SCIENCE

Biogemma, GenomeQuest, and SGI have announced a collaboration that has resulted in the first high-performance computing solution deployed for agriculture genomics. Specifically, here at their research headquarters and serving three international breeding companies and one French technical institute, Biogemma has deployed the GenomeQuest solution for sequence data management and analysis on the SGI Altix UV 1000, the world’s fastest, most scalable supercomputer.

Olivier DUGAS, head of Upstream Genomics, Biogemma, comments, "With the advent of next generation sequencing (NGS), our data delivery rate for species of interest is approaching hundreds of Gigabases per month and we will be dealing in Terabytes by the end of 2011. With this collaboration and the unique technologies from GenomeQuest and SGI, our researchers are equipped to handle these huge data sets and perform the complex analytical processes that will lead to powerful genomic-based discoveries." He adds, "For example, working at whole-genome resolution, we can now identify SNP and structural variations between individual plants and across hundreds of samples."

Biogemma performs genomic research activities worldwide across more than 200 collaborations. Pascual PEREZ, Biogemma CEO, remarks, "Large-scale comparative genomics greatly accelerates our gene discovery process and enables the molecular breeding efforts of our partners. We can better serve our shareholders by empowering them to select and produce seeds with properties that best meet the needs of the world – including higher yield, broader biodiversity, and lower impact on the environment."

GenomeQuest CEO, Richard Resnick, comments, "Genomics is at a major inflection point – with the blistering advances in sequencing and computing technology, we’re able to gain insight and understand the underlying science as never before. Our mission at GenomeQuest is to allow research organizations to rise above yesterday’s "scripting" details and focus on thriving in the new science. I’m happy to report that Biogemma and their progressive bioinformatics staff are fully exploiting the productivity and programmability of our genomic platform – at whole- and multi-genome scale."

Earlier this year, GenomeQuest and SGI announced a common software/hardware architecture for whole and multi-genome analysis, optimized for NGS scale. Also recently, SGI announced that the SGI Altix UV 1000 system achieved two world records for performance on the Standard Performance Evaluation Corporation’s SPECjbb2005 benchmark, an industry-standard measurement of Java-based application performance.

Dr. Eng Lim Goh, senior vice president and chief technology officer at SGI, remarks, "Congratulations to Biogemma for advancing the state-of-the art in deployed processing for agriculture genomics, and to GenomeQuest for continuing to lead the genomics industry in world-class, scalable SDM. We are proud to be an integral part of this collaboration and to provide the underlying, super-computer technology to power this deployment. Most importantly, SGI is quite inspired by the life science progress that will result."

Additional details of the collaborative deployment include:

• Initial crops in the research are maize, wheat, canola, and sunflower
• GenomeQuest workflows used are RNA-Seq analysis, multi-genome analysis, de novo   assembly, and polymorphisms discovery from SNP to large rearrangement Statistical and pathway tools will be integrated into the solution
• All existing sequence data is being converted and supported
• It is estimated that the system will support over 80TB of data by the end of 2011