P. Bauer (2017) Parallelism in Event-Based Computations with Applications in Biology. Doctoral thesis, Department of Information Technology, Uppsala University, Sweden. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-332009

S. Engblom, S. Widgren (2017) Chapter 11 - Data-Driven Computational Disease Spread Modeling: From Measurement to Parametrization and Control, Editor(s): Arni S.R. Srinivasa Rao, Saumyadipta Pyne, C.R. Rao, In Handbook of Statistics, Elsevier, Volume 36, Pages 305–328. DOI: 10.1016/bs.host.2017.05.005

P. Bauer, S. Engblom, and S. Widgren (2016) Fast event-based epidemiological simulations on national scales. International Journal of High Performance Computing Applications 30(4), 438-453. DOI: 10.1177/1094342016635723

S. Widgren, S. Engblom, P. Bauer, J. Frössling, U. Emanuelson, and A. Lindberg (2016) Data-driven network modeling of disease transmission using complete population movement data: Spread of VTEC O157 in Swedish cattle. Veterinary Research 47:81. DOI: 10.1186/s13567-016-0366-5

S. Widgren (2016) Studies on verotoxigenic Escherichia coli O157 in Swedish cattle: From sampling to disease spread modelling. Doctoral thesis, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Sweden. http://pub.epsilon.slu.se/13821/

S. Widgren, P. Bauer, and S. Engblom (2016) SimInf: An R package for Data-driven Stochastic Disease Spread Simulations. The SimInf manual available via arXiv.

P. Bauer (2015) Parallelism and Efficiency in Discrete-Event Simulation. Licentiate thesis, Department of Information Technology, Uppsala University, Sweden. http://www.it.uu.se/research/publications/lic/2015-004/

Talks

S. Engblom, Data-driven Epidemiological Simulations: Verotoxigenic E. coli O157 at the workshop Mathematical Biology for Understanding Emerging Infectious Diseases at the Human-Animal-Environment Interface: a “One Health” Approach“, November 20–25 2016 in Banff, Canada. The lecture was video recorded mp4.

S. Widgren, P. Bauer, and S. Engblom, “SimInf; an R-tool for data-driven modelling of disease spread and control” at the 14th ISVEE Conference - International Symposium on Veterinary Epidemiology and Economics, 6 November 2015 Merida, Mexico.

S. Widgren, P. Bauer, and S. Engblom, “Efficient data-driven simulation of infection spread in the Swedish cattle population” at the minisymposium “Data-driven modelling of epidemics” at the 9th European Conference on Mathematical and Theoretical Biology (ECMTB) 6 June 2014, Gothenburg, Sweden.

Workshops

Stefan Widgren and Thomas Rosendal, “Infectious disease modelling with SimInf” at the 2017 Society for Veterinary Epidemiology and Preventive Medicine (SVEPM) annual conference, 29 March 2017 Inverness, Scotland.

Posters

Robin Eriksson, “Towards Bayesian Parametrization of national scale epidemics” at Workshop IV: Uncertainty Quantification for Stochastic Systems and Applications. Part of the Long Program Complex High-Dimensional Energy Landscapes. 13–17 November 2017. IPAM at UCLA, Los Angeles, US.

A. Comin, S. Widgren, E. Ågren, A. Lindberg, “Data-driven stochastic modelling of Salmonella Dublin infection in dairy herds” at the 2015 Society for Veterinary Epidemiology and Preventive Medicine (SVEPM) annual conference, 25–27 March 2015 Gent, Belgium.


The SimInf software has been made possible by support from the Swedish Research Council within the UPMARC Linnaeus centre of Excellence (Pavol Bauer, Robin Eriksson and Stefan Engblom), the Swedish Research Council Formas (Stefan Engblom and Stefan Widgren), the Swedish Board of Agriculture (Stefan Widgren), and by the Swedish strategic research program eSSENCE (Stefan Widgren).