Seeker Spotlight: Life Technologies

Posted by TimOBrien on Sep 30, 2011 1:00:57 AM

Today we released a new round of four Life Technologies Grand Challenges. Matt Dyer, Ph.D., Senior Product Manager at Ion Torrent answers some questions about the Grand Challenge Program and offers tips for interested Solvers.

Can you tell us a bit about the Life Technologies Grand Challenge Program?

The Life Technologies Grand Challenge Program consists of three separate Challenges, each of which has a $1M prize associated with it. The three Challenges are Speed, Scalability, and Accuracy. The speed Challenge is centered on going from genomic DNA to pressing the start button on the Ion Torrent Personal Genome Machine(TM). If a Solver can do that in half the amount of time as we can do it, they win $1M. The focus on the scalability Challenge is to get more data from a single run of the PGM either by generating more reads or by my making the reads longer. If a Solver can double the throughput of a single run, you win $1M. Finally, the accuracy Challenge. The accuracy Challenge is unique in that it is purely a bioinformatics Challenge and Solvers don't need to have a PGM to participate. The goal here is to take a subset of reads in which the bases calls are 99% accurate and develop a better signal processing algorithm to make them 99.5% accurate. The Solver that can cut the error rate in half wins $1M.

In general the Life Technologies Grand Challenge Program is a typical crowd sourcing initiative (e.g., Netflix), but with one subtle difference. Since these Challenges all involve core pieces of the platform, we continue to work on them along side Solvers. Each quarter we release the current benchmarks along with protocols and software used to generate them and Solver have three months to work on and submit a solution. At the end of the three month if the Challenges remain unsolved, we update the benchmarks and the process starts over.

Wow, $1M that’s a pretty big prize pool? Why are these Challenges so important to Life Technologies?

It is about shared innovation, semiconductor sequencing in and of itself is built on innovations that happen from many others across a wide range of industries. For example the computing industry, semi-conductor industry, sequencing manufacturing industry, etc. Additionally, a lot of what we are doing is open source like our software where we release our source code. The Grand Challenges represent a continuation of shared innovation. We realize that there are a lot of really bright people in this world. Why not empower them and leverage their insights and innovation by building a community and platform where they can openly share their ideas.

Are there any other Grand Challenges from Life Sciences?

The fourth grand Challenge is again for $1M, but this time it's for an application on the 5500 genetic analyzer.

In this grand Challenge the winner will demonstrate the ability to isolate a single human cancer cell and then extract and analyze both the RNA and DNA, thus giving a complete genetic profile of the single cell transcriptome and genome. Completion of this Challenge will result in new methodologies for extracting single RNA and DNA whilst retaining the underlying genomic and transcriptome structure. We believe this will be a major breakthrough for cancer biology and coupled with the high throughput and accuracy of the SOLiD chemistry will enable many exciting questions about cancer development to be answered.

So far the Challenges have been open for 6 months, can you tell us what you've heard from the scientist and engineers that you've been in touch with during that period?

Solvers are really excited about semiconductor sequencing and the open source nature of the platform. Hundreds of labs now have access to semiconductor sequencing and everyone is digging into the data as more and more is produced and released. Several bloggers are following the Challenges and helping other start digesting the problem. Everyone likes the free exchange of ideas that the BlogTalk Radio interviews are providing. Ion Torrent R&D scientists are describing their views on the Grand Challenges. It really helps lower the bar to entry when someone explains their views on what's hard about each Grand Challenge.

We just reopened three of the Challenges on Semiconductor Sequencing. Can you tell us a bit about what is new in these Challenges for the current quarter?

The primary change for this quarter is that we are moving the Challenges from the Ion Torrent 314(TM) chip to the 316(TM) chip. So all of the benchmarks are now based off our best internal 316 run. In addition to that we have also released a couple of new tools. The first is Torrent Scout, which is designed to help accuracy Solvers. Torrent Scout allows users to access raw data generated by the PGM and view the data from the raw signal to the final alignment. The second is the PGM Flow Script editor. This is most applicable to scalability Solvers. The flow script editor allows Solver to change fluidic parameters on the PGM, for example if a Solver wanted to change the nucleotide flow order or flow times. This will enable Solvers to test different sequencing conditions. In addition to the tools, we are also releasing more dataset for accuracy Solvers. In addition to the Challenge dataset we are also posting three additional 316 datasets to use for testing.

Any tips that you'd offer to the Solvers?

Each Challenge is different. The Speed Challenge focuses primarily on molecular biology and particle chemistry. It involves representation and delivery of DNA to the semiconductor surface. The Scalability Challenge is about getting more and longer reads through the system, which could involve both chemistry and software enhancements. The Accuracy Challenge is about signal processing and phase correction. There is a series of recorded interviews with several Ion Torrent Scientists discussing which areas are likely to be most beneficial when approaching each of the Grand Challenges. Find out what Ion has been working on and what areas remain unexplored. All the interviews are available on Blog Talk Radio. In addition to that we also recommend that Solvers sign up for an account (it is free) on the Ion Community and visit the Grand Challenge space. It is a great knowledge sharing resource for accuracy Solvers to share ideas, tips, and tricks.

Topics: Challenges, Seekers

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