COMBINE Multicellular Modelling

This is the exchange platform of the COMBINE network.

COMBINE is an initiative to coordinate the development of various community standards and formats for computational models: BioPax, CellML, NeuroML, Synthetic Biology Open Language (SBOL), Systems Biology Graphical Notation (SBGN), Systems Biology Markup Language (SBML), Simulation Experiment Description Markup Language (SED-ML).

Virtual Tissues (VTs) are multi-scale, multi-cellular, mechanistic Agent Based Models (ABMs) that predict the spatio-temporal dynamics of biological tissues. While multiple platforms exist for constructing and executing VT models (listed below in the section on VT Modeling Frameworks), models developed for different platforms are currently incompatible and not accessible or executable in a common location, impeding model discovery, validation and reuse. FAIRSPACE will initially provide support ...

This mini-symposium, colocated at the ECMTB in Gothenburg, presents the state-of-the-art in computational methods for multicellular systems biology. It brings together developers and users of this software to identify common approaches and future challenges concerning multiscale integration, model specification, model exchange, scalability, workflow management as well as compliance to standards and guidelines. The session thus aims to provide an overview of the available modeling and simulation ...

For the spatio-temporal dynamics of bile transport, bile canalicular dilation, mechanical stimulation and transduction of YAP signaling during liver regeneration see the open access publication and its appendix: Meyer et al. (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985. https://doi.org/10.15252/msb.20198985

The model format is MorpheusML that can readily be loaded and run in the free and open source software ...

Spatio-temporal liver zonation in mouse and human with Wnt-Hh crosstalk and transport are modeled using coupled partial differential equations. The model file is in MorpheusML format and can be opened in the free, open-source multicellular modeling software Morpheus (https://morpheus.gitlab.io). In Morpheus, the model will simulate the time course (movie) of dynamic liver zonation for a 2D cross-section of several liver lobules, showing the patterns of Wnt ligands, intracellular Wnt signaling, ...

An overview over important lessons from the experience with SBML Level 3 extension for the MultiCellML language.

The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2022 will be a workshop-style event with oral presentations, breakout sessions and tutorials. The three meeting days will include talks about the COMBINE standards and associated or related standardization efforts, presentations of tools using these standards, breakout sessions for detailed discussions ...

Aim Multicellular spatial models have become an essential tool in quantitative biology and multiple model formalisms and simulation frameworks coexist. Progress towards software interoperability and reproducibility requires a novel model description language and conversion library, complementing SBML. Building on the community‘s practical experiences with multiple formalisms and simulators, we aim at (1) defining the concept for a multicellular language while simultaneously (2) exploring automated ...

This mini-symposium, colocated at the ECMTB in Gothenburg, presents the state-of-the-art in computational methods for multicellular systems biology. It brings together developers and users of this software to identify common approaches and future challenges concerning multiscale integration, model specification, model exchange, scalability, workflow management as well as compliance to standards and guidelines. The session thus aims to provide an overview of the available modeling and simulation ...

Program of COMBINE sessions on 6th, 7th Oct. 2022 and COMBINE Forum on 8th Oct. 2022.