Advanced Data Mining and Visualisation Approaches to Systems Biology
13 - 15 November 2003
University of Ulster, Jordanstown, Northern Ireland, UK

Organisers:

Francisco Azuaje, University of Ulster, Northern Ireland, United Kingdom.
Joaquin Dopazo, Spanish National Cancer Centre (CNIO)

Report

Scientific Content

This workshop brought experts from the areas of functional and structural genomics, bioinformatics and computer science to discuss advances, challenges and opportunities in biological data integration, analysis and visualisation.

The workshop covered two major themes.

Theme 1. Current challenges and opportunities in biological pattern discovery. It addressed key limitations exhibited by existing data mining approaches to systems biology, and requirements for the development of an advanced generation of techniques and applications.

Theme 2. Current challenges and opportunities in biological information visualisation. It covered the problems of displaying data mining results, navigating and browsing biological databases, and representing information extraction/retrieval outcomes based on multiple information resources, with special emphasis on a systemic scale view.

These themes were connected through the problem of integrating multiple data and information sources. This problem provided a common conceptual framework for the presentations and discussions of this workshop.

The presentations covered several biological problems originating from functional and structural genomics. They achieved a balance between the introduction of principles and methods and the discussion of applications. Moreover, they provided the audience with useful insights into the current state of the art, as well as emerging requirements. The meeting offered 13 presentations, including 11 given by invited speakers.

Final Programme

Day 1 (Thursday, 13/11)
10:00 am: Coffee
10:30 am: Welcome, introduction, summary of workshop's goals.
11:00 am: Jan Komorowski: Predicting Gene Ontology Biological Process From Temporal Gene Expression Patterns.
11:45 am: Patrick Aloy: The Third Dimension for Protein Interactions and Complexes.
12:30 pm: Lunch
2:00 pm: Graham Cameron: Strategies to Information Integration for Biological Research.
2:45 pm: Luis Serrano: In Silico Prediction of Functional Mutations and Partners Using Protein Design Algorithms.
3:30 pm: Coffee
4:00 pm: Alvis Brazma: Mining Gene Networks Derived from Microarray Data.
4:45 - 5:30 pm: Open discussion and summary.
7:30 pm: Dinner

Day 2 (Friday, 14/11)
10:00 am: Coffee
10:30 am: Terri Attwood: A UTOPIAn View of Protein Sequence Analysis.
11:15 am: Vincent Schächter: How Does Protein-Protein Interaction Data Complement Protein-DNA Interaction Data in the Yeast Transcriptional Regulation Network ?.
12:00 pm: Lunch
1:30 pm: Des Higgins: Multivariate Analysis of High Throughput Genomic Data.
2:15 pm: Joaquin Dopazo: Using Gene Ontology to Study Biological Processes that Account for Arrangements of Genes by Different Criteria.
3:00 pm: Coffee
3:30 pm: Inge Jonassen: Approaches to the Automatic Discovery of Patterns in Biological Sequences and Structures.
4:15 pm: Denis Shields: Multivariate Modelling of Genome-Linked Data to Define Proteins as Drug Targets
5:00 - 5:30 pm: Open discussion and summary.
7:30 pm: Dinner

Day 3 (Saturday, 15/11)
10:00 am: Coffee
10:15 am: Francisco Azuaje: Information-Theoretic Approaches to Functional Similarity.
10:45 am: Alessandro Guffanti: AntiHunter: A Web Tool for In Silico Detection of Anti-Sense Transcripts.
11:15 am: Open discussion and conclusions.
12:00 pm: Lunch/Departures

Assessment of the results and contributions

This workshop has provided the basis for consolidating and establishing new investigations on the discovery and visualisation of patterns that are novel and relevant for the systems biology research community. Participants discussed advances in data integration, which can significantly improve their data analysis and visualisation requirements. But also it was discussed how advanced data mining and visualisation techniques may facilitate more understandable and systematic data integration processes.

Most of the tools and resources discussed are freely available to support ongoing and future research. They are especially relevant to projects involving data originating from gene and protein sequence analysis, gene expression data, protein structure analysis and protein interactions across several model organisms.

One important factor for assessing the results of this event is the level and quality of discussion achieved during the workshop. Despite the multidisciplinary characteristics of the audience, participants actively expressed technical and conceptual concerns, discussed opportunities for improving solutions and shared expertise on different issues of interest for both system designers and users.

