IWPLS’09 International Workshop on Portals for Life Sciences

14 September, 09 10:00 AM - 15 September, 09 03:30 PM

e-Science Institute, 15 South College Street, Edinburgh

Organiser: Sandra Gesing and Jano van Hemert
e-Science Institute Logo

University of Tbingen

Any slides or other material generated as a result of this event can be found at: www.nesc.ac.uk/action/esi/contribution.cfm?Title=1000

New technologies and experimental methods in the field of life sciences have enabled researchers to create huge amounts of data in extremely short times. In turn, analysing this data demands a rise of compute power, storage, and transmission. An enormous number of complex and sophisticated algorithms and tools have been developed to aid research. The demand for compute power and storage is met with a rise in provision of infrastructure and High-Performance Computing facilities and has resulted in the popularity of novel utility computing infrastructures, such as grid and cloud computing. Despite the increasing available resources, the broad uptake of these facilities and infrastructures is not following the same pace. The main reasons for this lie in the complexity of the human-computer interface to these computing infrastructures. Partly these infrastructures are only accessible and popular in local or specific communities.

An approach to offer easy and intuitive access to computing infrastructures irrespective of their location is a portal. It is essentially a website specific for a community that shares resources, e.g., scientific data, scientific tools and underlying computing infrastructure. Through a portal, essentially a thin-client graphical interface, it is much easier to give a scientific community access to an underlying infrastructure as one can hide all the complexities of the technology involved.

Suggested Topics

The workshop aims to be a forum of discussion therefore we also encourage contributions describing work in progress and partial solutions. We invite the submission of papers related to various aspects of molecular and systems biology and portals. Suggested topics include, but are not limited to:

  • Management of biological high-throughput data
  • Modeling protein-carbohydrate recognition
  • Machine learning for computational immunomics
  • Molecular simulations for drug discovery
  • Portal technology and portal construction methods
  • Usage models and portal tools for life sciences
  • Security aspects of portals for life sciences
  • Usability studies of life sciences portals
  • Workflows and service composition for life sciences
  • Service discovery and ontologies for life sciences
  • Tools for managing grid and cloud portability
  • Integration of life sciences with e-infrastructures
  • Demonstrations/ success stories


IWPLS’09 will bring together scientists of the field of life sciences, bioinformaticians and computer scientists. The aim is to exchange experience, formulate ideas and introduce up-to-date technological advances in molecular and systems biology in the context of portals.

Additionally to participation at the workshop, there are three alternatives for researchers to present their work: talks, lightning talks, and poster sessions. Submission of a paper may result in a talk or a presentation of a poster, submission of an abstract may result in a lightning talk.


All abstracts will double-blind peer reviewed and evaluated on quality and relevance. Accepted submissions will be given a 10-minute time slot (plus 5 minutes for questions) in a lightning talk session. The schedule is planned with eight lightning talks.

Abstracts will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site. The abstract length must not exceed 200 words and the abstracts must be written in clear and readably English. As the workshop is hosted at the e-Science Institute in Edinburgh, every abstract will acknowledge support from the e-Science Institute. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work.


All papers will be double-blind peer reviewed and evaluated on quality and relevance. All submissions are held in confidentiality prior to publication in the proceedings. Accepted papers will be published as open access, online-only workshop proceedings under CEUR-WS.org and will result in fully citable articles. The proceedings will be available online approximately one week prior to the workshop opening.

The presentation of accepted papers is dependent on number and quality of submitted papers. The workshop schedule is planned with the best 10 papers for oral presentation. Presenters will be given a 20-minute time slot (plus 5 minutes for questions) to provide a summary and update to their work. About 10 papers will be presented in poster sessions.

Papers will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site. They have to be formatted according to the layout style required by the OUP bioinformatics journal. Formatting requirements can be found at: http://www.oxfordjournals.org/bioinformatics/for_authors/submission_online.html. The paper length must not exceed eight pages and the papers must be written in clear and readably English. As the workshop is hosted at the e-Science Institute in Edinburgh, every paper will acknowledge support from the e-Science Institute. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work.


This event is provisionally scheduled to start at 10:00 Monday 14 September 2009 and close at 15:30 on Tuesday 15 September 2009.

A social event will be held on the Monday evening at Malmaison. There will be a whisky tasting at 19:00 which will be followed by dinner at 20:00. Taxis will be organised from eSI to Malmaison however delegates will be expected to make their own way home from the hotel.

