From 3fdc62715cd38fdcdce8f6c0fac838a942577a1d Mon Sep 17 00:00:00 2001 From: Kilian Volmer <13285635+kilianvolmer@users.noreply.github.com> Date: Wed, 2 Sep 2026 18:20:53 +0200 Subject: [PATCH 1/3] Update MEmilio paper citation --- README.md | 2 +- docs/source/literature.rst | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index e99726ab43..5e90e73b08 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ MEmilio implements various models for infectious disease dynamics, from simple c If you use MEmilio, please cite our work -- Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H et al. (2026) *MEmilio - A high performance Modular Epidemics Simulation software for multi-scale and comparative simulations of infectious disease dynamics*. Submitted for publication. https://doi.org/10.48550/arXiv.2602.11381 +- Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H et al. (2026) *MEmilio: A high performance Modular Epidemics Simulation software for multi-scale and comparative simulations of infectious disease dynamics*. *Scientific Reports* 16, 26950. https://doi.org/10.1038/s41598-026-66481-6 and, in particular, for diff --git a/docs/source/literature.rst b/docs/source/literature.rst index 9adcfd57b4..b67cd187fa 100644 --- a/docs/source/literature.rst +++ b/docs/source/literature.rst @@ -1,6 +1,6 @@ -.. |MEmilio_citation| replace:: Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H, Abele D, Betz M, Nguyen K, Plötzke L, Volmer K, SchmidtA, Waßmuth N, Lenz P, Richter D, Tritzschak H, Hannemann-Tamas R, Litz J, Johannssen P, Borges M, Jungklaus A, Heger M, Lange A, Kluth E, Rack K, Wieland V, Arruda J, Binder S, Klitz M, Siggel M, Dahmen M, Basermann A, Meyer-Hermann M, Hasenauer J, Kühn MJ. (2026). *MEmilio -- A high performance Modular EpideMIcs simuLatIOn software for multi-scale and comparative simulations of infectious disease dynamics*. Submitted for publication. |MEmilio_DOI|_ -.. |MEmilio_DOI| replace:: DOI:10.48550/arXiv.2602.11381 -.. _MEmilio_DOI: https://doi.org/10.48550/arXiv.2602.11381 +.. |MEmilio_citation| replace:: Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H, Abele D, Betz M, Nguyen K, Plötzke L, Volmer K, SchmidtA, Waßmuth N, Lenz P, Richter D, Tritzschak H, Hannemann-Tamas R, Litz J, Johannssen P, Borges M, Jungklaus A, Heger M, Lange A, Kluth E, Rack K, Wieland V, Arruda J, Binder S, Klitz M, Siggel M, Dahmen M, Basermann A, Meyer-Hermann M, Hasenauer J, Kühn MJ. (2026). *MEmilio: A high performance Modular EpideMIcs simuLatIOn software for multi-scale and comparative simulations of infectious disease dynamics*. *Scientific Reports* 16, 26950. |MEmilio_DOI|_ +.. |MEmilio_DOI| replace:: DOI:10.1038/s41598-026-66481-6 +.. _MEmilio_DOI: https://doi.org/10.1038/s41598-026-66481-6 .. |Novel_travel_time_aware_metapopulation_models| replace:: Zunker H, Schmieding R, Kerkmann D, Schengen A, Diexer S, Mikolajczyk R, Meyer-Hermann M, Kühn MJ. (2024). *Novel travel time aware metapopulation models and multi-layer waning immunity for late-phase epidemic and endemic scenarios*. *PLOS Computational Biology* 20(12): e1012630. |Novel_travel_time_aware_metapopulation_models_DOI|_ .. |Novel_travel_time_aware_metapopulation_models_DOI| replace:: DOI:10.1371/journal.pcbi.1012630 From e34bb8872ed777aedc43ef6374e438fa64d7f5e6 Mon Sep 17 00:00:00 2001 From: HenrZu <69154294+HenrZu@users.noreply.github.com> Date: Thu, 3 Sep 2026 10:33:54 +0200 Subject: [PATCH 2/3] update doi traveler paper --- README.md | 2 +- docs/source/literature.rst | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 5e90e73b08..7811a8a00e 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ If you use MEmilio, please cite our work and, in particular, for -- Ordinary differential equation-based (ODE) and Graph-ODE models: Zunker H, Schmieding R, Hasenauer J, Kühn M J (2026). *Efficient numerical computation of traveler states in explicit mobility-based metapopulation models: Mathematical theory and application to epidemics*. arXiv. https://doi.org/10.48550/arXiv.2603.11275 +- Ordinary differential equation-based (ODE) and Graph-ODE models: Zunker H, Schmieding R, Hasenauer J, Kühn MJ. (2026). *Efficient numerical computation of traveler states in explicit mobility-based metapopulation models: Mathematical theory and application to epidemics*. *Mathematics and Computers in Simulation*. https://doi.org/10.1016/j.matcom.2026.08.029 - Integro-differential equation-based (IDE) models: Wendler A, Plötzke L, Tritzschak H, Kühn MJ. (2026). *A nonstandard numerical scheme for a novel SECIR integro differential equation-based model with nonexponentially distributed stay times*. *Applied Mathematics and Computation* 509: 129636. https://doi.org/10.1016/j.amc.2025.129636 - Agent-based models (ABMs): Kerkmann D, Korf S, Nguyen K, Abele D, Schengen A, et al. (2025). *Agent-based modeling for realistic reproduction of human mobility and contact behavior to evaluate test and isolation strategies in epidemic infectious disease spread*. *Computers in Biology and Medicine* 193: 110269. https://doi.org/10.1016/j.compbiomed.2025.110269 - Hybrid agent-metapopulation-based models: Bicker J, Schmieding R, Meyer-Hermann M, Kühn MJ. (2025). *Hybrid metapopulation agent-based epidemiological models for efficient insight on the individual scale: A contribution to green computing*. *Infectious Disease Modelling* 10(2): 571-590. https://doi.org/10.1016/j.idm.2024.12.015 diff --git a/docs/source/literature.rst b/docs/source/literature.rst index b67cd187fa..344e099bfa 100644 --- a/docs/source/literature.rst +++ b/docs/source/literature.rst @@ -66,7 +66,7 @@ .. |Missing_Transmission_Chains_DOI| replace:: DOI:10.1016/j.chaos.2026.118179 .. _Missing_Transmission_Chains_DOI: https://doi.org/10.1016/j.chaos.2026.118179 -.. |Traveler_estimation| replace:: Zunker H, Schmieding R, Hasenauer J, Kühn M J (2026). *Efficient numerical computation of traveler states in explicit mobility-based metapopulation models: Mathematical theory and application to epidemics*. arXiv. |Traveler_estimation_DOI|_ -.. |Traveler_estimation_DOI| replace:: DOI:10.1016/10.48550/arXiv.2603.11275 -.. _Traveler_estimation_DOI: https://doi.org/10.48550/arXiv.2603.11275 +.. |Traveler_estimation| replace:: Zunker H, Schmieding R, Hasenauer J, Kühn M J (2026). *Efficient numerical computation of traveler states in explicit mobility-based metapopulation models: Mathematical theory and application to epidemics*. *Mathematics and Computers in Simulation*. |Traveler_estimation_DOI|_ +.. |Traveler_estimation_DOI| replace:: DOI:10.1016/j.matcom.2026.08.029 +.. _Traveler_estimation_DOI: https://doi.org/10.1016/j.matcom.2026.08.029 From 997fc240c0bc36955949d34d5165fbe95deea0ae Mon Sep 17 00:00:00 2001 From: Henrik Zunker <69154294+HenrZu@users.noreply.github.com> Date: Thu, 3 Sep 2026 13:44:30 +0200 Subject: [PATCH 3/3] Apply batched suggestions from code review Co-authored-by: Carlotta Gerstein <100771374+charlie0614@users.noreply.github.com> --- README.md | 2 +- docs/source/literature.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 7811a8a00e..89d2546569 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ MEmilio implements various models for infectious disease dynamics, from simple c If you use MEmilio, please cite our work -- Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H et al. (2026) *MEmilio: A high performance Modular Epidemics Simulation software for multi-scale and comparative simulations of infectious disease dynamics*. *Scientific Reports* 16, 26950. https://doi.org/10.1038/s41598-026-66481-6 +- Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H et al. (2026) *MEmilio: a high performance Modular Epidemics Simulation software for multi-scale and comparative simulations of infectious disease dynamics*. *Scientific Reports* 16, 26950. https://doi.org/10.1038/s41598-026-66481-6 and, in particular, for diff --git a/docs/source/literature.rst b/docs/source/literature.rst index 344e099bfa..1d1beed978 100644 --- a/docs/source/literature.rst +++ b/docs/source/literature.rst @@ -1,4 +1,4 @@ -.. |MEmilio_citation| replace:: Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H, Abele D, Betz M, Nguyen K, Plötzke L, Volmer K, SchmidtA, Waßmuth N, Lenz P, Richter D, Tritzschak H, Hannemann-Tamas R, Litz J, Johannssen P, Borges M, Jungklaus A, Heger M, Lange A, Kluth E, Rack K, Wieland V, Arruda J, Binder S, Klitz M, Siggel M, Dahmen M, Basermann A, Meyer-Hermann M, Hasenauer J, Kühn MJ. (2026). *MEmilio: A high performance Modular EpideMIcs simuLatIOn software for multi-scale and comparative simulations of infectious disease dynamics*. *Scientific Reports* 16, 26950. |MEmilio_DOI|_ +.. |MEmilio_citation| replace:: Bicker J, Gerstein C, Kerkmann D, Korf S, Schmieding R, Wendler A, Zunker H, Abele D, Betz M, Nguyen K, Plötzke L, Volmer K, SchmidtA, Waßmuth N, Lenz P, Richter D, Tritzschak H, Hannemann-Tamas R, Litz J, Johannssen P, Borges M, Jungklaus A, Heger M, Lange A, Kluth E, Rack K, Wieland V, Arruda J, Binder S, Klitz M, Siggel M, Dahmen M, Basermann A, Meyer-Hermann M, Hasenauer J, Kühn MJ. (2026). *MEmilio: a high performance Modular EpideMIcs simuLatIOn software for multi-scale and comparative simulations of infectious disease dynamics*. *Scientific Reports* 16, 26950. |MEmilio_DOI|_ .. |MEmilio_DOI| replace:: DOI:10.1038/s41598-026-66481-6 .. _MEmilio_DOI: https://doi.org/10.1038/s41598-026-66481-6