One important conclusion derived from this event is that there exist multiple options to support knowledge discovery through data and knowledge integration. But at the same time novel and user-friendly data mining and visualisation tools may significantly facilitate integration tasks at different levels of biological complexity. Traditional statistical and bioinformatics fields have seen data mining and visualisation as two independent tasks. A systems biology era would require designers and users to understand data mining and visualisation as an integrative framework. Also there is the need to adopt, improve and expand current protocols and/or standards to represent and exchange data, which may significantly support meaningful data mining and visualisation. One important experience in this area has been MAGE-ML, which has been proposed for representing gene expression data.

This workshop has supported the consolidation of existing national and international collaborations by providing feedback and reviewing advances. It also represented an opportunity for discussing current and potential editorial projects, and the organisation of future meetings. Also it allowed some of the participants to discuss the development of new collaborations involving: Exchange of technical expertise, share of information resources and participation in existing projects. Furthermore, this meeting has significantly promoted potential interdisciplinary cooperation between bioscientists and computer scientists. Some of the participants would be interested in implementing activities such as research visits and exchanges. Options being considered include programmes such as the ESF travel fellowships, and funding provided by local or national organisations.

List of participants

Dr. Patrick Aloy, European Molecular Biology Laboratory, EMBL, Germany.
aloy@embl.de

Miss Fátima Al-Shahrour, Spanish National Cancer Centre - CNIO, Madrid, Spain.
falshahrour@cnio.es

Prof. Terri Attwood, University of Manchester, UMBER, U.K.
attwood@bioinf.man.ac.uk

Dr. Francisco Azuaje, University of Ulster, U.K
fj.azuaje@ulster.ac.uk

Dr. Alvis Brazma. The European Bioinformatics Institute, EBI, UK.
brazma@ebi.ac.uk

Dr. Graham Cameron, The European Bioinformatics Institute, EBI, UK.
cameron@ebi.ac.uk

Mr. Alban Chesneau, Institut de génétique moléculaire de Montpellier, IGMM, France.
chesneau@igm.cnrs-mop.fr

Dr. Aedin Culhane, Conway Institute, University College Dublin, Ireland.
a.culhane@ucc.ie

Prof. Padraig Cunningham, Trinity College Dublin, Ireland.
Padraig.Cunningham@cs.tcd.ie

Dr. Joaquin Dopazo, Spanish National Cancer Centre - CNIO, Madrid, Spain.
jdopazo@cnio.es

Dr. Jesualdo Fernandez, Universidad de Murcia, Spain.
jfernand@dif.um.es

Mr. Alessandro Guffanti, IFOM - FIRC Institute of Molecular Oncology, Italy.
guffanti@ifom-firc.it

Mr. Wilbert H.M. Heijne, TNO Nutrition and Food Research Institute & Wageningen University, The Netherlands.
Heijne@voeding.tno.nl

Dr. Des Higgins, Conway Institute, University College Dublin, Ireland.
des.higgins@ucd.ie

Dr. Inge Jonassen, University of Bergen, UIB, Norway.
Inge.Jonassen@ii.uib.no

Prof. Jan Komorowski, The Linnaeus Centre for Bioinformatics, LCB, Uppsala University, Sweden.
Jan.Komorowski@lcb.uu.se

Dr. Joan Marsh, John Wiley & Sons, U.K
JMarsh@wiley.co.uk

Dr. Patrick Job Ogao, University of Groningen, The Netherlands.
ogao@cs.rug.nl

Dr. Patricia M. Palagi, Swiss Institute of Bioinformatics, Geneva, Switzerland.
patricia.palagi@isb-sib.ch

Mr. Syed Asad Rahman, Cologne BioInformatics Center (CUBIC), Germany.
asad.rahman@uni-koeln.de

Dr. Olga Rigina, Center for Biological Sequence Analysis (CBS), DTU, Denmark.
olga@genome.cbs.dtu.dk

Dr. Vincent Schächter, Genoscope, National Consortium for Genomics Research, France.
vs@genoscope.cns.fr

Prof. Wolfgang Schreiner, University of Vienna, Austria.
Wolfgang.Schreiner@akh-wien.ac.at

Dr. Luis Serrano, European Molecular Biology Laboratory, EMBL, Germany.
serrano@embl-heidelberg.de

Dr. Mary Shapcott, University of Ulster, UK.
cm.shapcott@ulster.ac.uk

Dr. Denis Shields, Institute of Biopharmaceutical Sciences, IBS, at the RCSI, Ireland.
dshields@rcsi.ie

Mr. Hongzhi Song, University of Ulster, U.K
gh.song@ulster.ac.uk