Time Authors Title
September, 14th    
10:00 – 10:15 Sandra Gesing Welcome
10:15 – 11:15 Peter Kacsuk Keynote: P-GRADE Portal Family for e-Scientists
11:15 – 11:45 Jos Koetsier and Jano van Hemert Rapid Development of Computational Science Portals
11:45 – 12:15 Luciano Milanesi, Roberta Alfieri, Ettore Mosca, Federica Viti, Pasqualina D'Ursi and Ivan Merelli  Sys-Bio Gateway: a framework of bioinformatics database resources oriented to systems biology
12:15 – 13:30 Lunch break  
13:30 – 14:00 Richard Sinnott, Thomas Doherty, Jipu Jiang, Susan McCafferty, Anthony Stell and John Watt  Security-oriented Portals for the Life Sciences    
14:00 – 14:30 Livia Torterolo, Ivan Porro, Marco Fato, Maurizio Melato, Antonio Calanducci and Roberto Barbera Building Science Gateways with EnginFrame: a Life Science example  
14:30 – 15:00 Giuseppe La Rocca, Roberto Barbera, Alberto Falzone, Giacinto Donvito, Giorgio Pietro Maggi, Saverio Vicario and Luciano Milanesi On the Performance of Large Scale Bayesian Phylogenetic Analyses with Grid Portals and Robot Certificates
15:00 – 15:15 Coffee Break  
15:15 -15:30 Stuart Aitken, Kemian Dang and Jonathan Bard On the Design of BioSphere: A Grid Portal for Collaborative Ontology Creation 
15:30 – 15:45 Archie Campbell and David Liewald Generation Scotland Data Access Portal
15:45 – 16:00 Darren Oakley, Vivek Iyer and William Skarnes The New Sanger Mouse Resources Portal: a testbed for collaborative data integration
16:00 – 16:15 Morris A Swertz, K Joeri Van der Velde, Joris Lops, Martijn Dijkstra, Helen Parkinson and Ritsert C Jansen MOLGENIS: Generating Extensible Data Portals for Life Science Communities
16:15 – 16:30 Marco Roos, Matthew Gamble, Pieter Neerincx, Morris Swertz, Alexandra Nenadic and Carole A. Goble Applying the e-Laboratory Concept to Galaxy, a Portal for Genomics Researchers  
September, 15th    
9:00 – 10:00 Peter Brezany Keynote: Workflow Management for e-Science Analytics
10:00 - 10:30 Evert Lammerts Life Sciences & The Dutch Grid: An Analysis from a Grid Supporter's perspective
10:30 – 10:45 Coffee Break  
10:45 - 11:15  Eduardo Gutierrez, Alessandro Costantini, Javier Lopez Cacheiro and Aurelio Rodriguez. G-FLUXO: A workflow portal specialized in Computational BioChemistry
11:15 - 11:45 Ibrahim Elsayed, Thomas Ludescher, Konrad Schwarz, Thomas Feilhauer, Anton Amann and Peter Brezany Towards Realization of Scientific Dataspaces for the Breath Gas Analysis Research Community    
11:45 - 12:15 Jens Krüger and Gregor Fels Potential of Mean Force of Ion Permeation through alpha7 nAChR Ion Channel
12:15 - 13:15 Lunch break  
13:15 – 13:30 Andre Ribeiro  GROMACS Package within EELA-2  
13:30 – 13:45 Gregory Madey VectorBase: Biological Cyberinfrastructure for Research on Invertebrate Vectors of Human Pathogens
13:45 – 14:00 Peter Horvatovich, Isthiaq Ahmad, Frank Suits, Christin Christin, Berend Hoekman, Martijn Dijkstra and Rainer Bischoff Data Analysis Framework for High Throughput Analysis of Proteomics LC-MS Data 
14:00 - 14:15 Timothy Wright, David Cieslak, Gregory Madey and S M Niaz Arifin Garki Online:  E-Science Cyberinfrastructure for Research Data on Malaria Transmission
14:15 – 14:30 Sandra Gesing IWPLS'09: Summary and Outlook


Assistance with accommodation is offered once you have registered.


Registration for this event is now closed. To enquire about an application or to cancel a previous application please contact NeSC Administration.

Related Links

POSTER - www.nesc.ac.uk/esi/events/1000/posteriwpls20090625.pdf

Important Dates

25 Jun - Registration Opens
06 Aug - Abstract and paper submission
14 Aug - Notification of acceptance
24 Aug - Camera ready papers
07 Sep - Registration Deadline
07 Sep - Date we will respond to your application by (Please note this is the latest date we will respond to your application. It is normal policy for us to respond within 5 working days where possible.)
14 Sep - Event Starts at 10:00hrs


Workshop Chair
Sandra Gesing, University of Tübingen, Germany

Workshop Co-Chair Jano van Hemert, National e-Science Centre, University of Edinburgh, UK

Program Committee (preliminary)
Viktor Achter, University of Cologne, Germany
Stuart Aitken, University of Edinburgh, UK
Roberto Barbera, University of Catania and INFN, Italy
Maurice Bouwhuis, NBIC, Amsterdam, Netherlands
Antti Hyvärinen, Helsinki University of Technology, Finland
Ivan Janciak, University of Vienna, Austria
Phil Jones, EMBL EBI, Cambridge, UK
Joohyun Kim, Louisiana State University, Baton Rouge, US
Tamas Kiss, University of Westminster, UK
Jos Koetsier, National e-Science Centre, University of Edinburgh, UK
Oliver Kohlbacher, University of Tübingen, Germany
Miklos Kozlovszky, MTA SZTAKI, Budapest, Hungary
Tomasz Kuczynski, Poznan Supercomputing and Networking Center, Poland
Peter Kunszt, SystemsX.ch, Zürich, Switzerland
Luciano Milanesi, Institute of Biomedical Technologies, Milan, Italy
Steffen Müller, University of Lübeck, Germany
Jarek Nabrzyski, Center for Research Computing, University of Notre Dame, US
Lars Packschies, University of Cologne, Germany
Bengt Persson, Linköping University, Sweden
Richard Sinnott, National e-Science Centre, Glasgow, UK
Gergely Sipos, MTA SZTAKI, Budapest, Hungary
Chen Wang, CSIRO ICT Centre, Australia
Eric Yen, Academia Sinica Grid Computing Center, Taipei, Taiwan

Invited Speakers
Peter Brezany, University of Vienna, Austria
Peter Kacsuk, MTA SZTAKI, Budapest, Hungary


Full details on how to get to the e-Science Institute are available at:


Enquiries should be made directly to our Conference Administrator.



This event is sponsored by e-Science Institute in association with the following organisations:
  Scottish Bioinformatics Forum            
This is an archived website, preserved and hosted by the School of Physics and Astronomy at the University of Edinburgh. The School of Physics and Astronomy takes no responsibility for the content, accuracy or freshness of this website. Please email webmaster [at] ph [dot] ed [dot] ac [dot] uk for enquiries about this archive.