Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem

This model is based on the "Activator Model" in figure 4 and equations (5) through (8) of the following reference:

H Jonsson, M Heisler, GV Reddy, V Agrawal, V Gor, BE Shapiro, E Mjolsness & EM Meyerowitz (2005) "Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem," Bioinformatics, Vol. 21 Suppl. 1, 2005, pages i232-i240.

Download Paper

Supplementary Information for paper

Download zipped SBML Model (104 kB, expands to 3.4 MB) The SBML Level 2 Version 1 model consists of the following components: 254 Compartments 1265 Species 522 Parameters 4139 Reactions (2119 are diffusion, 2025 within a single compartment) 134,012 lines of text

(28 April 2010) Updated notebook compatible with Mathematica Version 7, xlr8r, and Cellzilla2D (6.4 MB Zip, expands to 33.4 MB). For more information on xlr8r and Cellzilla2D click here.

CellzillaML file (XML file: right click to save file - it will not display properly in a web browser. Also requires CelleratorML file, below.) This files contains the geometric information as an XML file and can be used, along with the CelleratorML file, by Cellzilla to reproduce the model in its entirety (for more information on CelleratorML/CellzillaML click here). This information is also contained in the three TSV files listed below so you don't need an xml decoder to retrieve the information.

CelleratorML file (XML file: right click to save file, it will not display properly in browser).

The following CSV files can be used to regenerate the template if you want to run the model in a different simulator. The files vertices.tsv, edges.tsv, and cells.tsv are equivalent to a Voronoi tessletation of centers given in centers.tsv (except along the L1 layers where the cells are truncated to give proper volume rather than extend to infinity).

• centers.tsv - this is a list of Voronoi Cell Centers, one x-y pair per line.
• vertices.tsv - this is a list of polygon vertices, that correspond to the vertices of the cells represented as polygons. Each line of the file contains one vertex as an x-y pair.
• edges.tsv - this is a list of the polygon edges, that correspond to the edges of the cells represented as polygons. Each line contains a pair of integers i,j, which means that there is an edge connecting the ith and jth vertex in the list in vertices.tsv.
• cells.tsv - this is a list of polygonal cells. Each line contains a list of integers. For example, the line "1 3 9 24 5 2" means that there is a cell composed of edges 1, 3, 9, 24, 5, and 2 in the list of edges in edges.tsv, which are on lines 1, 3, 9, 24, 5, and 2 of that file, respectively.

(3 May 2011) Updated Notebook compatible with Mathematica Version 8, Cellzilla2D, and Cambium v.09 generation. For SBML generation see Mathematica Version 7 Notebook above.

Cambium Model File (see Cambium Project Site for more information on Cambium)

(18 May 2011) Single Cell SBML file or Mathematica-8 nb for activator models. These represent the internal reactions within a single cell. Diffusion is not represented in this file. (Use "save link as" option to download files)

This page was last modified Wed May 18 09:01:05 2011, Please report any errors and address all inquiries to bshapiro at caltech dot edu