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riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data

Publishing date: 2018-08-13 Published on: PLOS Computational Biology summary: None authors: None link to paper: http://dx.doi.org/10.1371/journal.pcbi.1006169 Icons made by catkuro from www.flaticon.com

Digital open science—Teaching digital tools for reproducible and transparent research

Publishing date: 2018-07-26 Published on: PLOS Biology summary: An important hallmark of science is the transparency and reproducibility of scientific results. Over the last few years, internet-based technologies have emerged that allow for a representation of the scientific process that goes far beyond traditional methods and analysis descriptions.

OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement

Publishing date: 2018-07-26 Published on: PLOS Computational Biology summary: Movement is fundamental to human and animal life, emerging through interaction of complex neural, muscular, and skeletal systems. Study of movement draws from and contributes to diverse fields, including biology, neuroscience, mechanics, and robotics.

PyPhi: A toolbox for integrated information theory

Publishing date: 2018-07-26 Published on: PLOS Computational Biology summary: Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, the authors introduce PyPhi, a Python software package that implements this framework for causal analysis and unfolds the full cause-effect structure of discrete dynamical systems of binary elements.

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.

Shedding Light: A New Open Source Imaging System

Publishing date: 2018-07-04 Published on: PLOS Research News summary: An interview with Isaac Nuñez and Tamara Matute, authors of the research article that was awarded the 2018 PLOS Open Source Toolkit Channel Prize.

CellProfiler 3.0: Next-generation image processing for biology

Publishing date: 2018-07-03 Published on: PLOS Biology summary: CellProfiler is a free software that has enabled researchers, without training in computer vision or programming community to create flexible, modular image analysis pipelines since its release in 2005.

Why open source isn't just about code

Publishing date: 2018-06-01 Published on: TechRepublic summary: Abby Cabunoc Mayes of the Mozilla Foundation explains why open source is about culture as much as it is about code. authors: Dan Patterson & Abby Cabunoc Mayes