Initial steps towards a production platform for DNA sequence analysis on the grid

Background: Bioinformatics is confronted with a new data explosion due to the availability of high throughput DNA sequencers. Data storage and analysis becomes a problem on local servers, and therefore it is needed to switch to other IT infrastructures. Grid and workflow technology can help to handle the data more efficiently, as well as facilitate collaborations. However, interfaces to grids are often unfriendly to novice users. Results: In this study we reused a platform that was developed in the VL-e project for the analysis of medical images. Data transfer, workflow execution and job monitoring are operated from one graphical interface. We developed workflows for two sequence alignment tools (BLAST and BLAT) as a proof of concept. The analysis time was significantly reduced. All workflows and executables are available for the members of the Dutch Life Science Grid and the VL-e Medical virtual organizations All components are open source and can be transported to other grid infrast...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Angela C. M. Luyf, Barbera D. C. van Schaik, Michel de Vries, Frank Baas, Antoine H. C. van Kampen, Sílvia D. Olabarriaga
• Keywords: BMCBI 2010, Business, DNA Sequencers, Grid, Workflows