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Essential Open Source Software for Science

Publishing date: 2019-05-23 Published on: Chan Zuckerberg Science Initiative summary: Chan Zuckerberg Foundation design a new program to support open source software essential to modern scientific research. The Chan Zuckerberg Initiative will soon invite applications for open source software projects that are essential to biomedical research.

Machine learning to help researchers evaluate biases in clinical trials: a prospective, randomized user study

Publishing date: 2019-05-23 Published on: BMC Medical Informatics and Decision Making summary: Assessing risks of bias in randomized controlled trials (RCTs) is an important but laborious task when conducting systematic reviews.

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.

3D-printable portable open-source platform for low-cost lens-less holographic cellular imaging

Publishing date: 2019-05-02 Published on: arXiv summary: None authors: Stephan Amann, Max von Witzleben, Stefan Breuer link to paper: https://arxiv.org/pdf/1904.04497.pdf Icons made by catkuro from www.flaticon.com

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.