Multicellular Tissue Models Theme


Multicellular Tissue Models (Herbert M Sauro lead)

  • Multicellular modeling is a key element in developing models that span intracellular and tissue/organ models. There is growing interest among a number of biomedical communities in the US and Europe to develop tissue and organ models. Of particular interest is modeling and understanding the process of embryonic development, tumor development including vascularization, wound healing and in silico toxicity testing. A number of well development models have recently been published highlighting the growing interest in this area. However, there are currently a wide variety of approaches to building multicellular models, ranging from cellular Potts models that employ a lattice, to individual cell based models (IBM) and continuum models. Other differences include whether intracellular processes are modeled, whether cells can move, divide, die or change shape, etc. Many of these approaches are incompatible in the sense that one approach cannot be easily be compared to another. Their effectiveness, scope and computational tractability is therefore an open question. The purpose of this theme is to highlight some of the different modeling efforts and to find common ground between them.


Wednesday, September 3rd

3.00-3.05pm: Introduction to the session. Herbert M Sauro, Department of Bioengineering, University of Washington, Seattle, WA, 98195

3.05-3.30pm: Maciej Swat: Biocomplexity Institute Department of Physics, Indiana University, Bloomington, IN, 47405

Different approaches to modeling multicellular systems, their pros and cons, including published examples and the CompuCell3D based system.

3.30-3.55pm: Tony Hunt: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143

Critical multiscale modeling issues: from model uses to implementations and beyond See recent paper: Relational grounding facilitates development of scientifically useful multiscale models).

3.55-4.10pm: Jim Bassingthwaighte: Professor of Bioengineering and Radiology, Department of Bioengineering, University of Washington, Seattle, WA, 98195

Position talk on reproduciblilty in physiological and multcellular models

4.10-4.30pm: General Discussion



Maciej Swat: is lead developer of the CompuCell3D modeling framework. This application is geared towards multiscale and multicellular modelings. He works at Indiana University with Professor James Glazier.

Tony Hunt is a Professor of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, The University of California, San Francisco. He directs the BioSystems Group. A primary focus of his work is quantitative and systems pharmacology modeling and simulation.

Jim Bassingthwaighte os Professor of Bioengineering and Radiology at the University of Washington. He leads the development of JSim, a script based simulator for multiscaling modeling.


protein based multiscale models

Submitted by gkarniadakis on Wed, 09/03/2014 - 15:25

Software Tools Mentioned by Maciek

Submitted by jbarhak on Wed, 09/03/2014 - 15:32

partial reproducibility/replicability

Submitted by gepr on Wed, 09/03/2014 - 16:16

Reproducibility Definition

Submitted by jbarhak on Wed, 09/03/2014 - 16:24

Notes from Open Discussion

Submitted by gpeng on Wed, 09/03/2014 - 16:36

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