e-BioGrid Workshop 2011

e-Science Infrastructure for Life Science Research

Requirements and frameworks

Date: Thursday, November 10, 2011
Time: 10 - 17u
Location: Eulerzaal, Science Park Amsterdam Congreszalen, Science Park 125, Amsterdam. Directions.

Language: English
Participation: free. Please send an email to e-BioGrid if you would like to participate.

Life sciences today deals with data-intensive and high-throughput experimentation. When using data analysis or modeling software this can lead to long runtimes on a local computer infrastructure. e-BioGrid supports life-science research through the development and exploitation of a computing infrastructure that deals with these high demands. It makes the central Dutch BiG Grid infrastructure facilities such as Grid, cluster and Cloud available for Life Science research, allowing fast and efficient computing of life science software applications.

The focus of the workshop is primarily on the needs for e-science and computing infrastructure in life science research, and what is available on the Dutch e-science infrastructure. What are the typical needs for infrastructure in life sciences? Which computing infrastructure (Grid, Cloud) works best for next-generation sequencing data analyses? Which job submission framework is most scalable?

Requirements are presented from the technology application areas next-generation sequencing, microarray technology, mass spectrometry, nanoscopy, medical imaging, and structural modeling. We review and discuss the matching of requirements with technological frameworks and middleware, and identify standards and priorities for infrastructure developments where possible, with respect to current and upcoming data analysis and modeling requirements in life sciences.

We invite programmers and bioinformaticians as well as projectleaders and principical investigators, from the life science application areas

Program:

Introduction
9.45 – 10.00u Welcome reception.
10.00 – 10.05u Introduction. Irene Nooren (UvA/e-BioGrid)
10.05 – 10.20u Available Dutch computing infrastructure. Machiel Jansen (SARA/e-BioGrid)

Requirements and available e-infrastructure for the life science technology areas
10.20 – 10.35u Next generation sequencing, metagenomics. Sacha van Hijum (CMBI, RU).
10.35 – 10.50u Next generation sequencing, GWAS. Leon Mei (NBIC)
10.50 – 11.05u Biobanking. Morris Swertz (UMCG/BBMRI).
11.05 – 11.20u Microarray technology. Wim de Leeuw (UvA).

11.20 – 11.45u Coffee/tea break

11.45 – 12.00u Mass spectrometry, proteomics. Peter Horvatovich (UG).
12.00 – 12.15u Mass spectrometry, metabolomics. Kees van Bochove (NBIC/NMC).
12.15 – 12.30u Nanoscopy. Fons Verbeek (UL/NeCEN)
12.30 – 12.45u Medical Imaging. Silvia Delgado Olabarriaga (AMC).
12.45 – 13.00u NMR spectroscopy and modeling, We-NMR. Christoph Schmitz (UU).

13.00 - 14.00u Lunch

Overview and discussion of middleware and framework solutions + matching with requirements
14.00 – 14.30u Summary requirements and e-infrastructure life sciences. Irene Nooren (UvA/e-BioGrid)
14.30 – 15.00u Ibis e-Science Software Framework. Frank Seinstra (VU).

15.00 – 15.15u Coffee/tea break

15.15 – 15.45u Overview of middleware and framework solutions. Machiel Jansen (SARA/e-BioGrid)
15.45 – 16.30u Discussion.
16.30 – 17.00u Drinks.


The workshop is supported by BiG Grid and NBIC.