PLOS ONE

GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components

Publishing date: 2018-10-23 Published on: PLOS ONE summary: This paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development.

Testing for physical validity in molecular simulations

Publishing date: 2018-09-06 Published on: PLOS ONE summary: None authors: Pascal T. Merz, Michael R. Shirts link to paper: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202764 Icons made by catkuro from www.flaticon.com

PSoC-Stat: A single chip open source potentiostat based on a Programmable System on a Chip

Publishing date: 2018-07-25 Published on: PLOS ONE summary: The potentiostat presented here from Prattana Lopin and Kyle V. Lopin can measure the presence of chemicals including vitamin C and lead without any external electronic components.

Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization

Publishing date: 2018-07-17 Published on: PLOS ONE summary: None authors: None link to paper: http://dx.doi.org/10.1371/journal.pone.0199771 Icons made by catkuro from www.flaticon.com

OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer

Publishing date: 2018-07-11 Published on: PLOS ONE summary: The accurate quantification of cellular and mitochondrial bioenergetic activity is of great interest in medicine and biology. This study provides statistical good practices to support experimentalists in designing, analyzing, testing, and reporting the results of mitochondrial stress tests using this high throughput platform.

Efficient methods and readily customizable libraries for managing complexity of large networks

Publishing date: 2018-05-29 Published on: PLOS ONE summary: One common problem in visualizing real-life networks, including biological pathways, is the large size of these networks. Often times, users find themselves facing slow, non-scaling operations due to network size, if not a “hairball” network, hindering effective analysis.

Open-source micro-tensile testers via additive manufacturing for the mechanical characterization of thin films and papers

Publishing date: 2018-05-29 Published on: PLOS ONE summary: None authors: Krishanu Nandy, David W. Collinson, Charlie M. Scheftic, L. Catherine Brinson link to paper: 10.1371/journal.pone.0197999 Icons made by catkuro from www.

A ‘smart’ tube holder enables real-time sample monitoring in a standard lab centrifuge

Publishing date: 2018-04-16 Published on: PLOS ONE summary: In order to measure what happens to samples while being centrifuged, the authors created an adaptor that combines electronics and 3D printed parts to measure in real time how concentration changes along a tube containing samples, allowing protocol optimization.

pyBadlands: A framework to simulate sediment transport, landscape dynamics and basin stratigraphic evolution through space and time

Publishing date: 2018-04-12 Published on: PLOS ONE summary: Understanding Earth surface responses in terms of sediment dynamics to climatic variability and tectonics forcing is hindered by limited ability of current models to simulate long-term evolution of sediment transfer and associated morphological changes.

webpic: A flexible web application for collecting distance and count measurements from images

Publishing date: 2018-04-02 Published on: PLOS ONE summary: Despite increasing ability to store and analyze large amounts of data for organismal and ecological studies, the process of collecting distance and count measurements from images has largely remained time consuming and error-prone, particularly for tasks for which automation is difficult or impossible.