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...and for balance, here's a slightly more sceptical take on the announcement:

http://www.omespeak.com/blog/?p=507

'Until ONT demonstrates actual sequencing of a more complicated genome (a microbial one at minimum), there will be a healthy degree of skepticism,'

See also:

http://omicsomics.blogspot.com/2012/02/oxford-nanopore-doesnt-disappoint.html

'So, Oxford has unveiled an amazing pair of sequencers. Not one which completely clears the field of everyone else, but one which will offer a host of new opportunities for genomics. Now it is up to Oxford to deliver the instruments to the field, and for Oxford and its early access sites to start pumping out data for all to evaluate. '

and:

http://www.bio-itworld.com/news/02/17/12/Oxford-strikes-first-in-DNA-sequencing-nanopore-wars.html

'...he nanopore war is about to start.'

The world's most expensive iPod dock and it doesn't even come with speakers :-)

How are you finding it? Looks useful for smaller -scale (subgenomic or bug) projects where the capacity of a bigger machine would be wasted. And the concept of a 'massively parallel pH meter' is certainly cool.

For human whole-genome stuff there are already relatively cheap options. Illumina now offers a genome service for $4000 per sample in quantity:

http://www.bio-itworld.com/news/05/09/2011/Illumina-announces-five-thousand-dollar-genome.html

So the '$1000 genome' can't be far off, and may well be available as a commercial service before Ion Torrent can offer a competing solution for their machine. They already have a bit of a reputation for hype:

http://pathogenomics.bham.ac.uk/blog/2010/12/ion-torrent-hype-cycle-status-disappointment/

Note that the original article is misleading about the competing technologies, implying that the (existing) Ion Torrent costs $49000 because it uses 'optical based' technology. In fact the Ion Torrent (unlike the Illumina system, which does use an optical system) has always been semiconductor-based:

http://en.wikipedia.org/wiki/Ion_semiconductor_sequencing

The key issue, of course, is the cost and sequencing capacity of the (disposable) chips it uses, not the one-time cost of the machine. Right now, the comsumable costs are pretty high per sequenced base when compared to Illumina's. The Ion Torrent chip technology needs to be scaled up substantially if they want to offer a viable genome solution.

Early in 2007, GS FLX sequencer (a higher throughput iteration of GS20) from 454/Roche became available; in October 2007, Baylor college of medicine purchased 10 FLX instruments; also in 2007, Project Jim resulted in the first whole human genome to be sequenced using second-generation sequencing technology.

'The incoming data is image-based, so yes, it will be huge.'

The image data is routinely discarded by at least some major centres; the raw sequence and quality data alone is huge enough to be a major issue! See:

http://www.bio-itworld.com/news/09/16/10/Broad-approach-genome-sequencing-partI.html

'It's been a couple of years since we saved the primary [raw image] data. It is cheaper to redo the sequence and pull it out of the freezer. There are 5,000 tubes in a freezer. Storing a tube isn't very expensive. Storing 1 Terabyte of data that comes out of that tube costs half as much as the freezer! People [like Ewan Birney at EBI] are working on very elaborate algorithms for storing data, because you can't compress bases any more than nature already has. The new paradigm is, the bases are here, only indicate the places where the bases are different . . . In 2-3 years, you'll wonder about even storing the bases. And forget about quality scores.'

I think you are confusing actual research with ...

Then sit back down and shut up while you think about it. While you're sitting there, ostensibly thinking, here is some material to consider:

• Real-time cone-beam CT image reconstruction using a mercury's dual cell-based system (DCBS) and a Sony's Playstation 3 (PS3) cluster
• Playstation 3 Consoles Tackle Black Hole Vibrations
• PS3 boosts protein research plan
• Building Supercomputer Using Playstation 3
• PlayStation Cell Speeds Docking Programs
• Researchers Use PlayStation Cluster to Forge a Web Skeleton Key
• Playstation cluster creates cheap supercomputer
• and so on..

