Description
Life Sciences is a very active field of research using the EGEE infrastructure. Several EGEE related projects are also exploring the use of gLite middleware for bioinformatics and healthcare. The User Forum is a wonderful opportunity to get an overview of the present adoption of grids in the Life Sciences communities through the dedicated oral sessions session but also through the posters and demos exhibition. Complementary to the "medical imaging" session, the "bioinformatics and biomedicine" session programme reflects the variety of topics currently addressed on EGEE and its related projects in the field of life sciences.
Dr
Ignacio Blanquer-Espert
(UPV)
13/04/2010, 11:00
Experiences from application porting and deployment
Oral
Estimating the response time of large experiments is a key issue for achieving an efficient load balancing and minimizing the failure rate. This requires having a good knowledge of both the application and the infrastructure. This work describes a set of experiments that have conducted to the definition of a performance model that can be used to estimate the response time of the selected...
Dr
Christophe Blanchet
(CNRS IBCP)
13/04/2010, 11:15
Scientific results obtained using distributed computing technologies
Oral
Due to the present experimental limitations of solid-state NMR (ssNMR), 3D structure calculations of proteins using these NMR spectra as a source for structural constraints are demanding in terms of computing power. The application ARIA solid-state NMR is dealing with the automated assignment and structure calculation of large protein
systems in ssNMR context. We are currently adapting and...
Giacinto Donvito
(INFN-Bari)
13/04/2010, 11:30
Software services exploiting and/or extending grid middleware (gLite, ARC, UNICORE etc)
Oral
The Job Submitting Tool provides a solution for the submission of a large number of jobs to the grid in an unattended way. Indeed the tool is able to manage the grid submission, bookkeeping and resubmission of failed jobs.
It also allows the monitor in real time of the status of each job using the same framework. In this work we will introduce same key new features and application that we...
Dr
Maria Mirto
(CMCC, University of Salento, Lecce)
13/04/2010, 11:45
End-user environments, scientific gateways and portal technologies
Oral
Proteins are central to all biological processes: a very important problem in proteomics is the prediction of the three-dimensional (3D) structure of proteins from their amino acid sequence, because this information can be useful for determining the protein function, given by a specific spatial conformation that the protein assumes when it reaches the active state. We have integrated a...
Prof.
Bengt Persson
(IFM Bioinformatics, Linköping University, S-581 83 Linköping, Sweden; Dept of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden; National Supercomputer Centre (NSC), S-581 83 Linköping, Sweden),
Joel Hedlund
(IFM Bioinformatics, Linköping University, S-581 83 Linköping, Sweden)
13/04/2010, 12:00
Experiences from application porting and deployment
Oral
Life sciences have undergone an immense transformation during the recent years, where advances in genomics, proteomics and other high-throughput techniques produce floods of raw data that need to be stored, analysed and interpreted in various ways. Bioinformatics is crucial by providing tools to efficiently utilize these gold mines of data in order to better understand the roles of proteins...
Dr
Luciano Milanesi
(National Research Council - Institute of Biomedical Technologies)
13/04/2010, 14:00
End-user environments, scientific gateways and portal technologies
Oral
The Genetic Linkage Analysis of SNP markers aims to discover the genetic correlation in monogenic diseases by following their inheritance in families through the generations. The computational cost and memory requirements of the major algorithms in literature make large data sets very hard to be analyzed on a single CPU. The work here presented is a Grid implementation of a data pipeline...
Dr
Eberhard Schmitt
(University of Heidelberg, 69120 Heidelberg, Im Neuenheimer Feld 227)
13/04/2010, 14:20
Scientific results obtained using distributed computing technologies
Oral
A prominent means to detect genetic aberrations is the method of fluorescence in situ hybridization FISH. To avoid labelling large genomic regions by one polynucleotide like in standard FISH, for COMBO-FISH we search for a set of about 30 colocalizing short sequences with the requirement that no more than 4 of these stretches colocalize within 250 kb anywhere else in the genome. The exact...
Mrs
Barbera DC van Schaik
(Academic Medical Center)
13/04/2010, 14:40
End-user environments, scientific gateways and portal technologies
Oral
Current DNA sequencers produce a large amount of data. Because the amount of data is growing and the computation time for analysis is increasing, we initiated a pilot to run applications on the Dutch Grid (Big Grid, part of EGEE). We used the software platform that was developed for medical imaging in the VL-e project (e-BioInfra), and applied it to DNA sequence analysis. With the knowledge...
Ms
Ana Lucia DA COSTA
(HealthGrid)
13/04/2010, 15:00
Scientific results obtained using distributed computing technologies
Oral
Since the H1N1 outbreak lately, there has been a worldwide effort to isolate and sequence flu virus genomes. Specimens with a positive result are sequenced and deposited in influenza databases. The present EUAsiaGrid application, called g-INFO (Grid-based International Network for Flu Observation), shows the integration of existing data sources towards a global surveillance network for...
