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ya||a: GPU-powered Spheroid Models for Mesenchyme and Epithelium

15 Pages Posted: 5 Jun 2018 Sneak Peek Status: Published

See all articles by Philipp Germann

Philipp Germann

Barcelona Institute of Science and Technology (BIST) - Centre for Genomic Regulation (CRG); European Molecular Biology Laboratory; Universitat Pompeu Fabra

Miquel Marin-Riera

Barcelona Institute of Science and Technology (BIST) - Centre for Genomic Regulation (CRG); European Molecular Biology Laboratory; Universitat Pompeu Fabra

James Sharpe

Barcelona Institute of Science and Technology (BIST) - Centre for Genomic Regulation (CRG); European Molecular Biology Laboratory; Universitat Pompeu Fabra; Catalan Institution of Research and Advanced Studies (ICREA)

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Abstract

ya||a is yet another parallel agent-based model for morphogenesis. It is several orders of magnitude faster than conventional models, because it runs on GPUs and because it has been designed for performance: Previously only complex and therefore computationally expensive models could simulate both mesenchyme and epithelium. We chose to extend the simple spheroid model by the addition of spin-like polarities to simulate epithelial sheets and tissue polarity. We also incorporate recently developed models for protrusions and migration. ya||a is written in concise, plain CUDA/C++ and available at github dot com/germannp/yalla under the MIT license.

Suggested Citation

Germann, Philipp and Marin-Riera, Miquel and Sharpe, James, ya||a: GPU-powered Spheroid Models for Mesenchyme and Epithelium (April 25, 2018). Available at SSRN: https://ssrn.com/abstract=3188399 or http://dx.doi.org/10.2139/ssrn.3188399
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Philipp Germann (Contact Author)

Barcelona Institute of Science and Technology (BIST) - Centre for Genomic Regulation (CRG) ( email )

88 of Dr. Aiguader St.
Barcelona Biomedical Research Park Building
Barcelona, 08003
Spain

European Molecular Biology Laboratory ( email )

Meyerhofstraße 1
Heidelberg, 69117
Germany

Universitat Pompeu Fabra ( email )

Ramon Trias Fargas, 25-27
Barcelona, E-08005
Spain

Miquel Marin-Riera

Barcelona Institute of Science and Technology (BIST) - Centre for Genomic Regulation (CRG)

88 of Dr. Aiguader St.
Barcelona Biomedical Research Park Building
Barcelona, 08003
Spain

European Molecular Biology Laboratory

Meyerhofstraße 1
Heidelberg, 69117
Germany

Universitat Pompeu Fabra

Ramon Trias Fargas, 25-27
Barcelona, E-08005
Spain

James Sharpe

Barcelona Institute of Science and Technology (BIST) - Centre for Genomic Regulation (CRG) ( email )

88 of Dr. Aiguader St.
Barcelona Biomedical Research Park Building
Barcelona, 08003
Spain

European Molecular Biology Laboratory ( email )

Meyerhofstraße 1
Heidelberg, 69117
Germany

Universitat Pompeu Fabra ( email )

Ramon Trias Fargas, 25-27
Barcelona, E-08005
Spain

Catalan Institution of Research and Advanced Studies (ICREA) ( email )

Passeig Lluís Companys, 23
Barcelona, 08010
Spain

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