e-BioScience News

Perl script to generate Gasw xml and scufl file

This is a useful tool for anyone who is familiar with the syntax of the GasW configuration file. The command line script writes the user's input to the Gasw xml and scufl file for a single component.

http://bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/GASW?skin=clean.nat%2cpattern#Automatic_generation_of_XML_and

microRNA data analysis can now be run on the AMC Life Science Grid cluster

Marcel Willemsen, Angela Luijf and Silvia Olabarriaga from the Bioinformatics Laboratory successfully ported a software application (CORONA) for the analysis of microRNA data to run on the AMC computing cluster that is part of the Dutch Life Science Grid (http://www.biggrid.nl). CORONA was developed by Applied BioSystems (currently Life Technology) and is used as part of a collaboration with Nick Schopman (Laboratory of Experimental Virology, Department of Medical Microbiology) for the analysis of microRNA data. Recently, cellular miRNAs were shown to target viral mRNAs transcripts. Here, we studied miRNA expression profiles in HIV-1 infected T-cells using the SOLiD ultra deep sequencing method. We show that HIV-1 production significantly affected the expression of several miRNAs and found that some of these miRNAs had potential target sites in the HIV-1 genome. It was initially installed on the computing cluster that is used to process raw data acquired by the Solid sequencer at the AMC genomics facility headed by Frank Baas. However, this cluster didn't provide the compute capacity that was required for performing the data analysis on a regular basis. With the installation of CORONA on the AMC cluster, Marcel Willemsen can now run the analysis regularly, without being constrained by other users and applications of the Solid computing cluster. The use of high performance and GRID computing is increasingly used for AMC research through the development of expertise, methodology and computational infrastructure (e-BioInfra) in the e-Bioscience group headed by Dr. Silvia Olabarriaga from the Bioinformatics Laboratory of the KEBB.

See more information here.

Closing Workshop of the VL-e Medical project

The e-BioScience group organized the closing workshop for the Medical subprogram of the VL-e project. (more info)

Tristan Glatard at the Science Park

On 26 August 2009 Tristan Glatard presented a talk at an extra CT-Grid meeting (slides here)

My after-Dutch life: How much I miss grid.support ;-)

This talk will present our recent design, implementation, application porting and experimental efforts conducted at Creatis (Lyon, France) related to VL-e medical software. We will first present an integration of DIANE pilot jobs to improve quality of service in the biomed VO. Then, a service performing site monitoring and pre-selection will be described and experimental results will show how it complements pilot jobs. Besides, an interface of VL-e medical software with the ARC middleware will be presented, allowing application workflows to run both on EGEE/gLite and NorduGrid/ARC resources. Finally, three application use-cases (namely FIELD ultrasonic simulation, GATE radiotherapy simulation and CAVIAR cardiovascular analysis) will be presented, illustrating current achievements, remaining technical issues and on-going optimizations.

About the speaker:

Tristan Glatard worked in the Medical subprogram of VL-e (VLEMED) in 2007-2008. He is currently a CNRS researcher at the Creatis-LRMN lab, working on grid computing for medical imaging applications.

Contact with speaker:

Tristan Glatard
CNRS researcher
University of Lyon ; CREATIS-LRMN
http://www.creatis.insa-lyon.fr/~glatard
+33 (0) 472 43 72 99

This event is jointly organized by VL-e, Big Grid and the e-Bioscience group of the Bioinformatics Laboratory of the AMC.

1 July 2009

The paper by Silvia Olabarriaga, Tristan Glatard, Andreas Hoheisel, Aart Nederveen and Dagmar Krefting entitled Crossing HealthGrid Borders: Early Results in Medical Imaging was presented at the Healthgrid Workshop 2009 in Berlin. The paper obtained the third place in the "Best paper award" competition, which was based on votes of a jury of experts during the conference. In 2008 this competition was won by the same group from the e-BioScience group of the AMC with another paper (see 2008 paper abstract).

Abstract

Image analysis has been strongly present from the beginning in several healthgrid initiatives, and today we find many imaging projects with successful grid implementations and developments. An example is the analysis of functional MRI data on grids, which has been successfully done by several projects and that could be of interest for others. However, crossing the borders of existing grids is not trivial because the infrastructures being created for these projects differ, each adopting a (slightly) different software stack. This paper describes our early attempts to cross the borders between the German and Dutch grid infrastructures for medical imaging, motivated by a true wish to share expertise about fMRI analysis on grids between these two communities. We describe how we used off-the-shelf, production-level, grid technology to implement supporting mechanisms for cooperation in fMRI at several levels (users, data, software, workflows and computing resources). This simple exercise provided us valuable insights into the problems of crossing the borders of real grids from a user's perspective. Besides technical aspects, we observed that security and usability are very important for the success of inter-operation of Healthgrid.

This paper presents the results of a collaboration between the AMC, the Charite Hospital in Berlin, CREATIS in Lyon (FR) and the Fraunhoffer Institute in Berlin.