Customer and Partner Comments

Myriad Proteomics

To process and interpret protein interaction data, we analyze both nucleotide sequences collected from the yeast 2-hybrid workflow and protein sequences from the mass spectrometry workflow. We have to piece together hundreds of thousands of DNA fragments to identify where in the human genome the interacting sequences can be mapped to and what alternatively spliced form they are in. We also have to perform large-scale protein sequence analysis using sensitive multiple sequence alignment and domain search methods", explained Jake Yue Chen, Ph.D., Head of Computational Proteomics at Myriad Proteomics. "The DeCypher system's capacity for running algorithms optimized for protein sequence analysis ultimately brings a great advantage to the project", he added. More...

Virginia Bioinformatics Institute

"Disentangling the genetic workings of complicated diseases—such as malaria, Alzheimer's, tuberculosis (TB), and acquired immune deficiency syndrome (AIDS)—requires the examination of extremely large data sets," explained Dr. Bruno Sobral, Director of Virginia Bioinformatics Institute. "TimeLogic's DeCypher solution, implemented within the institute’s Sun Microsystems Sun Fire 15K server, delivers powerful bioinformatics analysis capabilities that allow broad comparisons between numerous host responses to different pathogens," he added. Read more...

Novartis Pharmaceuticals, Bio-ITWorld excerpt

One innovation [in the labs of Dr. Misha Reinhardt, Novartis Pharmaceuticals Global Head of Life Science Informatics, Basel] is the increasing use of dedicated microprocessors with built-in algorithms, such as Tera-BLAST from TimeLogic Corporation. Reinhardt's department uses a couple of TimeLogic's DeCypher accelerators..."Computational scientists use these [to speed up] the pipelines for gene annotation," he says.

MRC’s Laboratory of Molecular Biology

Dr. Julian Gough, of The MRC Laboratory of Molecular Biology, commented, “We will be using the TimeLogic system for Hidden Markov Model (HMM) work related to the Superfamily database (http://supfam.org), which includes analysis of all completely sequenced genomes, including projects focused on new procedures to detect and annotate genes in the human genome. We will also be experimenting with new HMM techniques. Without considerable computing power, these new types of investigations would be impossible.”

Dr. Gough continued, “We already have conventional computing resources, but have installed DeCypher rather than expanding existing systems because we believe it is the best solution for dedicated HMM-based computing." Read more...

University of Calgary, Sun Center of Excellence for Visual Genomics

"Unraveling the genetic components of complex diseases—such as diabetes, Alzheimer's and cancer—requires the analysis of huge data sets," explained Dr. Christoph Sensen, director of the Visual Genomics Center. "TimeLogic's DeCypher solution, running on Sun systems, delivers the powerful bioinformatics analysis capabilities that allow us to visualize pathways of cellular metabolism," he added.

Dr. Darrell Ricke, TimeLogic customer and Scientific Advisory Board Member

"TimeLogic's strategy and DeCypher product are extremely well positioned for the evolving bioinformatics market. I look forward to helping TimeLogic continue to accelerate the pace of scientific discovery."


San Diego Supercomputer Center, a TimeLogic/Sun HMM benchmark site

"This is the era of high-throughput biology where the same operation is repetitively performed on many thousands of data points,” said Philip E. Bourne, professor of Pharmacology at UCSD and the director of SDSC’s Integrative Biosciences program. “In these scenarios, results such as these [produced by DeCypher] are very significant. The speed improvement makes large scale analyses of this type much more achievable."

Sun Microsystems, platform partner

"Visualizing tremendously complex genomic data is a key challenge for discovery research today," said Loralyn Mears, market development manager for Life Sciences Market Development at Sun Microsystems, Inc. "TimeLogic on Sun solutions speed the mining and interpretation of genomic data in order to provide a clearer picture of the mechanisms of genetic-based diseases."

Department of Energy's Joint Genome Institute

"The Department of Energy's Joint Genome Institute (JGI) is one of the premier public sequencing centers in the world, decoding nearly 30 million base pairs per day. It is responsible for sequencing human chromosomes 5, 16, and 19, leads the international effort to sequence the puffer-fish genome, and has ongoing programs in microbial and comparative genomics. "Making sense of all the data we generate—going from the raw DNA sequence, to assembled genomes, to annotated proteomes, and finally to characterized biochemical and developmental pathways—requires computational tools that are both sensitive and fast," said Daniel Rokhsar, the JGI's Associate Director for Computational Genomics.

"With our capacity we can sequence a microbial genome in one day, which puts a premium on our ability to rapidly process this information and make it available to researchers at JGI and elsewhere. Our TimeLogic DeCypher system will play a central role in all of our internal genome analyses at JGI, and will allow researchers around the world to rapidly search our growing genomic databases."