OpenWorm: an open-science approach to modeling Caenorhabditis elegans.
OpenWorm: an open-science approach to modeling Caenorhabditis elegans.
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DOI：
10.3389/fncom.2014.00137
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发表时间：
2014
影响因子：
3.2
通讯作者：
Larson S
中科院分区：
文献类型：
--
作者：
Szigeti B;Gleeson P;Vella M;Khayrulin S;Palyanov A;Hokanson J;Currie M;Cantarelli M;Idili G;Larson S
OpenWorm 是一项国际合作项目，旨在了解秀丽隐杆线虫 (C. elegans) 的行为如何从其潜在的生理过程中显现出来。该项目开发了一个模块化仿真引擎来创建蠕虫的计算模型。引擎的模块化使得可以轻松修改模型、纳入新的实验数据和测试假设。该建模框架结合了生物物理神经元模拟和一种新颖的基于流体动力学的软组织模拟，用于物理环境与身体的相互作用。该项目的开放科学方法旨在克服传统学术环境中综合建模的困难。本文介绍了创建 OpenWorm 协作的基本原理，概述了迄今为止开发的工具和资源，并讨论了与该项目相关的独特挑战。
OpenWorm is an international collaboration with the aim of understanding how the behavior of Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modeling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modeling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.
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