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”.
Publishing date: 2018-10-23
Published on: PLOS Computational Biology
summary: In this paper, Gelfman et al. present an open-source R package ‘meaRtools’ that provides a platform for analyzing neuronal networks recorded on Microelectrode Arrays (MEAs).
Publishing date: 2018-10-23
Published on: PLOS Computational Biology
summary: Whilst many open source projects enter the spotlight as trend-setting new software packages, it’s nice to appreciate some of the long-lived projects as well.
Publishing date: 2018-08-17
Published on: PLOS Computational Biology
summary: Garrido-Martín et al. present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments, a feature unique to this software.
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
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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.
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.
Publishing date: 2018-05-10
Published on: PLOS Computational Biology
summary: The field of neuroimaging is rapidly adopting a more reproducible approach to data acquisition and analysis. Data structures and formats are being standardised and data analyses are getting more automated.
Publishing date: 2018-04-18
Published on: PLOS Computational Biology
summary: Pathogen genome sequencing can reveal details of transmission histories and is a powerful tool in the fight against infectious disease. In particular, within-host pathogen genomic variants identified through heterozygous nucleotide base calls are a potential source of information to identify linked cases and infer direction and time of transmission.
Publishing date: 2018-04-13
Published on: PLOS Computational Biology
summary: Modern microscopes allow us to acquire high quality external images of biological specimens, however, these can only be obtained at the very surface of the specimen.