Research Article

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA

Publishing date: 2019-02-27 Published on: PLOS ONE summary: The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data.

Design principles for open source bioinstrumentation: the poseidon syringe pump system as an example

Publishing date: 2019-02-01 Published on: bioRxiv summary: None authors: A. Sina Booeshaghi, Eduardo da Veiga Beltrame, Dylan Bannon, Jase Gehring, Lior Pachter link to paper: https://www.biorxiv.org/content/10.1101/521096v1 Icons made by catkuro from www.

Open-source automated chemical vapor deposition system for the production of two- dimensional nanomaterials

Publishing date: 2019-02-01 Published on: PLOS ONE summary: The study of two- dimensional (2D) materials is a rapidly growing area within nanomaterials research. However, the high equipment costs, which include the processing systems necessary for creating these materials, can be a barrier to entry for some researchers interested in studying these novel materials.

Open-Source Multiparametric Optocardiography

Publishing date: 2019-02-01 Published on: Scientific Reports summary: None authors: None link to paper: https://www.nature.com/articles/s41598-018-36809-y Icons made by catkuro from www.flaticon.com

optoPAD: a closed-loop optogenetics system to study the circuit basis of feeding behaviors

Publishing date: 2019-02-01 Published on: bioRxiv summary: The regulation of feeding plays a key role in determining the fitness of animals through its impact on nutrition. Elucidating the circuit basis of feeding and related behaviors is an important goal in neuroscience.

VasoTracker, a low-cost and open source pressure myograph system for vascular physiology

Publishing date: 2019-02-01 Published on: Physiology | Frontiers summary: None authors: Penelope F. Lawton, Matthew D. Lee, Christopher D. Saunter, John M. Girkin1, John G. McCarron and Calum Wilson link to paper: https://www.

Bayesian multiple logistic regression for case-control GWAS

Publishing date: 2019-01-17 Published on: PLOS Genetics summary: Genetic variants in genome-wide association studies (GWAS) are tested for disease association mostly using simple regression, one variant at a time. Standard approaches to improve power in detecting disease-associated SNPs use multiple regression with Bayesian variable selection in which a sparsity-enforcing prior on effect sizes is used to avoid overtraining and all effect sizes are integrated out for posterior inference.

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens

Publishing date: 2019-01-17 Published on: PLOS Computational Biology summary: Channel Editor’s Summary: To many, open source software means “free to use”, and to others it might mean “I can see and re-use the code freely”.

Validating quantum-classical programming models with tensor network simulations

Publishing date: 2019-01-17 Published on: PLOS ONE summary: The exploration of hybrid quantum-classical algorithms and programming models on noisy near-term quantum hardware has begun. As hybrid programs scale towards classical intractability, validation and benchmarking are critical to understanding the utility of the hybrid computational model.

Cell colony counter called CoCoNut

Publishing date: 2018-12-20 Published on: PLOS ONE summary: CoCoNut removes the need for slow and eye-straining manual counting of viable colonies under a microscope. It’s a semi-automated, image-based cell colony counting setup that combines 3D-printed hardware and an ImageJ plugin.