Posts Tagged ‘DNA’

Israeli Genome Compiler Creating Genetically Engineered Glowing Plants

May 6, 2013

The Israel based Genome Compiler received  $233,451 in Kickstarter to create plants that glow in the dark.

Glowing Plants

Glowing Plants

Check out this for more information and  in popular science magazine.

Pretty cool !

DNA sequencing and engineering is going to change what we are able to do , in multiple ways.

The fastest DNA Sequencer would soon cost under $1000 and plugs into USB…. you probably don’t even need USB 3.0

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Israel as a BioInformatics Super Power – Part One

December 1, 2012

Showing out, showing out, hit and run
Boy meets girl as beat goes on
Stitched up tight, can’t break free
Love is the drug, got a hook on me

Roxy Music,Love is the Drug

Israel is not (yet?) a super power in Bio-Informatics, but it should be.

We have 6000 PHD’s in biology and probably less than ten Bio-Informatics start-ups.

While Data Science is a great area for Israel , and some Israeli brains like to waste their time on SEO and gambling I think the Bio-Informatics industry is going to be huge , but the dominant players are still not set.

Genome viewer screenshot, Wikipedia

Genome viewer screenshot, Wikipedia

Israel can succeed because:

* Israel has some of the leading doctors and health-care research in the world (#3 in Life Expectancy , despite the wars)

* Many of the leading BioInformatics researchers in Boston and in Israel are originally Israelis 🙂

* Bio-Informatics requires new methodologies which are different than traditional biologiets are used to. This is a good scenario for Israelis who tend to be more adaptive in an unknown territory.

* Bio-Informatics is across domains. Math, Computer Science , Chemistry  ,Physics , Statistics and engineering all play a critical role.  While Israelis ,some times, are not as good in structured and well known engineering domains, they work well in teams and move between domains relatively easily.On a side note – Intel, Teva, IAI and Iskar demonstrate that manufacturing can work well in Israel.

* Bio-Informatics industry would probably be more cash efficient than traditional drugs design that requires FAB likes investments of Billions of Dollars.Moving from hardware into software and from manual experiments into virtual ones can reduce costs in an order of magnitude.

* M.Sc and PHD in Biology make very little money in Israel, due to the lack of opportunities.  This can get as bad as minimum wage or a high-school teacher salary.On the flip side, it means there is a large pool of extremely talented candidates.

On the next parts – what is the promise of bioinformatics? Why is Israel not there yet, and how can it get there?

Bar Refaeli, DNA Sequencing and Cloud Computing

December 7, 2009

Much like Bar Refaeli and Leonardo DiCaprio, DNA Sequencing and cloud computing go hand in hand together.

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I had a  very  interesting conversation with a friend yesterday about DNA Sequencing and cloud computing.

My friend is leading one of the largest cancer genome research projects in the world (and  yes, he is extremely  bright).

It appears that there is a great progress in DNA sequencing technology, based on chemical process. The pace is much faster than Moore’s law. As a result the budgets are shifting from the chemistry side to the computational side.

In the past, the budget would be 90% for biology and 10% for analyzing the data coming our of the DNA.

As the sequencing costs have fallen by orders of magnitude there is more and more data ( a single patient genome data is one TeraByte).

The more data , the more computing power needed to analyze it and hence the budget split becomes 50-50.

Each computation can take up to 24 hours, running on 100 cores mini grid.

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In theory, such tasks are great for cloud computing IAAS (Infra Structure as a Service) platforms or even PAAS (Platform as a service) solutions with Map-Redux capabilities.This EC2 Bioinformatics post provide interesting examples.

In practice there are three main challenges

  1. Since Cancer research facilities need this server power everyday, it is cheaper for them to build the solutions internally.
  1. To make things even more challenging, the highest cost in most clouds is the bandwidth in and out of the cloud. It would cost $150 to store one patient data on Amazon S3, but $170-$100 to transfer it into S3.
  1. Even if the cost gap can  be mitigated, there can be regulatory problems with privacy of patients data.After all its one person entire DNA we speak about. Encryption would probably be too expensive, but spiting and randomizing the data can probably solve this hurdle.

So, where do clouds make most sense for this kind of biological research ?

One use case is the testing of new improved  algorithm. Then, the researchers want to run the algorithm on all the existing data, not just the new one.

They need to compare the results  of the new algorithm with the old algorithms on same data set.They also need to finish the paper on time for the submission deadline :).

In such scenarios there is a huge burst of computation,needed on static data, at a very short period of time.Moreover,  if the data can be stored on shared cloud, and used by researchers form across the world, than data transport would not be so expensive in the overall calculation.

These ideas are fascinating and hopefully would drive new solutions, cures and treatments for cancer.

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