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虚拟植物组织：下一代植物生长模拟的构建模块

Virtual Plant Tissue: Building Blocks for Next-Generation Plant Growth Simulation.

作者信息

De Vos Dirk, Dzhurakhalov Abdiravuf, Stijven Sean, Klosiewicz Przemyslaw, Beemster Gerrit T S, Broeckhove Jan

机构信息

Integrated Molecular Plant Physiology Research, Department of Biology, University of AntwerpAntwerp, Belgium.

Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium.

出版信息

Front Plant Sci. 2017 May 4;8:686. doi: 10.3389/fpls.2017.00686. eCollection 2017.

DOI:10.3389/fpls.2017.00686
PMID:28523006
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5415617/
Abstract

Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks. Multiple levels of model integration and coordination enable combining existing and new models from different sources, with diverse options in terms of input/output. Besides the core simulator the toolset also comprises a tissue editor for manipulating tissue geometry and cell, wall, and node attributes in an interactive manner. A parameter exploration tool is available to study parameter dependence of simulation results by distributing calculations over multiple systems. Virtual Plant Tissue is available as open source (EUPL license) on Bitbucket (https://bitbucket.org/vptissue/vptissue). The project has a website https://vptissue.bitbucket.io.

摘要

植物发育过程的计算建模正变得越来越重要。已经开发出了细胞分辨率的植物组织模拟器，但它们通常以孤立的方式描述生理过程，在空间和时间上受到强烈限制。随着植物系统生物学朝着对发育的综合观点发展，我们构建了虚拟植物组织（VPTissue）软件包，以便在同一框架内以及跨不同框架耦合功能模块或模型。多层次的模型集成与协调能够将来自不同来源的现有模型和新模型结合起来，在输入/输出方面具有多种选择。除了核心模拟器之外，该工具集还包括一个组织编辑器，用于以交互方式操纵组织几何形状以及细胞、细胞壁和节点属性。有一个参数探索工具可通过在多个系统上分布计算来研究模拟结果的参数依赖性。虚拟植物组织以开源形式（欧盟公共许可证）在Bitbucket（https://bitbucket.org/vptissue/vptissue）上提供。该项目有一个网站https://vptissue.bitbucket.io。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/bfe93ea1338f/fpls-08-00686-g0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/148dfaf36f2a/fpls-08-00686-g0001.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/7cdda5bcc76f/fpls-08-00686-g0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/7691507e1892/fpls-08-00686-g0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/a72feb766eaa/fpls-08-00686-g0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/c80cac7db618/fpls-08-00686-g0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/bfe93ea1338f/fpls-08-00686-g0010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/148dfaf36f2a/fpls-08-00686-g0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/18233f15df99/fpls-08-00686-g0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/cba88cd5a625/fpls-08-00686-g0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/63b3fcbd509a/fpls-08-00686-g0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/4eb76e36fac1/fpls-08-00686-g0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/7cdda5bcc76f/fpls-08-00686-g0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/7691507e1892/fpls-08-00686-g0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/a72feb766eaa/fpls-08-00686-g0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/c80cac7db618/fpls-08-00686-g0009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d553/5415617/bfe93ea1338f/fpls-08-00686-g0010.jpg

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