ya||a: GPU-Powered spheroid models for mesenchyme and epithelium
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- dc.contributor.author Germann, Philipp
- dc.contributor.author Marin-Riera, Miquel
- dc.contributor.author Sharpe, James
- dc.date.accessioned 2019-09-17T16:00:46Z
- dc.date.available 2019-09-17T16:00:46Z
- dc.date.issued 2019
- dc.description.abstract Simulating morphogenesis of both mesenchyme and epithelium has typically required complex and computationally expensive models. To meet this challenge, we developed ya||a-yet another parallel agent-based model. Our model extends the spheroid model by the addition of spin-like polarities to simulate epithelial sheets and tissue polarity using pairwise interactions only. This design is simple and lends itself to parallelization, and we implemented it together with recent models for protrusions and migration for GPUs for high performance. ya||a is written in concise, plain CUDA/C++ and available at github.com/germannp/yalla under the MIT license.
- dc.description.sponsorship This work was supported by the Spanish Ministry of Economy and Competitiveness through Centro de Excelencia Severo Ochoa 2013-2017, SEV-2012-0208, the Swiss National Science Foundation through Sinergia grants CR23I3_156234 and CRSII3_141918, and the European Research Council through SIMBIONT (project no. 670555).
- dc.format.mimetype application/pdf
- dc.identifier.citation Germann P, Marin-Riera M, Sharpe J. ya||a: GPU-Powered spheroid models for mesenchyme and epithelium. Cell Syst. 2019 Mar 27; 8(3): 261-266.e3. DOI: 10.1016/j.cels.2019.02.007
- dc.identifier.doi http://dx.doi.org/10.1016/j.cels.2019.02.007
- dc.identifier.issn 2405-4712
- dc.identifier.uri http://hdl.handle.net/10230/42284
- dc.language.iso eng
- dc.publisher Elsevier
- dc.relation.ispartof Cell Systems. 2019 Mar 27;8(3):261-6
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/670555
- dc.rights © 2019 The Authors. Published by Elsevier Inc. This is an open access article under a CC BY license (http://creativecommons.org/licenses/by/4.0/)
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.keyword Morphogenesis
- dc.subject.keyword Agent-based modeling
- dc.subject.keyword Simulation
- dc.subject.keyword Epithelia
- dc.subject.keyword Mesenchyme
- dc.subject.keyword GPU computing
- dc.title ya||a: GPU-Powered spheroid models for mesenchyme and epithelium
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion