Publishing date: 2018-05-29
Published on: PLOS ONE
summary: One common problem in visualizing real-life networks, including biological pathways, is the large size of these networks. Often times, users find themselves facing slow, non-scaling operations due to network size, if not a “hairball” network, hindering effective analysis.
Publishing date: 2018-05-29
Published on: PLOS ONE
summary: None
authors: Krishanu Nandy, David W. Collinson, Charlie M. Scheftic, L. Catherine Brinson
link to paper: 10.1371/journal.pone.0197999
Icons made by catkuro from www.
Publishing date: 2018-05-20
Published on: Journal of Simulation
summary: This paper introduces Ciw, an open-source library for conducting discrete event simulations that has been developed in Python. The strengths of the library are illustrated in terms of best practice and reproducibility for computational research.
Publishing date: 2018-05-15
Published on: plasmotron.org
summary: PlasmoTron is an open-source robotic system built on top of the OpenTrons platform, to allow semi-automated culture of malaria parasites.
authors: Theo Sanderson and Julian C.
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: 2018-05-07
Published on: medium.com
summary: Mozilla’s fifth-annual Global Sprint is May 10 and 11. Open-source engineers and activists around the globe will swap code and ideas to make the internet a healthier place.
Publishing date: 2018-05-05
Published on: PLOS Synbio Community
summary: An interview with Addgene co-founder and current Chief Scientific Officer, Melina Fan.
authors: Aaron Dy
link to paper: http://blogs.plos.org/synbio/2016/05/05/if-sharing-is-caring-addgene-really-cares-about-plasmids/
Icons made by catkuro from www.
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: 2018-04-18
Published on: PLOS Blogs Network
summary: Difficulties reproducing scientific results are, in the vast majority of cases, not due to the authors having made mistakes or, even worse, forged data, writes Peter Wittek.
Publishing date: 2018-04-16
Published on: PLOS ONE
summary: In order to measure what happens to samples while being centrifuged, the authors created an adaptor that combines electronics and 3D printed parts to measure in real time how concentration changes along a tube containing samples, allowing protocol optimization.