HPCwire: Cartesian Gridspeed Turbocharges Genomic Searching

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April 21, 2006

Cartesian Gridspeed Turbocharges Genomic Searching

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New Zealand start-up, Cartesian Gridspeed, has developed a bioinformatics tool that supposedly searches gene databases 10,000 times faster than other existing genomic search engines. According to the company's CEO, Leonard Bloksberg, this allows industrial strength genomic searching to be performed on a standard PC instead of a multi-million dollar supercomputer cluster. HPCwire recently got an opportunity to ask Mr. Bloksberg about his company and the new technology that he helped develop.

HPCwire: What's the origin of your company and its name -- Cartesian Gridspeed?

Bloksberg: As a Senior Scientist at New Zealand's leading biotech company, Genesis Research, I was conducting research in systems biology when we encountered a need for significantly increased compute capacity. I got together with a group of programmers from Reel Two and we brainstormed a new way to get things done. Later I left Genesis and started Cartesian Gridspeed to work on bioinformatics technologies, and acquired the SLIM technology.

Genesis' core business is immunology. Systems biology and bioinformatics were a stretch for them. They have restructured and focused on their core immunology science.

The SLIM technology is based on very fast novel ways of working with data in arrays or grids. Rene Descartes created the concept of the grid, and the blue in our logo symbolizes the blue of the Fleur DeLis, which was the French flag at the time of Rene Descartes.

Cartesian Gridspeed was founded in April of 2005, and our alpha product was released exclusively in New Zealand in November of 2005. We are beginning a preliminary beta launch in Australia in April 2006, and the official beta launch is scheduled for May 2006 in the USA. The beta will be limited to no more than 24 companies world wide, and we are targeting the formal product launch for August 2006.

HPCwire: What does SLIM Search do and, without revealing any proprietary information, how does it do it?

Bloksberg: SLIM stands for Sequence Location Indexer and Matcher. SLIM Search is a super fast genomics search engine based on the SLIM technology. It is ten thousand times faster than a fully optimized implementation of Blast, the industry standard. SLIM Search offers more speed, more flexibility, and more sensitivity than anything else.

Ten thousand times faster is a ridiculous number, so here are some practical examples of what that means for a real biologist. SLIM Search can save you $100,000 per year in electricity costs if you run a Blast farm of 100 PCs where SLIM Search can do the job on a single PC. SLIM Search can assemble a human genome in half a day on a desktop workstation instead of months on a multi-million dollar cluster. SLIM Search can deliver daily updates of an orthogonal comparison comparative genomics database of every known gene on a single PC.

Modern genomics search tools break a search into 2 steps, a word search followed by an alignment. The word search phase is very simple, but must confront the entire dataset, so the need for speed is extreme. The fundamental concept of the word search is that you look for a short exact match -- the default in Blast is 11nt. If you find an exact match, you pass the hit on to an alignment phase as an HSP. SLIM Search is a significant improvement of how the computer carries out the word search, but the end result is the same. An exact match of 11nt does not vary no matter how the computer found it. SLIM Search then passes the pair on to the alignment program of Blast, so the biologist gets exactly the same results and statistics they are used to.

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