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Workflows management: new abilities for the biological information overflow

 5-7 October, 2005, Second University of Naples, Naples, Italy

Scientific Programme

NETTAB 2005 workshop intends to focus on the design and implementation of workflows by:

  • Introducing the basic knowledge in related technologies, in a non trivial way (invited lectures)
  • Outlining the promising features of workflows in bioinformatics (invited lectures, open discussion)
  • Showing some valuable examples in bioinformatics (invited lectures, oral communications, posters)
  • Allowing for as much discussion as possible (open discussions, panel discussion, contest)
  • Demonstrating "how it works" practically (tutorials)

For this reason, the workshop will include:

  • Invited lectures on technological issues, perspectives and examples in bioinformatics
  • Oral communications on applications, tools and examples in bioinformatics
  • A panel discussion on perspectives of workflows in bioinformatics
  • A poster session
  • Tutorials, both on implementation of tools and technologies and on the best practice in workflows management in bioinformatics

Invited Lectures

  • Workflow management in bioinformatics: the possibilities and the challenges
    Francis Ouellette, University of British Columbia, Canada
  • Web Services Choreography: Building Peer-to-Peer Relationships
    Steve Ross-Talbot, Pi4 Technology, London, UK
    Chair W3C Web Services Coordination Group and co-chair W3C Web Services Choreography Working Group
  • Semantics in data integration processes
    Guido Vetere, Research Director, Center of Advanced Studies, IBM, Italy
  • Survey and categorization of existing workflow management systems and their main features / limitations
    Elia Stupka, TIGEM, Naples, Italy
  • Application of automated bioinformatics procedures for the analysis of biological data
    Luciano Milanesi, Biomedical Technologies Institute, National Research Council, Milan, Italy

Tutorials

  • Taverna Workbench
    Tom Oinn, European Bioinformatics Institute - EBI, United Kingdom
  • Designing, setting up and accessing Web Services
    Martin Senger, International Rice Research Institute - IRRI, Philippines
  • The Pegasys workflow manager software system for high-throughput sequence analysis
    Sohrab Shah, University of British Columbia, Canada

Detailed Scientific Programme

Wednesday October 5, 2005
10.00 - 17.30 Registration and poster hang up
11.00 - 13.00 Tutorial 1
Taverna Workbench
Tom Oinn, European Bioinformatics Institute EBI, UK
Manual in PDF format [1,364 KB]
13.00 - 14.00 Time for free lunch
14.00 - 16.00 Tutorial 2
Designing, setting up and accessing Web Services
Martin Senger, International Rice Research Institute IRRI, Philippines
Slides in PDF format [3,760 KB]
16.15 - 16.30 Welcome and introduction to the workshop
Welcome
Giovanni Colonna, Second University of Naples, Italy
NETTAB workshop aims and structure
Paolo Romano, National Cancer Research Institute, Genoa, Italy,
and Angelo Facchiano, ISA/CNR, Avellino, Italy
16.30 - 17.20 Opening Lecture
Workflow management in bioinformatics: the possibilities and the challenges
Francis Ouellette, University of British Columbia, Canada
17.20 - 17.50 Coffee break
17.50 - 19.00 Posters' session (see the list with abstracts and posters)
 
Thursday October 6, 2005
09.00 - 10.20 1st Session:
Technologies and technological platforms for web services and workflow management
Two invited lectures (40' each, including questions and discussion)
10.20 - 10.50 Coffee break
10.50 - 12.10 1st Session (cont.):
Technologies and technological platforms for web services and workflow management
Four oral communications (20' each, including questions)
  • User-designed web services to support heterogeneous biological data retrieval
    Marie-Dominique Devignes1, Hervé de Palma1, Laurent Pierron1, Lionel Domenjoud2 and Malika Smaïl-Tabbone1
    1LORIA, CNRS INRIA Université Henry Poincaré, Vandoeuvre-les-Nancy, France
    2UPRES EA3446, Université Henry Poincaré, Vandoeuvre-les-Nancy, France
    Abstract in PDF format [304 KB] - Slides in PDF format [1,452 KB]


  • A proposed semantic framework for reporting omics investigations
    Alexander Garcia1,2,3, Jennifer Fostel4, Norman Morrison5, Philippe Rocca-Serra1 and Susanna-Assunta Sansone1 (The MGED RSBI Working Group)
    1EMBL-EBI The European Bioinformatics Institute, The Wellcome Trust Genome Campus. Cambridge, UK
    2The Institute for Molecular Bioscience, The University of Queenslan, Brisbane, Australia
    3Australian Center for Functional Plant Genomics
    4National Institute of Environmental Health Sciences, National Center for Toxicogenomics, Research Triangle Park, USA
    5The University of Manchester, School of Computer Science, Oxford Road, Manchester, UK
    Abstract in PDF format [180 KB] -


