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Compartmental Modeling Software: A Fast, Discrete Stochastic Framework for Biochemical and Epidemiological Simulation
The compartmental modeling software (CMS) is an open source computational framework that can simulate discrete, stochastic reaction models which are often utilized to describe complex systems from epidemiology and systems biology. In this article, we report the computational requirements, the novel input model language, the available numerical solvers, and the output file format for CMS.… Read more
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2019-nCoV: Preliminary estimates of the confirmed-case-fatality-ration and infection-fatality-ratio, and intial pandemic risk assesment
Preliminary estimates of the confirmed-case-fatality-ratio and infection-fatality-ratio, and intial pandemic risk assesment. Read more
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Sabin vaccine reversion in the field: a comprehensive analysis of Sabin-like poliovirus isolates in Nigeria
To assess the dynamics of genetic reversion of live poliovirus vaccine in humans, we studied molecular evolution in Sabin-like poliovirus isolates from Nigerian acute flaccid paralysis cases obtained from routine surveillance. We employed a novel modeling approach to infer substitution and recombination rates from whole-genome sequences and information about poliovirus infection dynamics and individual vaccination… Read more
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Deterministic Analysis of Extrinsic and Intrinsic Noise in an Epidemiological Model
We couple a stochastic collocation method with an analytical expansion of the canonical epidemiological master equation to analyze the effects of both extrinsic and intrinsic noise. It is shown that depending on the distribution of the extrinsic noise, the master equation yields quantitatively different results compared to using the expectation of the distribution for the… Read more