Research Article

FlexGraph: Flexible partitioning and storage for scalable graph mining

Publishing date: 2020-01-24 Published on: PLOS ONE summary: None authors: Chiwan Park, Ha-Myung Park, U. Kang link to paper: 10.1371/journal.pone.0227032 Icons made by catkuro from www.flaticon.com

A network-centric approach for estimating trust between open source software developers

Publishing date: 2020-01-15 Published on: PLOS ONE summary: None authors: Hitesh Sapkota, Pradeep K. Murukannaiah, Yi Wang link to paper: 10.1371/journal.pone.0226281 Icons made by catkuro from www.flaticon.com

Assemblage of Focal Species Recognizers—AFSR: A technique for decreasing false indications of presence from acoustic automatic identification in a multiple species context

Publishing date: 2020-01-15 Published on: PLOS ONE summary: None authors: Ivan Braga Campos, Todd J. Landers, Kate D. Lee, William George Lee, Megan R. Friesen, Anne C. Gaskett, Louis Ranjard

Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives

Publishing date: 2020-01-15 Published on: PLOS Genetics summary: None authors: Madison Caballero, Daniel N. Seidman, Ying Qiao, Jens Sannerud, Thomas D. Dyer, Donna M. Lehman, Joanne E. Curran, Ravindranath Duggirala, John Blangero, Shai Carmi, Amy L.

EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data

Publishing date: 2020-01-15 Published on: BMC Bioinformatics summary: This software article presents “https://github.com/MathOnco/EvoFreq">EvoFreq<, a comprehensive tool to visualise the evolutionary and population frequency dynamics of clones at a single point in time or as population frequencies over time using a variety of informative methods.

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data

Publishing date: 2020-01-15 Published on: PLOS ONE summary: Analysis of microbiome data involves identifying co-occurring groups of taxa associated with sample features of interest such as disease state. A key challenge in this is the composition and dimensionality of microbiome data.

Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data

Publishing date: 2020-01-15 Published on: BMC Bioinformatics summary: None authors: Shifu Chen, Yanqing Zhou, Yaru Chen, Tanxiao Huang, Wenting Liao, Yun Xu, Zhicheng Li & Jia Gu link to paper: https://bmcbioinformatics.

NUFEB: A massively parallel simulator for individual-based modelling of microbial communities

Publishing date: 2020-01-15 Published on: PLOS Computational Biology summary: None authors: Bowen Li, Denis Taniguchi, Jayathilake Pahala Gedara, Valentina Gogulancea, Rebeca Gonzalez-Cabaleiro, Jinju Chen, Andrew Stephen McGough, Irina Dana Ofiteru, Thomas P.

PyLandStats: An open-source Pythonic library to compute landscape metrics

Publishing date: 2020-01-15 Published on: PLOS ONE summary: Channel Editor Summary: PyLandStats is a fantastic example of an open source scientific package, with an open licence (GPL), clear documentation for both users and developers, and a source code repository set up to easily enable contributions and bug reports.

Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software

Publishing date: 2019-11-14 Published on: Giga Science summary: The authors have developed Bionitio, a tool that automates the process of starting new bioinformatics software projects following recommended best practices. With a single command, the user can create a new well-structured project in 1 of 12 programming languages.