May 17: Paper published: E. Blom, S. Engblom: Morphological stability for in silico models of avascular tumors in Bull. Math. Biol, 86 (2024) (doi). Also check out the associated SMB blog post.
Sept 15: paper submitted, E. Blom, S. Engblom: Morphological stability for in silico models of avascular tumors, available via arXiv.
Sept 12: paper finally published! R. Marin, H. Runvik, A. Medvedev, and S. Engblom: Bayesian Monitoring of COVID-19 in Sweden, in Epidemics, 45 (2023) (doi). Note the extensive Supporting Information. The associated software and data can be downloaded at GitHub. Update: Sara Hamis made a nice illustration of this paper in the form of a movie poster. “An elite spy embarks on a covert mission. In a twist of fate, he starts to suspect that the target is his own life which leads him to question everything he knows.”
Dec 22: New paper published! The reference is S. Bronstein, S. Engblom, and R. Marin: Bayesian inference in Epidemics: linear noise analysis in Math. Biosci. Eng., 20(2) (2023):4128–4152 (doi). Open access! Reproduce the numerical experiments: BISDE.tar (requires Matlab, R, and relies on URDME and SimInf).
May 31: Guest-lecture entitled Computational modeling of populations of cells: applications to tumor behavior in the Advanced Cancer Biology course organized by Femke Heindryckx.
May 3: new preprint submitted! R. Marin, H. Runvik, A. Medvedev, and S. Engblom: Bayesian Monitoring of COVID-19 in Sweden, can be downloaded from arXiv. This was work conducted during an extended period of time and part of this was reported within the CRUSH Covid collboration, see also their data portal. Our software can be downloaded at GitHub.
Mar 21: new preprint submitted! S. Bronstein, S. Engblom, and R. Marin: Bayesian inference in Epidemics: linear noise analysis, can be downloaded from arXiv.
June 10: I gave a guest-lecture entitled Computational modeling of populations of cells: applications to tumor behavior in the Advanced Cancer Biology course organized by Femke Heindryckx.
Jan 26 (12.00–13.00): I participated in UPPTALK on the topic CRUSH Covid - samverkan för att dämpa smittspridning i Uppsala. See the recorded talk at YouTube.
Oct 12: today CRUSH Covid starts! This project aims to trace cluster spread of Covid-19 in the Uppsala Region, helping with the local test-and-trace strategy and with the optimization of resource allocation. CRUSH Covid has got some coverage:
Sept 30: paper published. The reference is J. Liu, S. Engblom, C. Nettelblad: Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline in J. Opt. Soc. Amer. A 37(10):1673–1686 (2020) (doi).
Sept 8: Organizing the “mini kick-off” for SysCon.
Aug 13: Paper finally published! We have developed a procedure for Bayesian posterior exploration of parameters in epidemiological models defined over contact networks. Find out more in S. Engblom, R. Eriksson, S. Widgren: Bayesian epidemiological modeling over high-resolution network data in Epidemics 32 (2020) (doi). Open access!
Aug 10: Welcome week for the Master’s program Computational Science Class 2020. Welcome!
Jul 17: new preprint available from arXiv. Håkan Runvik, Alexander Medvedev, Robin Eriksson, Stefan Engblom: Initialization of a Disease Transmission Model. Here we study the problem of initializing a large epidemiological model with many hidden states using recorded disease data.
Dec 12: I gave a short talk concerning in silico alternatives to animal experiments entitled Scientific computing and the single cell… the cell population. Host: SciLife Lab.
Dec 10: meeting with The Young Korean Academy of Science and Technology (Y-KAST) in Stockholm hosted at KVA.
Nov 7–8: I visited the University of Stuttgart and gave a seminar entitled Stochastic modeling for the single cell and the cell population: considerations for data-driven methodologies in the Systems Biology Seminar series. Thanks Nicole Radde for hosting!
Oct 30: a new preprint submitted. The item is Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline by J. Liu, S. Engblom, and C. Nettelblad, and it can be found on arXiv.
Oct 25: a new preprint submitted. This manuscript is the result of quite extensive work and a productive collaboration. Doing something with real data is hard! The item is Bayesian epidemiological modeling over high-resolution network data by S. Engblom, R. Eriksson, and S. Widgren, and it can be found on arXiv.
Sept 30–Oct 4: I participated in the conference ENUMATH in Egmond aan Zee, The Netherlands. I gave a talk entitled Bridging the single cell with the cell population: opening up for data-driven methodologies.
Aug 28: conference proceedings paper on our (early) results of modeling African swine fever published. S. Widgren, T. Rosendal, S. Engblom, and K. Ståhl: SimInf for spatio-temporal data-driven modeling of African swine fever in Swedish wildboar, in GeoVet 2019. Novel spatio-temporal approaches in the era of Big Data (url).
Mar 28: I acted as chairman of the committe for the Unga forskare (Young researcher) competition, in Stockholm. Read their own summary of the event. Congratulations!
