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A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project

Gor, V. and Shapiro, B. E. and Jönsson, H. and Heisler, M. and Reddy, G. V. and Meyerowitz, E. M. and Mjolsness, E. (2006) A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project. In: Bioinformatics of Genome Regulation and Structure II. Springer , New York, NY, pp. 345-354. ISBN 978-0-387-29450-6. https://resolver.caltech.edu/CaltechAUTHORS:20161207-110017153

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Abstract

We present the software architecture of the Computable Plant Project, a multidisciplinary computationally based approach to the study of plant development. Arabidopsis thaliana is used as a model organism, and shoot apical meristem (SAM) development as a model process. SAMs are the plant tissues where regulated cell division and differentiation lead to plant parts such as flowers and leaves. We are using green fluorescent proteins to mark specific cell types and acquire time series of three-dimensional images via laser scanning confocal microscopy. To support this, we have developed an interoperable architecture for experiment design that involves automated code generation, computational modeling, and image analysis. Automated image analysis, model fitting, and code generation allow us to explore alternative hypothesis in silico and guide in vivo experimental design. These predictions are tested using standard techniques, such as inducible mutants and altered hormone gradients. The present paper focuses on the automated code generation architecture.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1007/0-387-29455-4_33DOIArticle
http://link.springer.com/chapter/10.1007%2F0-387-29455-4_33PublisherArticle
http://rdcu.be/v0k5PublisherFree ReadCube access
ORCID:
AuthorORCID
Jönsson, H.0000-0003-2340-588X
Heisler, M.0000-0001-5644-8398
Meyerowitz, E. M.0000-0003-4798-5153
Additional Information:© 2006 Springer Science+Business Media, Inc. This work was supported by the United States National Science Foundation (NSF) under Frontiers in Integrative Biological Research (FIBR) grant No. EF-0330786. HJ was supported, in part, by the Knut and Alice Wallenberg Foundation through Swegene. Portions of the research described in this paper were performed at the California Institute of Technology.
Funders:
Funding AgencyGrant Number
NSFEF-0330786
Knut and Alice Wallenberg FoundationUNSPECIFIED
Subject Keywords:Arabidopsis; Cellerator; correspondence; Delaunay triangulation; meristem; SAM; SBML; softassign; Voronoi diagram
Record Number:CaltechAUTHORS:20161207-110017153
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20161207-110017153
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:72627
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:07 Dec 2016 19:09
Last Modified:03 Oct 2019 16:19

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