Today's Highlights -

Today's Highlights - "The Other Side of Academic Freedom"

A. The other side of “academic freedom” h/t: @genetics_blog

When we wrote “When to Leave the Academia (University Cartel)?”, we learned that commentaries on leaving academia gets far more attention that commentaries about science, genome assembly and, God forbid, complex bioinformatics algorithms.

In the linked commentary, Harvard CS professor Matt Welsh told readers, why he left academia to join Google. Even though he got tenure and was ‘free to do anything’, he explained that he was not really ‘free’, because his innovative, non-mainstream ideas did not get funding. That had been a less acknowledged aspect of academia that is being mentioned more often these days with funding cuts for small projects. Interestingly, it gets reinforced by cowardly behavior of those at relatively high positions, such as Sean Eddy. When he gives tacit support for ‘big science’ projects, such as ENCODE and human brain mapping, it results in more funding being sucked away from small, innovative ideas and more Matt Welshes leaving for ad companies.

Suggestion from Titus Brown based on Matt Welsh’s commentary -

Some advice to young graduate students

If you are a gradate student, and whether or not you are definitely planning to go into academia, or toying with going into biotech or a startup, or completely uncertain, write a professional blog.

B. Good Seqanswers Discussion on Aligning Ion Torrent Data h/t: lex


TMAP works very well. Bowtie pretty bad. CLC (commercial) worked just as good as TMAP. Mosaic worked fine, too. I generally find if you follow the manufacturers recommendations things seem to work pretty well. Our strategy is looking to be TMAP for on “torrent” server analysis and CLC for off server custom analysis. I haven’t really tested anything more since everything is working just fine and compares well with previous work we’ve done.

C. Deanna Church on the Reference Genome Past, Present and Future

D. An Introduction to Social Media for Scientists h/t: @genetics_blog

E. In biggest business news, Roche quit collaborating with IBM on nanopore sequencing.

Here are a set of press releases from 2010-2013:


Roche and IBM Collaborate to Develop Nanopore-Based DNA Sequencing Technology

YORKTOWN HEIGHTS, N.Y. & BRANFORD, Conn. - 01 Jul 2010: Roche (SIX: RO, ROG; OTCQX: RHHBY) and IBM (NYSE: IBM) announced today an agreement to develop a nanopore-based technology that will directly read and sequence human DNA quickly and efficiently. Focused on advancing IBM’s recently published “DNA Transistor” technology, the collaboration will take advantage of IBM’s leadership in microelectronics, information technology and computational biology and Roche’s expertise in medical diagnostics and genome sequencing.

The novel technology, developed by IBM Research, offers true single molecule sequencing by decoding molecules of DNA as they are threaded through a nanometer-sized pore in a silicon chip. The approach holds the promise of significant advantages in cost, throughput, scalability, and speed compared to sequencing technologies currently available or in development.


Roche Acquires License to Nanopore Technology with Sights on $1,000 Whole Genome Sequencing

Roche negotiated a license to nanopore-based DNA base sensing and reading technologies from the Biodesign Institute at Arizona State University and the Columbia University Nanoscience Center. The firm claims that these new technologies could help take the cost of sequencing a whole human genome down to well under $1,000.

The technologies will be used by Roches sequencing center and collaborators 454 Life Sciences and IBM to develop and commercialize a single-molecule nanopore DNA sequencer. The deal was brokered by Arizona State Universitys technology transfer arm, Arizona Technology Enterprises, and includes sponsored research funding to help the academic researchers progress development of the technology toward commercialization.


Nanopore Genome Sequencer Makes its Debut- Technique Promises it will Produce a human genome in 15 Minutes

Technology that its parent company says will sequence a human genome in just 15 minutes opened its first data run to scrutiny today.

Oxford Nanopore Technologies, based in Oxford, UK, revealed the initial results from its GridION system at the Advances in Genome Biology and Technology meeting in Marco Island, Florida. The firm expects to start selling its new machine in the second half of this year and also plans to launch the worlds first miniaturized, disposable sequencer the MinION which will retail for less than US$900.

Did you notice that the price went down from $1000 to $900?


Roche Dissolves Applied Science Unit as It Ends IBM Alliance

Roche Holding AG (ROG) will dissolve its Applied Science unit as it sees further price pressure and funding cuts in life-science research and said its ended an alliance with International Business Machines Corp. (IBM)

Even $900-$1000 is too high a price for vaporware !!!

DNA Electronics confirms continued development of its DNA sequencing solutions using semiconductor technology

Regius Professor Chris Toumazou, CEO and founder of DNA Electronics, a thought-leader in the semiconductor technology, commented I would like to thank Roche for our fruitful collaboration and for handing us back the project. Harnessing additional unlicensed IP, and without any limitations on field of use, DNAe will now continue the development of the platform but with a new focus to create a disruptive total solution.

Four Lessons From IBM And Roche’s Failed DNA Collaboration

This is a lesson weve learned over and over again. Its even true for startups that take a Silicon-Valley approach. Take Pacific Biosciences of California, another DNA sequencer maker. The company announced vaporware, raised huge amounts of venture capital, and made an pedal-on-the-gas push to try to take over the DNA sequencing market. Its machine came up short, and the failure to find a niche has left it looking for a purposes.

**We do not think our readers from PacBio will be too happy to read the above text! PacBio instrument is not vaporware. **

Written by M. //