U de Montréal Researchers Simulate ‘World’s Largest Heart Model’ with SGI Technology
Researchers at the Université de Montréal have run what they consider to be the largest mathematical simulation of a heart ever assembled – a 2 billion-element model – on a high-performance computing system from SGI. The UdM model is up to 1,000 times more detailed than the university’s previous models, according to SGI.
Over the past nine months, Mark Potse and Alain Vinet, both with the Research Center of Sacré-Cœur Hospital and the Biomedical Engineering department at UdM, began running 100-to-120 million-point models as part of their heart disease research on an SGI Altix 4700 system, a shared memory computing system. They use 60 of the 768 Intel Itanium 2 processors running on the SGI Altix which, as part of the Quebec Network for High-Performance Computing, is shared by many researchers from across Canada.
In late October, Potse and Vinet ran their custom electrocardiography code to solve the largest, most detailed heart model ever, using the entire SGI Altix system and 1.2TB of shared memory. Originally written by them on an older SGI system and ported to the SGI Altix system’s Linux environment in 2003, the ECG code jumped from 120 million to 2 billion points easily, according to SGI in a statement.
Genedata Provides Expressionist Platform to Eisai Research Institute
The Eisai Research Institute has agreed to work with Genedata’s Expressionist biomarker discovery platform, it was announced this week.
Genedata Expressionist is a modular computational platform for biomarker discovery that integrates transcriptomics, proteomics and metabolomics data in an enterprise software system. It uses high-throughput data processing and automated workflows to perform assessments, statistical analysis, and interpretation functionalities.
The platform provides a single point-of-access for all experimental data, including sample information, raw and pre-processed data, analysis, results and documentation with reports.
Simulations Plus Releases 1st Q 2008 Earnings
Simulations Plus released its first quarter 2008 earnings this week, conducting a webcast later released on its website.
Results for the quarter show that revenues increased 36 percent with earnings up by 232 percent, the company said.
CFO Momoko Beran said that consolidated gross profit increased increased 47.6 percent to $1,498,000 in 1Q08 from $1,015,000 in 1Q07. R&D expense increased 23.0 percent to $226,000 in 1Q08 from $184,000 in 1Q07, primarily “due to expansion of our life sciences staff,” said Momoko Beran, CFO.
CLC bio and Danish Research Institutions Start Next-Gen Network
CLC bio and some Danish research institutions have established SEQNET – a national network for developing a software platform for the analysis of data from next-gen sequencers.
CLC bio said in a statement that the platform will integrate bioinformatics algorithms with a user-friendly and graphical user interface.”
The statement continued, mentioning that “a significant amount of new or optimized bioinformatics algorithms will be developed in this project. They will all be bundled into a comprehensive bioinformatics package based on CLC bio's present platform, the workbench, facilitating analysis of new sequencing technology data by research groups in companies and large corporations, as well as public and private research institutions.
The network is funded by the Danish Agency for Science Technology and Innovation, with a total of $3 million USD and will initially operate for three years, commencing this month.
The founding partners of the Danish SEQNET are Department of Life Sciences at Aalborg University, Faculty of Agricultural Sciences at Aarhus University, Department of Biology at University of Copenhagen, University of Southern Denmark, Aalborg University Hospital, and CLC bio.