5 ms·

Great interview and optimism. The $1,000 genome is indeed within sight. Let us hope that software will be evolving as fast to handle the data.

by yannis 17y ago

njm 17y ago
It's not as much data as one might think, especially if you store the deltas -- there's not that much variation between individuals. That fact has actually been exploited to a great extent in enabling the $1,000 genome.
- coderdude 17y ago
  How much is "not much?" How many "values?" If stored as byte strings delimited by \n, how many lines? (I don't know if these are even answerable questions at this point, just wondering.)
  - yannis 17y ago
    Put it that way you can store the genome of 8 people on an 8GB SanDisk Cruzer Micro USB flash drive. It is not that large.
    - coderdude 17y ago
      Very specific brand of flash drive. ;) Thanks for the figure.
      - yannis 17y ago
        It's optimized for cost!
- bbgm 17y ago
  The raw data (the original image files), while mostly transient today, is massive. At some of the big genome centers they are in the double digit TB's of data processing per day
acg 17y ago
Isn't this what the Genomics X Prize is about? Complete Genomics does not appear to be a team: http://genomics.xprize.org/ http://genomics.xprize.org/
ericb 17y ago
So DNA is a long string, with certain identified parts that have meaning (code for something we know). What would a layman like myself need to get myself to a hello world program that could take an actual DNA string(file) as input and give a hello for the presence an actual known gene? Not code-wise, that's obvious. I'm asking where I could get a sample genome, information about a gene, fill in the gaps of my understanding, etc. Anyone know?
- bbgm 17y ago
  While not genome centric (it's genotype-based) Promethease is one example http://www.snpedia.com/index.php/Promethease http://www.snpedia.com/index.php/Promethease 23andme's software does a pretty good job. You can also use the UCSC genome browser although it probably as a learning curve for most. http://genome.ucsc.edu/ http://genome.ucsc.edu/ Honestly, I believe that people need to understand the biology, some depth of what genes are, and what SNPs are etc. It's important as molecular medicine becomes the norm (still some ways away).
- yannis 17y ago
  You can start with your favorite language by downloading a library, there is bioPerl, bioPython, bioRuby and even bioPHP! The libraries have all the routines to connect to public sources. The National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/nuccore/89889045?report=fasta&log$=seqview http://www.ncbi.nlm.nih.gov/nuccore/89889045?report=fasta&#3... has an enormous database and is all open source. The link I quoted lists the genome for a virus. I wrote a short program in JavaScript that did frequency analysis on the pairs. It took 30ms in Chrome. It is actually not all that difficult at a certain level of analysis. In my mind the big question is, how can we understand how it works? It is like giving you a binary for windows to reverse engineer it. My own question is; does my DNA makes me? If my grandkids have it on a memory stick (it can actually fit), would they be able to 're-construct' me in some form of virtual reality? A potential area for hackers to get involved in my opinion - is the potential of the Cloud. You can imagine say 10 million genomes stored out there at the not so distant future and distributed software analyzing it and indexing it and all the ethical and other problems that come from it.

Great interview and optimism. The $1,000 genome is indeed within sight. Let us hope that software will be evolving as fast to handle the data.

by yannis 17y ago

Great interview and optimism. The $1,000 genome is indeed within sight. Let us hope that software will be evolving as fast to handle the data.

njm 17y ago

It's not as much data as one might think, especially if you store the deltas -- there's not that much variation between individuals. That fact has actually been exploited to a great extent in enabling the $1,000 genome.

coderdude 17y ago
How much is "not much?" How many "values?" If stored as byte strings delimited by \n, how many lines? (I don't know if these are even answerable questions at this point, just wondering.)
- yannis 17y ago
  Put it that way you can store the genome of 8 people on an 8GB SanDisk Cruzer Micro USB flash drive. It is not that large.
  - coderdude 17y ago
    Very specific brand of flash drive. ;) Thanks for the figure.
    - yannis 17y ago
      It's optimized for cost!
bbgm 17y ago
The raw data (the original image files), while mostly transient today, is massive. At some of the big genome centers they are in the double digit TB's of data processing per day

acg 17y ago

Isn't this what the Genomics X Prize is about? Complete Genomics does not appear to be a team: http://genomics.xprize.org/ http://genomics.xprize.org/

ericb 17y ago

So DNA is a long string, with certain identified parts that have meaning (code for something we know). What would a layman like myself need to get myself to a hello world program that could take an actual DNA string(file) as input and give a hello for the presence an actual known gene? Not code-wise, that's obvious. I'm asking where I could get a sample genome, information about a gene, fill in the gaps of my understanding, etc. Anyone know?

bbgm 17y ago
While not genome centric (it's genotype-based) Promethease is one example http://www.snpedia.com/index.php/Promethease http://www.snpedia.com/index.php/Promethease 23andme's software does a pretty good job. You can also use the UCSC genome browser although it probably as a learning curve for most. http://genome.ucsc.edu/ http://genome.ucsc.edu/ Honestly, I believe that people need to understand the biology, some depth of what genes are, and what SNPs are etc. It's important as molecular medicine becomes the norm (still some ways away).
yannis 17y ago
You can start with your favorite language by downloading a library, there is bioPerl, bioPython, bioRuby and even bioPHP! The libraries have all the routines to connect to public sources. The National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/nuccore/89889045?report=fasta&log$=seqview http://www.ncbi.nlm.nih.gov/nuccore/89889045?report=fasta&#3... has an enormous database and is all open source. The link I quoted lists the genome for a virus. I wrote a short program in JavaScript that did frequency analysis on the pairs. It took 30ms in Chrome. It is actually not all that difficult at a certain level of analysis. In my mind the big question is, how can we understand how it works? It is like giving you a binary for windows to reverse engineer it. My own question is; does my DNA makes me? If my grandkids have it on a memory stick (it can actually fit), would they be able to 're-construct' me in some form of virtual reality? A potential area for hackers to get involved in my opinion - is the potential of the Cloud. You can imagine say 10 million genomes stored out there at the not so distant future and distributed software analyzing it and indexing it and all the ethical and other problems that come from it.