Bocchi, Diego Bonura, Paolo Bresciani, Tony Brooks, Thomas Bruce, Kevin Bryson, Greg Butler, Paolo Ciancarini, Mick Correl, Brooks, Thomas Bruce, Kevin Bryson, Greg Butler, Paolo Ciancarini, Mick Correl, Rosario Culmone, Keith Decker, Angelo Facchiano, Michele Finelli, Paolo Fontana, Rosario Culmone, Keith Decker, Angelo Facchiano, Michele Finelli, Paolo Fontana,

Phil Gardner, Alfredo Garro, Robin Gras, Karlheinz GroPhil Gardner, Alfredo Garro, Robin Gras, Karlheinz Groß, Alessandro Guffanti, ß, Alessandro Guffanti, Frederic Guinand, François Guissart, Midori Harris, Patricia Hernandez, Ian Horrocks, Frederic Guinand, François Guissart, Midori Harris, Patricia Hernandez, Ian Horrocks, Beatrice Iannotta, Cosimo Laneve, Davide Lorenzoli, Michael Luck, Federico Malusa, Beatrice Iannotta, Cosimo Laneve, Davide Lorenzoli, Michael Luck, Federico Malusa,

Gianmaria Mancosu, Assunta Manniello, Leonardo Mariani, Domenico Marra, Andreas Gianmaria Mancosu, Assunta Manniello, Leonardo Mariani, Domenico Marra, Andreas Matern, Daniel McShan, Emanuela Merelli, Audrius Meskauskas, Luciano Milanesi, Matern, Daniel McShan, Emanuela Merelli, Audrius Meskauskas, Luciano Milanesi,

Michel Millot, Steffen MMichel Millot, Steffen Möller, Luc Moreau, öller, Luc Moreau, Christine Nardini, Tom Oinn, Andrea Christine Nardini, Tom Oinn, Andrea Omicini, Francesca Piersigilli, Joke Reumers, Paolo Romano, Elda Rossi, Edith Omicini, Francesca Piersigilli, Joke Reumers, Paolo Romano, Elda Rossi, Edith

Schlagenhauf, Daniel Schober, Michael Schroeder, Cinzia Segala, Martin Senger, Schlagenhauf, Daniel Schober, Michael Schroeder, Cinzia Segala, Martin Senger, Padmini Srinivasan, V. S. Subrahmanian, Padmini Srinivasan, V. S. Subrahmanian, Carsten Tham, Luca Toldo, Carsten Tham, Luca Toldo, Nadine ZanggerNadine Zangger

Many thanks to all participants!Many thanks to all participants!

This presentation will soon be available in the NETTAB 2002 web site:This presentation will soon be available in the NETTAB 2002 web site:http://www.nettab.org/2002/ http://www.nettab.org/2002/

Thanks!Thanks!

bologna, 15/7/2002bixmas workshop nettab 2002 workshop paolo romano 1 & emanuela merelli 2 &...

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