Software

Blogs about software

An illustration of SeqScreen's workflow (A) and the machine learning training framework (B)

An article published in the journal “Genome Biology” reports the results of tests conducted with SeqScreen, a free / open source software developed to recognize genetic sequences existing in pathogenic microorganisms. A team of researchers led by computer scientist Todd Treangen of Rice University and genomics specialist Krista Ternus of the scientific consultancy firm Signature Science, LLC developed SeqScreen to analyze the characteristics of short DNA sequences often called oligonucleotides and improve the recognition techniques of sequences present in a sample that are at least potentially dangerous.

Some cabinets of the Frontier supercomputer (Photo courtesy Carlos Jones/ORNL, U.S. Dept. of Energy)

The American Frontier supercomputer has been crowned the new king of the Top 500 ranking. It has a speed that is more than twice that of the Japanese Fugaku, the previous king. This is the first exascale supercomputer, which means that it’s capable of exceeding the calculation capacity of 1 exaflop with 10^18 floating point operations per second. Frontier reaches 1.102 exaflops per second.

Hock E. Tan (Photo courtesy Broadcom)

Semiconductor giant Broadcom Inc. announced that it has reached an agreement to buy virtualization and cloud software maker VMware in a deal worth approximately $61 billion that will be paid partly in cash and partly in shares. Broadcom takes over VMware’s debts, which amount to approximately $8 billion. Broadcom Software Group, the software subsidiary, will be integrated into VMware. With this acquisition, Broadcom can extend its business solutions offering.

Linus Torvalds in 2014

On August 25, 1991, Linus Torvalds (photo ┬ęKrd) announced in a message on the comp.os.minix newsgroup the project of a new operating system that actually diverged considerably from Minix. Unhappy with the Minix license, Torvalds adopted a license from the GNU project, the GPL, which seemed to him free enough. After a few weeks, the first Linux kernel was released. The availability of various components released by the GNU project and the contributions of several people who joined the project helped to spread it. Thirty years later, Linux is being used by virtually everyone in one way or another, even if only a small minority realize it.

A schematic of how the system called genomatnn recognizes adaptive introgression

An article published in the journal “eLife” reports the development of an approach based on convolutional neural networks (CNNs) to identify genes inherited from other species such as Neanderthals that brought positive effects. A team of researchers led by Graham Gower of the Danish University of Copenhagen developed this deep learning technique to examine genomes of modern humans for examples of what is technically called introgression, which means genes that a hybrid between two species brought into one of his parents’ species. Various possible examples have been found, for example, genes inherited from Denisovans have been found in Melanesians that affect various metabolic and disease-related traits.