Technologies


Illumina Offers to Donate Pacbio Patents, But Will That Save Oxford Nanopore?

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

Woodford's WEIF Dead, Oxford Nanopore IPO Doubtful

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

All Against All Fight Breaks Out among the Sequencing Businesses

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

Uncertainty over Pacbio-Illumina Deal May Spill over to Oxford Nanopore

A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.

Illumina Buys Pacbio, What Are the Implications?

How does Multi-threaded Code Run in Assembly Language?

In the traditional model of computing, programmers write their codes in C or other high-level (i.e. human-readable) languages. Then a compiler (e.g. gcc) converts that code into assembly and machine (byte) instructions. This is because the microprocessor can understand only 0s and 1s, whereas the humans tend go crazy trying to make sense of such code. The assembly language is a happy compromise between the two. It presents the machine or byte-instructions in human-readable format.

After Docker

The Lab That Invented Nanopore Sequencing

Yesterday, I attended an interesting talk by Ian Derrington, who is currently working as a post-doctoral researcher in the lab of professor Jens Gundlach at the University of Washington (UW). For those who do not know, Gundlach lab is the first to identify and use MspA as an efficient pore molecule for nanopore sequencing, and they published several key papers related to development of the technology over the years. In my understanding, Illumina’s licensing of MspA-related patents from UW is the basis of their IP lawsuit against Oxford Nanopore.

Illumina's 'Surprise' Announcement is not Surprising

Disclaimer: The following post is not financial advice. It is only for entertainment purpose.

Sequencing Technology Comparison Chart - 2016

Is "Huge" Business Downturn Coming in the Sequencing Industry?

[Note: Following post is not investment advice.]

Growing Human Brain on a Petri Dish

In a remarkable feat, Professor Rene Anand of Ohio State University, one of our collaborators from the electric eel genome project, grew near complete human brain organoids on a petri dish in his lab. Here is how the method works. He starts from the skin cells of a person (could be you) and reprograms them into induced pluripotent stem cells (iPSCs) using Yamanaka’s method. Then he grows those stem cells into neural organoid, and you can see your ‘baby brain’ sitting in a test tube. It is truly your brain, because it has the identical genome as yours.

CRISPR-directed mitotic recombination enables genetic mapping without crosses

Linkage and association studies have mapped thousands of genomic regions that contribute to phenotypic variation, but narrowing these regions to the underlying causal genes and variants has proven much more challenging. Resolution of genetic mapping is limited by the recombination rate. We developed a method that uses CRISPR to build mapping panels with targeted recombination events. We tested the method by generating a panel with recombination events spaced along a yeast chromosome arm, mapping trait variation, and then targeting a high density of recombination events to the region of interest. Using this approach, we fine-mapped manganese sensitivity to a single polymorphism in the transporter Pmr1. Targeting recombination events to regions of interest allows us to rapidly and systematically identify causal variants underlying trait differences.

Illumina Sues Britain's 'Most Highly Valued Company' at US International Trade

Forbes reports -

Patents vs GPL, Who Wins? A Case Study

Between 2000-2005, computer company SUN Microsystems developed a number of major improvements (zones, ZFS, dtrace) to Solaris, which was their version of the unix operating system. Then in 2005, SUN released all Solaris code publicly through a CDDL license along with 1600 patents. The CDDL license was GPL incompatible, and therefore linux authors could not copy Solaris code and claim as their own.

War of Standards - XML vs JSON

By mid-90s, software companies started to think about ways to make sure millions of would be internet-connected devices talk to each other. XML, a generalized version of highly popular HTML, was one possible option. In fact, for many years it was the only option. XML standards were designed in mid-90s by a committee of eleven well-respected programmers and had widespread backing from companies.

Major Security Hole Discovered in Popular Library glibc

The Most Important Part of Flatley's #AGBT16 Talk

Capture

Two Potentially Important Developments on Nanopore

The first paper demonstrates selective sequencing, whereas the second ones improves accuracy by introducing circularization.

Genomic Analysis with Spark - A Few Examples

Yesterday’s post on Spark mentioned that the technology is not being used in bioinformatics. That is not entirely correct, and we came across a (small) number of mentions here and there.

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