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Creating an accessible and understandable modelling language for cell-based simulations

Published: 26 October 2020 Publication History

Abstract

The study of morphogenesis has increasingly entailed the use of computer simulations to predict intricate behaviours from these systems, which has led to the development of tools for computational biologists to build their own simulations. However, uptake of these tools by experimental biologists has been slow and concerns remain over the assumptions underlying such tools, which are not readily explicable to a domain expert without prior programming knowledge. To demonstrate how these concerns might be addressed, we propose the creation of a domain-specific language (DSL) of one such simulation, the MemAgent-Spring model (MSM). By designing this DSL around regimented biological concepts identified by observing discussions between experimentalists and modellers, we hope to better understand how the usability and reproducibility of the MSM might be improved, therefore potentially increasing its usage by experimentalists.

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cover image ACM Conferences
MODELS '20: Proceedings of the 23rd ACM/IEEE International Conference on Model Driven Engineering Languages and Systems: Companion Proceedings
October 2020
713 pages
ISBN:9781450381352
DOI:10.1145/3417990
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 26 October 2020

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  1. agent-based models
  2. biological simulation
  3. domain specific languages
  4. interaction design

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