Literature DB >> 33512399

Epidemiological modeling in StochSS Live!

Richard Jiang1, Bruno Jacob2, Matthew Geiger3, Sean Matthew3, Bryan Rumsey3, Prashant Singh4, Fredrik Wrede4, Tau-Mu Yi5, Brian Drawert6, Andreas Hellander4, Linda Petzold1,2.   

Abstract

SUMMARY: We present StochSS Live!, a web-based service for modeling, simulation, and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters, and analyze the results. AVAILABILITY: StochSS Live! is freely available at https://live.stochss.org/. SUPPLEMENTARY INFORMATION: Available at https://github.com/StochSS/Covid19_Modeling.
© The Author(s) 2021. Published by Oxford University Press.

Entities:  

Year:  2021        PMID： 33512399      PMCID： PMC7929247          DOI： 10.1093/bioinformatics/btab061

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  11 in total

Review 1.  Principles of epidemiological modelling.

Authors:  M G Garner; S A Hamilton
Journal:  Rev Sci Tech       Date:  2011-08       Impact factor: 1.181

2.  COPASI--a COmplex PAthway SImulator.

Authors:  Stefan Hoops; Sven Sahle; Ralph Gauges; Christine Lee; Jürgen Pahle; Natalia Simus; Mudita Singhal; Liang Xu; Pedro Mendes; Ursula Kummer
Journal:  Bioinformatics       Date:  2006-10-10       Impact factor: 6.937

3.  GillesPy: A Python Package for Stochastic Model Building and Simulation.

Authors:  John H Abel; Brian Drawert; Andreas Hellander; Linda R Petzold
Journal:  IEEE Life Sci Lett       Date:  2016-09

4.  Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe.

Authors:  Seth Flaxman; Swapnil Mishra; Axel Gandy; H Juliette T Unwin; Thomas A Mellan; Helen Coupland; Charles Whittaker; Harrison Zhu; Tresnia Berah; Jeffrey W Eaton; Mélodie Monod; Azra C Ghani; Christl A Donnelly; Steven Riley; Michaela A C Vollmer; Neil M Ferguson; Lucy C Okell; Samir Bhatt
Journal:  Nature       Date:  2020-06-08       Impact factor: 49.962

5.  Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist.

Authors:  Brian Drawert; Andreas Hellander; Ben Bales; Debjani Banerjee; Giovanni Bellesia; Bernie J Daigle; Geoffrey Douglas; Mengyuan Gu; Anand Gupta; Stefan Hellander; Chris Horuk; Dibyendu Nath; Aviral Takkar; Sheng Wu; Per Lötstedt; Chandra Krintz; Linda R Petzold
Journal:  PLoS Comput Biol       Date:  2016-12-08       Impact factor: 4.475

6.  Scalable machine learning-assisted model exploration and inference using Sciope.

Authors:  Prashant Singh; Fredrik Wrede; Andreas Hellander
Journal:  Bioinformatics       Date:  2021-04-19       Impact factor: 6.937

7.  Programming biological models in Python using PySB.

Authors:  Carlos F Lopez; Jeremy L Muhlich; John A Bachman; Peter K Sorger
Journal:  Mol Syst Biol       Date:  2013       Impact factor: 11.429

8.  PyDREAM: high-dimensional parameter inference for biological models in python.

Authors:  Erin M Shockley; Jasper A Vrugt; Carlos F Lopez
Journal:  Bioinformatics       Date:  2018-02-15       Impact factor: 6.937

9.  PyBioNetFit and the Biological Property Specification Language.

Authors:  Eshan D Mitra; Ryan Suderman; Joshua Colvin; Alexander Ionkov; Andrew Hu; Herbert M Sauro; Richard G Posner; William S Hlavacek
Journal:  iScience       Date:  2019-08-28

10.  An interactive web-based dashboard to track COVID-19 in real time.

Authors:  Ensheng Dong; Hongru Du; Lauren Gardner
Journal:  Lancet Infect Dis       Date:  2020-02-19       Impact factor: 25.071
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