Research Article

Reproducible big data science: A case study in continuous FAIRness

Publishing date: 2019-05-23 Published on: PLOS ONE summary: In recent years, researchers have access to larger volumes of data. More and more hypotheses are now developed and tested against existing data rather than by generating new data.

Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments

Publishing date: 2019-05-23 Published on: PLOS Computational Biology summary: This paper presents Stytra, a flexible, open-source software package, written in Python and designed to cover all the general requirements involved in larval zebrafish behavioral experiments.

Automating multimodal microscopy with NanoJ-Fluidics

Publishing date: 2019-05-02 Published on: Nature Communications summary: Channel Editor Summary: The authors have developed an open source and low-cost device for automated control of labelling and washing cells while under the microscope.

IntensityCheck – The light measuring app for microscope performance checks and consistent fluorescence imaging

Publishing date: 2019-05-02 Published on: PLOS ONE summary: Quantitative fluorescence imaging is an essential tool in biomedical research. It requires consistent and repeatable conditions such as constant sample illumination. Even on a confocal microscope this can usually only be achieved by using an external laser power meter.

BioModelos: A collaborative online system to map species distributions

Publishing date: 2019-04-11 Published on: PLOS ONE summary: Information on species distribution is recognized as a crucial input for biodiversity conservation and management. To that end, considerable resources have been dedicated towards increasing the quantity and availability of species occurrence data, boosting their use in species distribution modeling and online platforms for their dissemination.

Community-led data collection using Open Data Kit for surveillance of animal African trypanosomiasis in Shimba hills, Kenya

Publishing date: 2019-04-11 Published on: BMC Research Notes summary: In Sub-Saharan Africa, there is an increase in trypanosome non-susceptibility to multiple trypanocides, but limited information on judicious trypanocide use is accessible to smallholder farmers and agricultural stakeholders in disease endemic regions, resulting in widespread multi-drug resistance.

ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

Publishing date: 2019-04-11 Published on: PLOS Computational Biology summary: Interacting-particle reaction dynamics (iPRD) combines the simulation of dynamical trajectories of interacting particles as in molecular dynamics (MD) simulations with reaction kinetics, in which particles appear, disappear, or change their type and interactions based on a set of reaction rules.

RMut: R package for a Boolean sensitivity analysis against various types of mutations

Publishing date: 2019-04-11 Published on: PLOS ONE summary: There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones.

RUPEE: A fast and accurate purely geometric protein structure search

Publishing date: 2019-04-11 Published on: PLOS ONE summary: Given the close relationship between protein structure and function, protein structure searches have long played an established role in bioinformatics. Despite their maturity, existing protein structure searches either use simplifying assumptions or compromise between fast response times and quality of results.

CLEESE: An open-source audio-transformation toolbox for data-driven experiments in speech and music cognition

Publishing date: 2019-04-04 Published on: PLOS ONE summary: None authors: Juan José Burred, Emmanuel Ponsot, Louise Goupil, Marco Liuni, Jean-Julien Aucouturier link to paper: 10.1371/journal.pone.0205943 Icons made by catkuro from www.