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.

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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!

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!

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.

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.

Stefan Engblom

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