Blog posts

2024

Calendar of 2024

1 minute read

Published: December 31, 2024

Dec 6: open position Postdoc in Computational Epidemiology. Welcome to apply using the online system. Deadline: 28th February 2025.
Nov 19: Visit by MP Monica Haider as part of RIFO.
Nov 18: new preprint! G. Menz, S. Engblom: Modelling Population-Level Hes1 Dynamics: Insights from a Multi-Framework Approach, available via arXiv.
Nov 4: Start of the Project course in Computational Science. Welcome!
Oct 23–24: SWEDCOMP24.
Oct 22: leadership in science, arranged by Sweden’s young academy.
Oct 16–17: participating in the Swedish e-Science Academy 2024.
Oct 7–8: participating in the DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Diseases
Oct 2–3: visit to the Swedish parliament within the RIFO-program. I had the honour of following MP Monica Haider during this visit. Thanks a lot!
Sep 13: I organized a kick-off for the eSSENCE grad-school.
Sep 6: I was the chairman on Tuan Anh Dao’s PhD defence. He defended his PhD thesis Invariant domain preserving schemes for magnetohydrodynamics. Congrats!.
Sep 5: organized a Mini Workshop in Computational Fusion and Plasma together with Murtazo Nazarov.
Aug 29–30: visiting the Pandemic Laboratory Preparedness Retreat 2024.
May 28: visiting eSSENCE Lund.
May 27: visiting eSSENCE Umeå.
May 25: annual day of SUA in Umeå.
May 24: participating in the Doctoral Degree Conferment Ceremony for Robin Marin. Congrats!.
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.
Mar 26: Erik Blom gave his halftime seminar. External reviewer was Philip Gerlee.
Mar 8: I was the chairman on Camille Clouard’s PhD defence. She defended her PhD thesis A computational and statistical framework for cost-effective genotyping combining pooling and imputation. Congrats!.
Feb 20: I was formally appointed the new Director of eSSENCE. Lots of things to take care of, stay tuned…
Feb 2: new preprint, E. Blom, S. Engblom, G. Menz: Modeling the hallmarks of avascular tumors, available via arXiv.

2023

Calendar of 2023

1 minute read

Published: December 31, 2023

Oct 31: I will be the course responsible for the advanced level course Project course in Computational Science
Oct 23: I will give the module “Foundations of probabilistic modelling” in the PhD level course Mathematical Foundations for Computational Science.
Oct 11–12: eSSENCE Academy.
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.”
Sept 4–8: organizing an ENUMATH minisymposium entitled Mathematical and computational models of cells, cell-populations, and applications thereof joint with Fred Vermolen. Also giving a talk in the minisymposium Analysis and Numerics for Systems of Nonlinear PDEs in Mathematical Biology.
Aug 31–Sept 1: participated in the SciLifeLab Pandemic Laboratory Preparedness retreat.
Aug 21: We have written an essay on CRUSH Covid in the current issue of Qvintensen, the journal of Statistikfrämjandet.
Jan 18: First lecture in the course Scientific Computing II. Welcome!

2022

Calendar of 2022

1 minute read

Published: December 31, 2022

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).
Nov 29: Guest lecture Results of computations: communication and responsibility in the project course in Computational Science.
Nov 14–18: Installation week for new full Professors at Uppsala university.
Oct 5–6: eSSENCE Academy.
Sep 28: Served as a member of a PhD grading committe for Peter Brommesson at Linköping’s university who defended his thesis Cattle Shipments and Disease Spread Modeling.
Aug 22–26: I was one of the key speakers at Hausdorff School: “Inverse problems for multi-scale models” organized by Lorenzo Contento, Jan Hasenauer, and Yannik Schälte.
Aug 19: Robin Marin publicly defended his PhD thesis Computational Modeling, Parameterization, and Evaluation of the Spread of Diseases. Congratulations! Faculty opponent was T. J. McKinley, members of the grading committe included Ullrika Sahlin, Uno Wennergren, and Umberto Picchini.
Aug 18: I arranged a miniworkshop entitled Surrounded by data, starved for insight with some external and internal guests.
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.
Feb 4: Acting as the chairman at the dissertation defense of Viktor Bro who defended his thesis Volterra Modeling and Estimation of the Human Smooth Pursuit. Congratulations!
Feb 3: First lecture in the course Numerical Functional Analysis. Welcome!
Jan 18: First lecture in the course Scientific Computing III. Welcome!

