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
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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: 2018-05-10
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: 2018-04-16
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.
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.
Publishing date: 2018-04-12
Published on: PLOS ONE
summary: Understanding Earth surface responses in terms of sediment dynamics to climatic variability and tectonics forcing is hindered by limited ability of current models to simulate long-term evolution of sediment transfer and associated morphological changes.
Publishing date: 2018-04-11
Published on: PLOS Computational Biology
summary: Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment.
Publishing date: 2018-04-02
Published on: PLOS ONE
summary: Despite increasing ability to store and analyze large amounts of data for organismal and ecological studies, the process of collecting distance and count measurements from images has largely remained time consuming and error-prone, particularly for tasks for which automation is difficult or impossible.