Feb 2: New paper published. The reference is J. Liu, G. Schot, and S. Engblom: Supervised classification methods for flash X-ray single particle diffraction imaging in Opt. Express, 27(4):3884–3899 (2019) (doi). Open access!
Oct 26: a new preprint submitted. The item is Supervised Classification Methods for Flash X-ray single particle diffraction Imaging by J. Liu. G. van der Schot and S. Engblom, and it can be found on arXiv.
Sept 11: a new paper published. The paper is S. Engblom, P. Lötstedt, L. Meinecke: Mesoscopic Modeling of Random Walk and Reactions in Crowded Media in Phys. Rev. E 98(3):033304 (2018): (doi).
Aug 2: yet another paper published today. The reference is S. Widgren, S. Engblom, U. Emanuelson, and A. Lindberg: “Spatio-temporal modelling of verotoxigenic _Escherichia coli O157 in cattle in Sweden: Exploring options for control”_ in Veterinary Res. 49(78), 2018: (doi). Open access!
Aug 1: two new papers published this very day. The first one is P. Bauer, S. Engblom, S. Mikulovic, and A. Senek: “Multiscale modeling via split-step methods in neural firing” in Math. Comput. Model. Dyn. Syst. 24(4):409–425, 2018: (doi). The second one is S. Engblom, D. Wilson, R. Baker: Scalable population-level modeling of biological cells incorporating mechanics and kinetics in continuous time in Roy. Soc. Open Sci. 5(8), 2018: (doi). Both are open access!
Jul 5: New paper published (finally)! The reference is J. Liu, S. Engblom, and C. Nettelblad: “Assessing Uncertainties in X-ray Single-particle Three-dimensional reconstructions” in Phys. Rev. E. 98(1):013303 2018: (doi)
June 20: New paper published! The reference is “Stochastic simulation of pattern formation in growing tissue: a multilevel approach” in Bull. Math. Biol., 2018, (doi). Open access!
Feb 1: Finally published! The work conducted together with Augustin Chevallier has now arrived in final form. The formal journal reference is A. Chevallier and S. Engblom: Pathwise error bounds in multiscale variable splitting methods for spatial stochastic kinetics , SIAM J. Numer. Anal. 56(1):469–498, (2018) (doi).
Jan 24: organizing (together with Sanna Koskiniemi) the Young Academy’s Interdisciplinary Scientific salon on the theme Antimicrobial Resistance (by invitation only).
Sept 4: we just published a chapter on SimInf. The reference is S. Engblom and S. Widgren: Data-driven computational disease spread modeling: from measurement to parametrisation and control, Chapter 11 (doi) in Disease Modelling and Public Health, Part A, Volume 36 of Handbook of Statistics by Elsevier.
Jul 20: a preprint with Per Lötstedt and Lina Meinecke was posted on arXiv. The title of the paper is Mesoscopic Modeling of Random Walk and Reactions in Crowded Media and here we develop a multiscale modeling method wherby the diffusion in a crowded environment may be simulated via a highly efficient mesoscopic model. An implementation of this method, including the numerical experiments performed in the paper, is scheduled for release with URDME version 1.4.
June 13: a paper with Dan Wilson and Ruth Baker was posted on arXiv. The title of the paper is Scalable population-level modeling of biological cells incorporating mechanics and kinetics in continuous time. Selected examples of the method are presented in the paper. An implementation of the method is scheduled for release with URDME version 1.4.
June 12: Robin Eriksson joined as a PhD student. The title of his project is Computational Modeling, Parameterization, and Evaluation of the spread of Diseases. Welcome!
May 12: a paper with Anders Goude was posted on arXiv. The paper concerns a high order panel method with applications in airfoil design. The actual method has been implemented in our GPU-branch of the FMM2D-code and the experiments of the paper may be reproduced using the scripts distributed. Download here: freeware page.
May 9: I hosted a visit to Uppsala by Andreas Milias-Argeitis from the University of Groningen.
Mar 8: Jing Liu gave her 1/2-time seminar entitled Flash X-ray single particle imaging in 3D: computational scalability and resolution assessment 10–12 in B/A7:111. The external reviewer was Silvelyn Zwanzig.
Jan 13: a paper with Vikram Sunkara was published. The paper is “Preconditioned Metropolis sampling as a strategy to improve efficiency in posterior exploration” and discusses a kind of two-level strategy to obtain full posterior exploration in stochastic models of chemical kinetics. See IFAC-PapersOnLine 49(26):89–94 (2016): (doi).
Jan 2: a paper we have worked on during some time (with Carl Nettelblad and Jing Liu) was submitted and posted on arXiv. The title is “Assessing Uncertainties in X-ray Single-particle Three-dimensional reconstructions” and here we design a method by which the accuracy of reconstructions using X-ray lasers can be determined. See the arXiv-post.
