Craic has published a detailed tutorial on using Google's BERT language representation model to classify biomedical research papers.

This approach combines the large pre-trained dataset in BERT with fine-tuning using domain-specific set of Pubmed abstracts. The resulting model is able to distinguish between papers that describe therapeutic antibodies against human antigens from other papers with an accuracy of around 91%, much higher than other approaches using term frequencies, etc.

The tutorial and associated data preparation scripts can be found on GitHub.

Arduino Power provides an open-source hardware and software solution to managing the power for portable systems using Arduino microcontrollers.

The hardware links an Adafruit PowerBoost Shield and a Data Logging Shield to an Arduino, with software that monitors and logs battery voltage to an SD card.

The circuits and software are available on GitHub and are distributed freely under the MIT license.

Pi Power provides a hardware and software solution to managing the power sources for portable Raspberry Pi projects that works like many mobile phones.

It implements the functions that we have grown to expect on mobile phones:

• Power up / Power down by pushing a button
• Automatic charging when a USB power cord is connected
• A simple status showing how much battery life remains
• An alert when the battery is very low
• Safe shutdown when the battery runs out

The hardware links an Adafruit PowerBoost 1000C charger to the Pi and two background scripts monitor the battery and update the status LEDs.

Pi Power appears to be the first complete solution to powering portable Pi systems.

The circuits and software are available on GitHub and are distributed freely under the MIT license.

Our paper describing the genome of the nitrogen-fixing soil bacterium Azotobacter chroococcum has been published in the journal PLoS One.

Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)

Robert L. Robson, Robert Jones, R. Moyra Robson, Ariel Schwartz, Toby H. Richardson

You can find the paper HERE

Rob Robson has worked on A.chroococcum since the 1980s, back when he was my Ph.D. supervisor. Working together on this project to sequence and characterize the entire genome has been an excellent way to mark his research career.

GenBank has released the genome sequence of the nitrogen fixing bacterium Azotobacter chroococcum and its six plasmids.

A.chroococcum NCIMB 8003 (ATCC 4412) is a free-living member of the gamma-proteobacteria used in studies of nitrogen fixation and hydrogen metabolism. This strain contains six plasmids.

The project has been a collaboration between Rob Jones (Craic), Rob and Moy Robson (Univ. Reading, UK) and Ariel Schwartz and Toby Richardson (Synthetic Genomics, USA).

Links to the Sequence data and other resources can be found at azotobacter.craic.com.