  • Bioinformatics Workflow using ASSIST on GRID
    Ivan Merelli, Giulia Morra and Luciano Milanesi
    Biomedical Technologies Institute, National Research Council, Milan, Italy
    Abstract in PDF format [196 KB] - Slides in PDF format [412 KB]


  • Retrieving factual data and documents using IMGT-ML in the IMGT information system
    D. Chaume, K. Combres, V. Giudicelli and M.-P. Lefranc,
    Laboratoire d'ImmunoGénétique Moléculaire, LIGM, UPR CNRS 1142, Institut de Génétique Humaine, Montpellier, France
    Abstract in PDF format [164 KB] -
12.30 - 14.00 Lunch
14.00 - 15.40 2nd Session
Workflow management systems in bioinformatics
Invited lecture (40' including questions and discussion)
  • Survey and categorization of existing workflow management systems and their main features / limitations
    Elia Stupka, TIGEM, Italy
Three oral communications (20' each, including questions)
  • A Workflow Management System for Bioinformatics Grid
    Giovanni Aloisio, Massimo Cafaro, Sandro Fiore and Maria Mirto
    Center for Advanced Computational Technologies/ISUFI and Southern Partnership for Advanced Computational Infrastructure Consortium, University of Lecce, Lecce, Italy
    Abstract in PDF format [292 KB] - Slides in PDF format [1,216 KB]


  • Bioinformatic workflows: G-PIPE as an implementation
    Alexander Garcia1,2, Samuel Thoraval1,3 , Leyla J. Garcia4, Yi-Ping Phoebe Chen2,5, and Mark A. Ragan1,2
    1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia;
    2Australian Research Council (ARC) Centre in Bioinformatics
    3Current address: Bioinformatique, Université Montpellier II, Montpellier, France
    4Faculty of Information Technology, Fundacion Universitaria San Martin, Bogota, Columbia
    5School of Information Technology, Deakin University, Burwood, Australia
    Abstract in PDF format [160 KB] -


  • Easy and user-friendly workflow management based on the data-morphing concept
    Stéphane Graziani
    ISoft, Gif-sur-Yvette, France
    Abstract in PDF format [348 KB] - Slides in PDF format [1,816 KB]
15.40 - 16.10 Coffee break
16.10 - 17.30 2nd Session (cont.)
Workflow management systems in bioinformatics
Four oral communications (20' each, including questions)
18.00 - 19.30 Guided Tour of Naples
20.00 - Social Dinner
 
Friday October 7, 2005
09.00 - 10.20 3rd Session
Applications of workflow management systems in bioinformatics
Invited lecture (40' including questions and discussion) Two oral communications (20' each, including questions)
  • A LIMS to support quantitative data acquisition and numerical simulations of dynamics of segment determination in Drosophila early embryo
    M. Samsonova1, E.Poustelnikova1, A.Pisarev1, E. Myasnikova1, K.Kozlov1, J. Reinitz2
    1State Polytechnical University, St. Petersburg, Russia
    2Dept. Applied Mathematics and Statistics and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, USA
    Abstract in PDF format [224 KB] - Slides in PDF format [3,296 KB]


  • The IGIPI Ontological Framework: integrating gene interactions with protein interactions
    Bill Andreopoulos1, Aijun An1 and Jimmy Huang2
    1Department of Computer Science and Engineering, York University, Toronto, Canada
    2Department of Information Technology, York University, Toronto, Canada
    Abstract in PDF format [232 KB] - Slides in PDF format [416 KB]
10.20 - 10.50 Coffee break
10.50 - 11.30 3rd Session (cont.)
Applications of workflow management systems in bioinformatics
Two oral communications (20' each, including questions)
  • Workflow Scenarios for a Semantic Web for Fungal Genomics
    Greg Butler
    Department of Computer Science and Software Engineering, Centre the Structural and Functional Genomics, Concordia University, Montréal, Canada
    Abstract in PDF format [132 KB]


  • Preprocessing, Management and Analysis of Mass Spectrometry Proteomics Data
    M. Cannataro, P. H. Guzzi, T. Mazza, and P. Veltri
    University "Magna Græcia" of Catanzaro, Italy
    Abstract in PDF format [148 KB] - Slides in PDF format [444 KB]
11.30 - 12.30 Panel Discussion
Limitations, problems and perspectives in the setting up and use of workflow management systems in bioinformatics
All invited speakers and members of the Scientific Committee
12.30 - 13.00 Introduction to NETTAB 2006 and Farewell
Presentation of NETTAB 2006 on "Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics"
Luciano Milanesi, ITB/CNR and LITBIO, Italy
Giuliano Armano, University of Cagliari, Italy
Slides in PDF format [1,408 KB]
13.00 - 14.15 Time for free lunch
14.15 - 16.15 Tutorial 3
Using Pegasys to create custom workflows for sequence analysis and genome annotation
Sohrab Shah, University of British Columbia, Canada
Slides in PDF format [3,024 KB]

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