First HPC Solution Deployed for Agriculture Genomics
Biogemma, GenomeQuest and SGI have announced a collaboration resulting in the first high performance computing solution deployed for agriculture genomics. Specifically, Biogemma has deployed the GenomeQuest solution for sequence data management and analysis on the SGI Altix UV 1000 scalable supercomputer at their research headquarters, and serving three international breeding companies and one French technical institute.
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.”
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, supercomputer 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
Biogemma is a biotech company in Europe involved in genomics applied to field crops. The company is the result of the merger of the biotech activity of three major seed companies, Vilmorin & Cie (Limagrain Group), Euralis and RAGT; with the help of two financial institutions, Sofiproteol and Unigrains; and the support of the technical agency Arvalis. Its R&D programs for field crops (corn, wheat, sunflower and oilseed rape) are developed with its partners and focused on yield improvement, biotic and abiotic stress resistance, and specialty grain compounds.
GenomeQuest, a sequence data management company, helps life science organizations realize the full promise of genomics. Over 160 health and agriculture companies use GenomeQuest for mission-critical work, including nine of the top 10 pharmaceuticals. The core technology of the company is the GQ-Engine — a sequence database engine that is purpose-built for storing, managing, and analyzing sequence data at whole- and multi-genome scale.