MulticellML
Development of a standardized exchange of multicellular models in computational systems medicine
The "MulticellML" alliance is part of the networking fonds to strengthen the interdisciplinary interactions between the five modules of the research and support concept "e:Med - Establishing systems medicine in Germany". A general aim of systems medicine is to better understand the complex processes and structures in cell aggregates, tissues and organs. It is already possible to mathematically model these multicellular processes and structures to spatially simulate the interaction of the various elements.
Several different multicellular models and the associated simulation software have already been developed within the research and funding concept “e:Med - Establishing systems medicine in Germany”. So far, the exchange of these computer models among the different project groups is not possible. Exchange, reproducibility and archiving of these models have hampered by the lack of a standard for the declarative model description and the elements used in them.
Portion of a declarative xml-description for a multicellular model.
© Lutz Brusch
In this joint project, three e:Med groups are working together to develop a declarative description language for multicellular models (multicell markup language = multicellML) and to create an infrastructure for the exchange of models. In addition, a so-called hackathon (a collaborative software and hardware development event) will be organized and a course will be offered for educating the users of MulticellML in existing e:Med projects. Thereby, the multicellML project directly promotes networking and enables the transferability of computer models and software to a wide variety of systems medicine research areas.
Subprojects
SP1 Development of a standard and a MulticellML interface to Morpheus
SP2 Development of a standard and archiving of multicellular models
SP3 Development of a standard and a MulticellML interface to Simulator M3
Publications
Alfonso, J. C. L., L. A. Papaxenopoulou, P. Mascheroni, M. Meyer-Hermann, and H. Hatzikirou (2020). "On the Immunological Consequences of Conventionally Fractionated Radiotherapy." iScience 23(3): 100897. www.sciencedirect.com/science/article/pii/S258900422030081X.
Barua, A., S. Syga, P. Mascheroni, N. Kavallaris, M. Meyer-Hermann, A. Deutsch, and H. Hatzikirou (2020). "Entropy-driven cell decision-making predicts ‘fluid-to-solid’ transition in multicellular systems." New J Phys 22(12): 123034. doi.org/10.1088/1367-2630/abcb2e.
Deutsch, A., J. M. Nava-Sedeno, S. Syga, and H. Hatzikirou (2021). "BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration." PLoS Comput Biol 17(6): e1009066. www.ncbi.nlm.nih.gov/pubmed/34129639.
Mascheroni, P., J. C. Lopez Alfonso, M. Kalli, T. Stylianopoulos, M. Meyer-Hermann, and H. Hatzikirou (2019). "On the Impact of Chemo-Mechanically Induced Phenotypic Transitions in Gliomas." Cancers (Basel) 11(5). www.ncbi.nlm.nih.gov/pubmed/31137643.
Papaxenopoulou, L. A., G. Zhao, S. Khailaie, K. Katsoulis-Dimitriou, I. Schmitz, E. Medina, H. Hatzikirou, and M. Meyer-Hermann (2022). "In silico predicted therapy against chronic Staphylococcus aureus infection leads to bacterial clearance in vivo." iScience: 105522. doi.org/10.1016/j.isci.2022.105522.
Sego, T. J., J. O. Aponte-Serrano, J. F. Gianlupi, S. R. Heaps, K. Breithaupt, L. Brusch, J. Crawshaw, J. M. Osborne, E. M. Quardokus, R. K. Plemper, and J. A. Glazier (2020). "A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness." PLoS Comput Biol 16(12): e1008451. doi.org/10.1371/journal.pcbi.1008451.
Vu, H. T., S. Mansour, M. Kucken, C. Blasse, C. Basquin, J. Azimzadeh, E. W. Myers, L. Brusch, and J. C. Rink (2019). "Dynamic Polarization of the Multiciliated Planarian Epidermis between Body Plan Landmarks." Dev Cell 51(4): 526-542 e526. www.ncbi.nlm.nih.gov/pubmed/31743666.