Garbage products like xbox have gone down in flames (pun intended) and MS has to make smoke (no pun intended) and noise to distract from the situation. Same crowd is going on attack against OpenOffice.org and other key products. The universal office format, OpenDocument Format, is getting specialized attackers. Repeat lies often enough that people believe them seems to be an ongoing theme from MS.

Whether 1-, 8-. 16, or 32-node clusters, PS3s are useful in computationally intensive tasks. I'd like to see an add-on for Blender or other 3D software that allows adding a PS3 as a single node cluster. If it's there and you're working with a desktop, why not also use the processors of the otherwise idle gaming machine

I think that David Shaw, founder of D.E. Shaw, would be a very good choice for either position. His background is in computer science, yet he is a true renaissance man -- after building one of the largest hedge funds in the world (you've probably noticed the recruiting ads on /. by now!), he is working on building the world's fastest protein folding computer. The man is truly a genius, and undoubtedly has knowhow. I think he'd be a great candidate. He also seems to be quite humble, I went to one of his talks on molecular simulations recently.

Hopelessly out of date :-) I think your talking about Expressed sequence tags (EST)

The central dogma of biology is DNA makes RNA makes Protein (but since this is biology there are exceptions :-)

• Think of DNA as the source code (Exons) with lots and lots of commented out text (Introns)

• RNA is the executable with all the commented out text has been removed

• the RNA provides the patten to make protein by, so if you know what RNA molecules are in a cell you know to a first approximation what proteins are in that cell.

Its possible to decompile the RNA executable back into DNA (using Reverse transcriptase (this is important because RNA is unstable and easily breaks down).

I think thats enough background ... What you do is take some living tissue flash freeze in in liquid nitrogen extract the RNA convert it back to DNA, clone all the resultant DNA molecules (yielding ~50 thousand clones)then pick one at random and do a quick and dirty sequencing on it. Wash rince repeat dump the results in a database

Back when sequenceing was expensive it was a useful way of snagging genes without having to struggle though mega bases of DNA. Now you can sequence whole genomes (small ones:) in a week and are talking about doing the individual human genomes in a matter of months/. EST data provides support for computational gene predections (just because something looks like a gene, quacks like a gene doesn't mean that it is ever expressed (used) like a gene:-)

The coverage was 8x (average). This was done with complete de novo ( i.e. from scratch ) sequencing and did not use the human genome except as a reference at the end.

http://www.bio-itworld.com/newsitems/2007/may/05-3 1-07-watson-genome

As for the 2 DVD's, most people are correct. If you just transmitted the base pairs and compressed it with bz2 (or whatever), you could get ~ 600 MB. But the file includes some meta-data (mostly having to do with read quality, etc.)

In any case, if you want to DO anything with the data, you have to get it onto a workstation to manipulate it. 1 DVD, 2 DVD's, doesn't really matter. There really isn't a push to make it smaller - the push is to make it simpler/faster to work with subsets of the data. Nothin's easier than a nice, flat ASCII file for that.

I work at 454, a totally kick-ass company, BTW. The people here put in an incredible effort getting this job done. Publicity stunt or not, $1M for a human genome in 3 months is quite an accomplishment. Human Genome Project? $3B and it took 13 years. You do the math.

Caroline Benner is a fellow at the University of Washingtons Institute for International Policy. From 2001 to 2003, Ms. Benner was a consultant with the geopolitical policy and strategy group at Microsoft.

