SGI® UV: Biogemma - Case Study

May 2012

Biogemma Uses Improved Memory Sharing to Minimize Research Time with SGI® UV 1000 High Performance Computer.

SGI UV 1000 Enables Rapid Results

Biogemma is, today, the only European plant biotechnology research company that has been founded and is financed by the agricultural world. The company‘s shareholders are specialists in plant improvement and representatives of the major plant production chains in France: the cooperative groups Limagrain and Euralis, the firm RAGT, and the financial institutions Sofiprotéol and Unigrains.

These partners share the same strong convictions about the challenges set for agriculture today and the ways to go about tackling them.

Biogemma has more than 60 researchers and technicians specialized in genetic engineering, cellular and molecular biology, genome analysis, molecular marking, bioinformatics, plant physiology and pathology.

 

Case studies:

Biogemma works on major crop species, such as maize, wheat, oilseed rape and sunflower. Except for maize, those species are not fully sequenced, highly repetitive, poorly polymorphic and polyploid (wheat, rapeseed).  This makes it a real challenge to develop markers,that are necessary for the identification of trait-related candidate genes. Most of Biogemma’s marker development projects rely on DNA sequencing and de novo sequence assembly.

Case Study 1: whole genome SNP discovery on non-sequenced species.
Biogemma developed for the scientific community a very comprehensive sequence and SNP database for the species Pisum sativum. This was achieved by whole exome sequencing and required several computing days for de novo assembly using the Mira assembler, an analysis which was impossible without the SGI UV1000. The study resulted in more than 30,000 markers for a species on which only 384 SNP were publicly available.

 Figure 1: whole exome assembly and SNP detection

 

Case study 2: Trait-associated genes targeted sequencing on non-sequenced species.

Biogemma developed targeted sequencing based on sequence capture for all its species of interest.

The advantage of the strategy is that it can help to reconstruct complete genes for species for which only ESTs are available, allowing the access to intron sequence polymorphism. A bioinformatic pipeline was developed for de novo assembly and SNP discovery dedicated to polyploid species, and is routinely run for thousands of genes in parallel. The assembly is made individually for each targeted gene, and the computing time was significantly reduced using parallelization with the SGI UV1000 coupled to PBSpro.

Figure 2: Parallelized de novo assembly for targeted sequencing


Configuration

To support its research mission of improving plants in order to contribute to the progress of agriculture, Biogemma purchased an SGI UV 1000 in 2011. This system is configured as follows:

•    SGI UV 1000 with 22 compute blades
•    264 cores of Intel® Xeon® processor 7542 running at 2.66GHz
•    2,560MB of coherent shared memory

Biogemma uses many bioinformatics tools, mainly in the DNA sequence alignment and assembly area. The purchase of the UV 1000 was driven by the company‘s need for coherent shared memory, because their research projects now require handling huge amonts of data. In some cases, like sequence assembly, an entire dataset needs to be accessible in memory at one time — it cannot be split in chunks.

“We recently optimized one of our analysis pipelines for the UV 1000 with PBSpro, and we managed to make it run in 50 hours instead of the previous 130 hours, by parallelizing PBS job submissions”, according to Franck Pignard, IT Manager at Biogemma.

The UV 1000 replaced a Red Hat® cluster with 48 processor cores. Pignard states, “With this new installation, we are able to run some jobs which could not fit in memory at all on our previous cluster. I am very happy with this solution.“ The great advantage of our solution is that it allows both high performance computing for jobs like whole genome data assembly, as well as highly parallelized analyses and multiple users efficient management.

 

SGI Professional Services Led the Implementation

Françoise Lecomte, IT engineer at BIOGEMMA explains, “A lot of custom work was done to enable this solution to work in our environment, especially in the area of training us on PBSpro, the software solution used for managing HPC workloads. We also needed to integrate the system into our web portal to enable researchers to submit processes to the system.“

“With the UV 1000”, she continues, “we are now able to get results in a few hours instead of multiple days. This is really important for us since we always have new research projects to do. We need to be able to tune the system parameters to get the best results, which is something we can do easily with the UV. Without the UV, this would not be possible with jobs taking more than a few hours.”