2021

Calendar of 2021

1 minute read

Published: December 31, 2021

Dec 23: Opinion piece with Krister Forsberg and Tove Fall.
Dec 10: Member of the grading committe for Lena Leitenmaiers defense of the thesis Analysis and numerical methods for multiscale problems in magnetization dynamics.Congratulations!
Nov 30: Guest lecture Results of computations: communication and responsibility in the project course in Computational Science.
Oct 8: Opinion piece with Tove Fall and Mats Martinell.
Sept 23: Academy meeting, my final one! Thanks for these 5 years!
Aug 30: I will start giving the course Scientific Computing III. Welcome!
June 29: Member of the grading committee for Carl Lundholm’s PhD-defence for the thesis Cut Finite Element Methods on Overlapping Meshes: Analysis and Applications, Chalmers University of Technology. Congrats!
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.
May 6–7: Two short interviews for local-TV concerning the decline of COVID-19 in Uppsala and the decline in fatality of the disease.
Apr 30: Contributed with a talk at MIT IDSS: Paths from Research to Impact: A Year of Collaborative Research on COVID-19.
Mar 25 Chairman of the Jury in the Unga forskare (Young researcher) competition. A short summary by the Young Academy.
Jan 29 Member of a Aku Kammonen’s grading committe at KTH. The thesis was entitled Numerical algorithms for high dimensional integration with application to machine learning and molecular dynamics. Congrats!
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.

2020

Calendar of 2020

2 minute read

Published: December 31, 2020

Dec 14: I was the opponent at the PhD defense of Naeimeh Atabaki-Pasdar, Lund. Congrats!. Link to thesis: (here).
Dec 1: Promoted to full Professor in Scientific Computing!
Oct 30: I gave a lecture in the Applied Mathematics Seminars-series at the University of Warwick.
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:
- Press release by Uppsala university
- Description by Uppsala university
- Short report by Swedish Television
- Mats Martinell interviewed by TV4
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 23–24: Academy meeting, Stockholm.
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.
June 15: Opinion piece with Tove Fall, Paul Franks, Maria Gomez, and Alexander Medvedev.
June 4: I gave an invited guest-lecture in the Cancer Biology course organized by Femke Heindryckx.
June 2: an opinion piece on the Swedish Covid-19 strategy published with Lars Calmfors, Tove Fall and others.
Apr 22–23: (Online) Academy meeting.
Apr 3: (Online) Chairman of the Jury in the Unga forskare (Young researcher) competition, in Stockholm.
Apr 1: another opinion piece published with Tove Fall and others.
Mar 31: Jing Liu successfully defended her PhD thesis Towards Fast and Robust Algorithms in Flash X-ray single-particle Imaging. The opponent was Helmut Grubmueller. Congratulations!
Mar 20: an opinion piece published with Tove Fall and others.
Feb 13: preprint with Jonathan Bull released: Distributed and Adaptive Fast Multipole Method In Three Dimensions. Download the daFMM3D-software at stenglib.
Feb 5–6: Academy meeting in Stockholm.
Jan 27: release of URDME 1.4.0 at www.urdme.org.
Jan 16: start of graduate course Numerical methods in stochastic modeling and simulations (7.5hp). Welcome!
Jan 13–14: TDB Internal conference 2020.

2019

Calendar of 2019

3 minute read

Published: December 31, 2019

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.
Dec 4–5: Academy meeting, London, UK.
Dec 2: Half-time seminar by Robin Eriksson entitled Bayesian epidemiological modeling over network data. External reviewer Umberto Picchini.
Nov 27: Opinion piece published in Curie: Forskare hinner inte meritera sig på fem år (in Swedish).
Nov 26: Guest lecture Results of computations: communication and responsibility in the project course in Computational Science.
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.
Oct 23: together with Carolina Wählby I hosted one of the IT-department’s 20 year anniversary seminar. See the Facebook-post here.
Oct 15–16: Swedish e-Science Academy, Lund.
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.
Sept 11–12: Academy meeting, Stockholm.
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).
Aug 12–14: I participated in the organization of the Young Academy’s Research Summer School.
June 3–5: I participated in the conference Multiscale Modelling of Materials and Molecules in Uppsala where I gave a short talk entitled Bayesian epidemiologial modeling: with little and without data.
May 27: Member of the grading commiittee for M. Ghahremanpour who successfully defended his PhD thesis Alexandria: A General Drude Polarizable Force Field with Spherical Charge Density. Congratulations!.
May 25th: Academy meeting, Uppsala.
May 3rd: Start of the PhD-level course in Numerical Functional Analysis (5–7.5hp)! Welcome! Please visit the course web-page.
May 2nd: I arranged (with Tove Fall and Aryo Makko) the meeting Stand up for the scientific perspective, in Stockholm, Gamla Stan.
Apr 24–25: Academy meeting, Luleå.
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!
Mar 20–21: Meeting with the Baltic and Nordic Young Academies, in Stockholm.
Feb 6–7: Academy meeting, Stockholm.
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!

