Magic Touch of Roche, New Convey Server, 'Deep Understanding' of Variants and

Magic Touch of Roche, New Convey Server, 'Deep Understanding' of Variants and

1. Pacific Biosciences to Partner With Roche on In Vitro Diagnostics Products

The previous commentary is updated with information on what the deal may imply on the operational front. At least some key engineers and bioinformaticians will get diverted, but we hope they continue to keep the highly informative PacBio github page updated.

In the bigger picture, we get cold shivers, when three words come together - (i) diagnostics, (ii) human, (iii) Roche. Lex Nederbragt seems to have similar fear.


Several years back, we used to work with the products of an array company that was way ahead of its time. Then the technology disappeared. Part of that disappearance is due to the untimely passing away of founder Franco Cerrina. However, Nimblegen made a mess by trying to chase the diagnostics market, while underinvesting in keeping up with the Moore’s law. Franco told us in 2007 that he had a prototype for next-generation custom oligo-array instrument that could be affordable by individual labs at $10 or below per array. Here is what followed instead.

Roche NimbleGen to Quit Array Market, Lay off Majority of Staff, Close European Facilities

Roche has decided to shutter its NimbleGen microarray business, and will phase out array production and services by the end of the year. At the same time, the firm will continue to provide target enrichment products for use with next-generation sequencing, a spokesperson confirmed last week.

2. On the hardware front, Convey computer announces new hybrid-core server. This new server is currently being used by the San Diego Supercomputer Center to accelerate a key layer of their storage hierarchy.

Convey Computer , the leader in hybrid-core computing, today announced the latest addition to their hybrid-core (HC) series. The Convey HC Memcached appliance provides an order of magnitude higher throughput than commodity servers, while maintaining sub-millisecond response time. Additionally, the new Convey HC Memcached server dramatically reduces cost of ownership by slashing power, cooling, and maintenance costs.

Full press release can be accessed here. Does any reader of our blog have experience of working on Convey machines? Please feel free to comment.

3. Transcriptome and genome sequencing uncovers functional variation in humans

We love their claim in the abstract -

Altogether, this study provides a deep understanding of the cellular mechanisms of transcriptome variation and of the landscape of functional variants in the human genome.

Does ‘deep sequencing’ equate ‘deep understanding’, or is there anything more? Dan Graur says -


4. Mike White Chimes in on GMO Debate

The Scientific Debate About GM Foods Is Over: Theyre Safe

A focus on the risks and benefits of all new crops could move the debate in a direction that would prompt scientists, companies, and regulators to more clearly justify the role GMOs play in our food supply. To date, consumers nervous about GMOs have been given little reason to think that companies like Monsanto are designing GM crops to solve any problem other than the one of patents and profits. As journalist Mark Lynas put it in his rousing defense of GM foods, for most people GMOs are about a big American corporation with a nasty track record, putting something new and experimental into our food without telling us.

But many researchers working on GM crops are in fact trying to solve important problems, such as feeding a growing population, keeping food prices affordable worldwide, making healthier fruits and vegetables widely available, confronting the challenging growing conditions of a changing climate, saving Floridas oranges or Hawaiis papaya from pests, and fighting malnourishment in the developing world. For many of these problems, genetic engineering is faster, more cost-effective, and more reliable than conventional breeding methods.

We disagree with him, because ‘scientific debate’ is a non-issue. The articles like his are symptoms of our compartmentalized society, where scientists refuse to learn about economics but are still allowed to talk as ‘experts’ in their narrow areas of expertise. Food prices are rising all over globe due to disastrous money-printing policies of the central banks. Since the 2008 crash, ‘inflation’ or printing money has been suggested as the only prescription for fixing things, whereas sending the banskters to jail could have done the job much better. Scientists either do not have much understanding of how money is created, or choose to look the other way, thus condoning behavior of the banker. It is even worse, when they try to push various techno-narcissist solutions for an economic evil.

Written by M. //