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 Commission

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


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.

Apache Spark

Yesterday I attended a seminar on Apache Spark, and thought the readers may find this new technology interesting for their programming and data analysis. There is no bioinformatics connection at the moment, and I am simply mentioning it as a type of fault-tolerant software- hardware technology with a lot of development work going on, and may turn out to be useful in the future.

CRISPR Fight and the Corrosive Role of Bayh-Dole Act in Damaging Basic Science

Readers wanted us to comment on the ongoing dogfight related to CRISPR patents. Only thing we can say is that patents related to publicly funded research should be placed in the public domain, because otherwise the patent fight damages basic research at several levels.

The Heroes of CRISPR - Lander

Eric Lander wrote an excellent article reviewing the history of CRISPR. It is well-written and covers fascinating stories about the early scientific work of some of the key players. A take-home message is that unusual discoveries in basic science do not start from the heavily funded famous labs. Kudos to Lander for recognizing the roles of young, unknown and risk-taking scientists in pursuing such discoveries.

Protip - Don't Shout at Your Computer

Amazing video -

Bringing Arbitrary Compute to Authoritative Data

Computation on large data sets often require copying files from ‘storage’ to the ‘computing node’. That leads to creation of second copy of original data file, which itself is large, and the process is inefficient. There could be another model, where ‘compute’ is brought to data stored only once. In this context, readers may enjoy the following two papers -

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