Just what does a software company need a Geopolitical Policy and Strategy Group for anyway? Gobal FUD? Creepy, and she's got a long history of M$ apologies and FUD to her name. Let's review,

• Not embarrassed by M$ virus penetration of Pentagon systems or disruption of NASA communications endagering the Space Shuttle and five months before the 9/11 attacks she tells us not to worry about cyber terrorists because the mighty M$ can deal with such unskilled attackers through patches., " time and access one needs to create a devastating attack, like crashing an airplane. In "Six Nightmares," Lake doesn't consider the checks that protect infrastructure from such threats. He also fails to ask an obvious question: If there are so many malicious hackers at work (19 million, by Lake's count), why have their attacks been, by and large, fairly innocuous?" M$ forsight. Let's review what happened next:
  • 9/11 demonstrated to the world that there were indeed many well organized terrorists wanting to harm US citizens and how venerable rescue efforts were to disruption of communications.
  • US Government drafts defense plan
  • Chinese attack plans are revealed by the CIA
  • Still M$ languishes and languishes working on DRM and other lock out crap.
  • M$ incompetence contributes to the biggest US blackout ever by disrupting critical company communications and overloading network. The whole thing could have been prevented.
  • North Korea launches cracker schools.
  • The US Air force Mission is updated to include net dominance
  • US Government turns to superior Free Software
  • Home and business users lag, causing havoc in hospitals, threatening medical and accounting records and creating a hotbed of exploitable computers for spam and spam and spam and denial of service attacks used against EVERYONE.
• 2004 apologies, security is too hard! Duhhhhh, if M$ is not up to task no one is, right? Wrong.
• The FUD rolls on to this day check out Her new Blog! as she spews forth Pressing Questions.
  • Get the facts about how expensive and non free software is helping India and other developing coun

XMilkProject said: "...and it's also fair to say that most of the 4% of OSX users are in very non-technical fields, and far less likely to be capable of the technical mischief"

On the contrary it's Windows that is not up the task of running in highly technical areas. The University of Virginia built the currently 20th fastest supper computer in the world out of essentially stock Mac Xserves see: http://www.top500.org/lists/2005/11/basic

How many Windows boxes are on the top 500 list, hint, zero because Windows is not a supper computer class operating system. The BSD based Darwin is a real Unix, it can run XII and in fact G5 powermacs are used in genetics research as a full fledged workstation, despite being a consumer "desktop" computer etc.

See for example: http://www.bio-itworld.com/products/041604_finch.h tml

http://www.macobserver.com/article/2004/01/13.4.sh tml

Microsoft does make a decent word processor I wrote this in word, that's about as "technical" as I'd like to get with M$ software.

Please do some research before you just spout off a troll M'K?

I don't have a large library of such documents or links on hand, but you might try something like this (found near top of search list by by Google w/"large jury awards frequency" search):

http://www.rand.org/publications/RB/RB9025/RB9025. html
http://www.rand.org/publications/CT/CT143/

They are a little old, but I haven't heard any evidence to dispute that the trends have changed since then.

You'll note that although they do say that size of punitive damage awards is going up, they also say that "Despite the attention they have received from policymakers and from the media, punitive damages are rarely awarded". Rand isn't well-known for being a liberal think tank.

Many of the other links are heavily biased & seem to be oriented toward manipulating public perception - often by pointing out the increasing size of jury awards, and then stating without proof that both size AND frequency of jury awards are going up, and that's why we need tort reform.

Here's a link that is admittedly selected because it supports my viewpoint, but seems to list some cases to back up their claims:

http://cms.bio-itworld.com/newsitems/2005/Aug2005/ 08-30-05-opinion-merck/talkback/1125443244/discuss ionitem_view

... not every processor is documented. In fact, the documentation for a lot of high volume processors isn't available. I'd like PSP docs, or docs on the processor in the ipod, or even the processor in the disposable digital cameras or the VMU game system -- but none of these docs are publicly available. The hardware manual for the G5 PowerPC was finally published last November, over a year after apple started selling the hardware.

So, no, the documentation doesn't always get released.

Here is another article about Venter's journey:

Venter Makes Waves -- Again

The talk was his acceptance speech for the 2004 Benjamin Franklin Award at the BioIT-World conference.

The award was presented by bioinformatics.org. In his speech Lincoln talked about essentially open sourcing the R&D process and leaving the manufacturing and distribution to big Pharma. Thus, in theory, allowing academic R&D to push new drugs towards current public health concerns versus the money making drugs big Pharma produces now.

Not likely to happen but interesting to think about.