2018

Calendar of 2018

3 minute read

Published: December 31, 2018

Dec 13: Guest lecturer on the course Project in computational science on the topic Results of computations: communication and responsibility
Dec 7: I served as a member of the grading committee at the PhD defense of Gabriela Malenova entitled Uncertainty quantification for high frequency waves. Congratulations!.
Nov 28–29: Academy meeting
Nov 13: UPMARC day.
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.
Oct 16–17: eSSENCE Academy, Uppsala.
Oct 1–5: workshop Multidisciplinary and multiscale approaches to bridge the gap between molecular and cellular level at the Centro di Ricerca Mathematica (CRM) Ennio De Giorgio in Pisa, Italy. I gave a talk entitled From the bottom and up: bridging the single cell with the cell population.
Sept 13–14: Academy meeting, Kristineberg.
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!
June 11–13: I took part in the eSSENCE-Multiscale Modelling Meeting in Uppsala.
May 30–June 2: I participated in the Wenner-Gren symposia Antibiotic resistance: Evolutionary concepts versus clinical realities in Stockholm.
May 29: Served as a member of the PhD grading committe for Kristin Kirchner who successfully defended her thesis Numerical approximation of solutions to stochastic partial differential equations and their moments at Chalmer’s University of Technology.
May 4: Served as a member of the PhD grading committe for Markus Wahlsten who successfully defended his thesis Uncertainty quantification for wave propagation and flow problems with random data at Linköping’s university.
Apr 18–19: Academy meeting, Stockholm.
Mar 23: Served as a member of a PhD grading committe for Stefan Sellman at Linköping’s university who defended his thesis Quantifying Risk in Epidemiological and Ecological Contexts.
Mar 22: Chairman of the committe for the Unga forskare (Young researcher) competition, in Stockholm. See their description of the event, and the Young Academy’s summary.
Feb 6–7: Academy meeting, Norrköping.
Feb 3: A new preprint entitled Stochastic simulation of pattern formation in growing tissue: a multilevel approach was released on arXiv.
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).
Jan 16–17: Acting as the external reviewer on the PhD viva by Juan Kuntz Nussio at Imperial College, London. The thesis: Deterministic approximation schemes with computable errors for the distributions of Markov chains.

2017

Calendar of 2017

4 minute read

Published: December 31, 2017

Dec 14: I served as a member of the PhD grading committee of Ranjita Dutta Roy who successfully defended her thesis Allosteric regulation of synaptic processes at Karolinska Institutet.
Dec 11: Pavol Bauer successfully defended his thesis Parallelism in Event-Based Computations with Applications in Biology. The opponent was Markos Katsoulakis. Congratulations!
Nov 13–17: I was one of the speaker at the Workshop IV: Uncertainty Quantification for Stochastic Systems and Applications, part of the Program Complex High-Dimensional Energy Landscapes at IPAM, UCLA, CA, USA. See the talk here.
Oct 10–11: I participated in the international policy arena Uppsala Health Summit.
Oct 5: I just published two chapters related to ongoing research in URDME. The first one is S. Engblom: Stability and Strong Convergence for Spatial Stochastic Kinetics (Chapter 3.3, (doi)). The second is S. Engblom, A. Hellander, P. Lötstedt: Multiscale Simulation of Stochastic Reaction-Diffusion Networks, (Chapter 2.4, (doi)), both in Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, by Springer.
Sept 26–27: Academy meeting in Uppsala.
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 26: Major version 5.0.0 of SimInf released on CRAN. As before the manual is available at arXiv. For a quick example, see the animation Modeling and simulation of the spread of VTEC.
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.
Apr 26–27: Academy meeting in Stockholm.
Mar 28: I was one of the jury members in the Young Researcher’s Finale Week. See the post at the Young Academy.
Mar 16: new release of URDME! Version 1.3 can now be downloaded at www.urdme.org. The new manual can be retrieved via arXiv.
Mar 9–10: I was involved in organizing Expedition Mundus at SciFest.
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.
Mar 6–7: visit to Lund University, hosted by Alexandros Sopasakis. I gave a talk with the title Data-driven computational Epidemics.
Feb 8–9: Academy meeting in Gothenburg.
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.

Stefan Engblom

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