At this page we give a short description of these partners' activities within EDGeS.

Erasmus Medical Centre consists of 2 hospitals with 10.000 PC's. 1500 PC's are already connected in a Condor Grid cluster.

EDGeS candidate applications:

1. MRI-Morph: 15.000 elderly people are MRI-scanned each half year and compared to ATLAS scans to detect the reasons behind Alzheimer's Disease
2. HTS-Analysis: the aim is to power up a new sequencer that will produce a lot of data
3. DNA-ORG: sequence comparison
4. VirtNuc: 3D distribution of large molecules. It is able to simulate extremely large structures. Currenly, it is used to predict the architectural 3D organisation of the human genome by simulating all chromosomes in the cell nucleus assuming the chromatin.

ViSAGE application for Video Stream Analysis in a Grid Environment.

Video Analysis is a general term used to describe the use of advanced algorithms to process video data. ViSAGe processes image pairs over the BOINC Grid and paints movement in yellow.

Advantages of image processing with EDGeS:
the processing time of one image pair + the transfer time of all images = the processing time of image stream with EDGeS.

This performance will be greatly improved as the development of EDGeS continues.
The advantage of processing images by EDGeS will take place when the processing time of one image will be bigger than the transfer time on the Internet.

Porting and testing has been completed in October 2008.
 

PLINK application for genomic research and massive genotyping for the study of human hereditary diseases.

The first round of the parallelization is finished.

The objectives are to:
- distribute the computation: execution time reduction, optimising the IT budget
- improve the GUI to reduce human effort
- launch many processes in a single step and easily retrieve results

There are two applications: one for data preparations and one for parallel analysis. Detailed design and final implementation using the EDGeS methodology are underway.

At this page we give a short description of these partners' activities within EDGeS.

Material Science Applications - experimental and simulation activities focused on strength, plasticity, fracture and defects of crystal growth:

1. Monte Carlo simulation of defects in metals
2. Image and video processing of experimental data

The code is parallelized and plans are being made to determine the porting strategy based on detailed analysis and experiences.  Further work consists in adopting the applications to the EDGeS platform.

 

Protein Functional Analysis with InterproScan

CNR has adopted a computational tool for functional characterization of protein and gene sequences.  The InterproScan application is used for screening (annotation of whole genomes) or for more specific analyses:
- input: one sequence; output: the same sequence with one or more annotations (function associated with regions)
- combines results of several tools. Each tool scans a specific dataset against a sequence in order to find out similarities

The goal of the project is to port InterproScan to a desktop Grid infrastructure in three phases:
1. CNR started with the BOiNC infrastructure (almost finished)
2. Install the application into the EDGeS infrastructure
3. CNR plans to port to the XtremWeb infrastructure
 

Signal and Image Processing in Ultrasound Computer Tomography and Distributed Grid applications for early breast cancer detection.

FZK aims to:
1. achieve computation in near real-time because batch systems in conventional Grid approaches are not feasible
2. deploy a solution in which no knowledge of Grid technologies is required

The FZK scientists develop new methods and algorithms. Therefore a client - server approach is needed using SOA architecture.
 

Fusion Physics Application - ISDEP: Integrator of Stochastic Differential Equations in Plasmas to calculate the trajectories of the particles inside a fusion device (ITER)

ISDEP has been ported to BOINC:
- C application crosscompiled for Windows, Linux, Mac
- BOINC API calls, templates fixed, validation mechanism

ISDEP has been validated in this Public Desktop Grid and the performance fits the requirements.

Next steps are the validation of the XtremWeb runs and the porting to the production EDGeS platform.