PLOS ONE

Assessing the impact of introductory programming workshops on the computational reproducibility of biomedical workflows

Publishing date: 2020-08-18 Published on: PLOS ONE summary: This mixed methods study consisted of in-depth interviews with 14 biomedical researchers before and after participation in an introductory programming workshop. During the interviews, participants described their research workflows and responded to a quantitative checklist measuring reproducible behaviors.

RefShannon: A genome-guided transcriptome assembler using sparse flow decomposition

Publishing date: 2020-08-18 Published on: PLOS ONE summary: High throughput RNA-Seq has become a staple in modern molecular biology, with applications not only in quantifying gene expression but also in isoform-level analysis of the RNA transcripts.

Development of a low-cost, user-customizable, high-speed camera

Publishing date: 2020-06-15 Published on: PLOS ONE summary: Channel Editor Summary: The paper describes a high speed camera system, capable of reaching frame rates of ~2300 frames per second in its max speed setting.

A practical 3D-printed soft robotic prosthetic hand with multi-articulating capabilities

Publishing date: 2020-05-14 Published on: PLOS ONE summary: None authors: Alireza Mohammadi, Jim Lavranos, Hao Zhou, Rahim Mutlu, Gursel Alici, Ying Tan, Peter Choong, Denny Oetomo link to paper: 10.1371/journal.pone.0232766

Dataflow programming for the analysis of molecular dynamics with AViS, an analysis and visualization software application

Publishing date: 2020-04-21 Published on: PLOS ONE summary: None authors: Kai Pua, Daisuke Yuhara, Sho Ayuba, Kenji Yasuoka link to paper: 10.1371/journal.pone.0231714 Icons made by catkuro from www.flaticon.com

Multiple social platforms reveal actionable signals for software vulnerability awareness: A study of GitHub, Twitter and Reddit

Publishing date: 2020-03-24 Published on: PLOS ONE summary: None authors: Prasha Shrestha, Arun Sathanur, Suraj Maharjan, Emily Saldanha, Dustin Arendt, Svitlana Volkova link to paper: 10.1371/journal.pone.0230250 Icons made by catkuro from www.

A portable, low-cost device for precise control of specimen temperature under stereomicroscopes

Publishing date: 2020-03-11 Published on: PLOS ONE summary: None authors: Nicholas D. Testa, Samiksha Kaul, Kim N. Le, Mei Zhan, Hang Lu, Annalise B. Paaby link to paper: 10.1371/journal.pone.0230241 Icons made by catkuro from www.

Metrics for graph comparison: A practitioner’s guide

Publishing date: 2020-03-03 Published on: PLOS ONE summary: Comparison of graph structure is a ubiquitous task in data analysis and machine learning, with diverse applications in fields such as neuroscience, cyber security, social network analysis, and bioinformatics.

pyKNEEr: An image analysis workflow for open and reproducible research on femoral knee cartilage

Publishing date: 2020-03-03 Published on: PLOS ONE summary: Channel Editor Summary: Sometimes, all the available algorithms to perform a scientific task are either closed source, or just too complex to easily be re-used by others.

Repository-based plasmid design

Publishing date: 2020-03-03 Published on: PLOS ONE summary: There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU.