About Utopia

When using Utopia for your own work, please consider citing these articles.

• Lukas Riedel, Benjamin Herdeanu, Harald Mack, Yunus Sevinchan, and Julian Weninger. 2020.
  Utopia: A Comprehensive and Collaborative Modeling Framework for Complex and Evolving Systems.
  Journal of Open Source Software 5 (53): 2165. DOI: 10.21105/joss.02165.

• Yunus Sevinchan, Benjamin Herdeanu, Harald Mack, Lukas Riedel, and Kurt Roth. 2020.
  Boosting Group-Level Synergies by Using a Shared Modeling Framework.
  Computational Science – ICCS 2020, edited by VV. Krzhizhanovskaya, G. Závodszky, MH. Lees, JJ. Dongarra, PMA. Sloot, S. Brissos, and J. Teixeira, 12143:442–456. Lecture Notes in Computer Science. Cham, Switzerland: Springer International Publishing. DOI: 10.1007/978-3-030-50436-6_32

• Yunus Sevinchan, Benjamin Herdeanu, and Jeremias Traub. 2020.
  dantro: a Python package for handling, transforming, and visualizing hierarchically structured data.
  Journal of Open Source Software 5 (52): 2316. DOI: 10.21105/joss.02316.

To download the corresponding BibTeX data, please refer to this page in the project documentation.

Using Utopia

The following works made substantial use of Utopia for the implementation, simulation, and analysis of computer models.

• Petro Sarkanych, Yunus Sevinchan, Marjana Krasnytska, Pawel Romanczuk, Yurij Holovatch. 2024. Consensus decision making on a complete graph: complex behaviour from simple assumptions, Condensed Matter Physics, 27(3). DOI: 10.5488/cmp.27.33801 — Model repository

• Thomas Gaskin, Grigorios A. Pavliotis, Mark Girolami. 2024. Inferring networks from time series: A neural approach, PNAS Nexus, 3(4). DOI: 10.1093/pnasnexus/pgae063 — utopya model repository

• Thomas Gaskin, Tim Conrad, Grigorios A. Pavliotis, Christof Schütte. 2024. Neural parameter calibration and uncertainty quantification for epidemic forecasting, PLOS ONE, 19(10), e0306704. DOI: 10.1371/journal.pone.0306704, arXiV preprint — utopya model repository

• Harald Mack. 2023. Evolution from the ground up with Amee: from basic concepts to explorative modeling, Doctoral dissertation. heiDOK. Heidelberg University. DOI: 10.11588/heidok.00033914 — Model repository

• Julian Weninger. 2023. Mechanical Insights into the Development of Positional and Orientational Order in Multi-Cell-Type Tissues, Doctoral dissertation. Université de Genève. DOI: 10.13097/archive-ouverte/unige:174312 — Model repository

• Raj Ladher, Anubhav Prakash, Julian Weninger, Nishant Singh, Sukanya Raman, Karsten Kruse, Madan Rao, 2023. Junctional Force Patterning drives both Positional and Orientational Order in Auditory Epithelia, Research Square preprint (v1). DOI: 10.21203/rs.3.rs-2508957/v1 — Model repository

• Thomas Gaskin, Grigorios A. Pavliotis, and Mark Girolami. 2023. Neural parameter calibration for large-scale multiagent models, PNAS 120 (7). DOI: 10.1073/pnas.2216415120 — utopya model repository

• Benjamin Herdeanu. 2021. Emergence of Cooperation in Evolutionary Social Interaction Networks,
  Doctoral dissertation. heiDOK. Heidelberg University. DOI: 10.11588/heidok.00030725 — Model repository

• Yunus Sevinchan. 2021. Evolution Mechanics and Perspectives on Food Web Ecology,
  Doctoral dissertation. heiDOK. Heidelberg University. DOI: 10.11588/heidok.00030750. — Model repository