Cellzilla


Cellzilla2D performs xCellerator (xlr8r) simulations on two-dimensional tissue objects. Each cell is treated as a separate polygonal compartment. The tissue object itself consists of three parts: a list of vertex coordinates; a list of edges, composed of integer pairs of vertex numbers; and a list of cells consisting of integer lists of edge numbers. Tissues may be defined externally by the user, or one of a collection of preddfined templates may be used. For an annotated example see: [html or Zipped Mathematica Notebook].

Cellzilla2D models are compatible with CelleratorML and CellzillaML, XML-based file formats for transferring models. Cellzilla models can also be saved to SBML using xlr8r2sbml.

Stochastic models can be simulated using xSSA.


Cellzilla Reference

Quick Start
Download
Install
Examples
Bug Report (Tracker)
Feature Request
Protocols

AddCell
AddEdge
AddVertex
Area
BellCurve
Boundary
BoundaryCell
BoundedCellVoronoi
CelleratorNetwork
CellNeighbors
CellsOnBoundary
CellsOnTop,Bottom,
  Left,Right

CellOutwardVector
CellsInsidePolygon
CellVertexCoordinates
CellVertexNumbers
Cellzilla Arrows
Centroid
Centeroid
CommonTimeDomain
ConnectionList
ConnectionMatrix
ConvexHullVertices
CSVFile
DanglingEdges
DanglingVertices
DelaunayEdges
DelaunayMean
DelaunayPairs
DeleteCell
DisentangleVertices
distance
DivideCell
DivideEdge(s)
DropPerpendicular
DTissue
EdgeBetween
EdgeLength(s)
EdgesNotOnBoundary
EdgesOnBoundary
EdgesUsed
EdgesOnTop,Bottom,
  Left,Right

EdgeVertices
EntangledVertices
FitEllipse
FlatTissue
GenerateBoundaryLayer
GeometricSnapShot
GetSavedFile
GetTissueInsidePolygon
grow
InertiaMatrix
Inside
IsoPerimetricRatio LineageAnimate
LineageShow
LineEdgeIntersection
MergeCells
MergeEdges
MergeVertices
MidPoint
Movies
NeighborQ
NormalVector
NTissueCells
NTissueEdges
NTissueVertices
NumericPointQ
OutwardNormalVector
Perimeter
PointOnLineSegment
PointQ
PolygonIntersection
PrimaryAxes
PrimaryAxesVectors
PrunedDelaunayEdges
PrunedDelaunayPairs
RandomizeTemplate
Rectangularize
RegularPolygon
RegularStar
RemoveCell
RemoveEdge
RemoveShortEdges
RemoveVertex
RunSim
SaveFrames
ShowEdgeNormal
ShowOutwardNormals
ShowSavedFiles
ShowTissue
ShowTissueCells
SimAnimate
SimInterpolate
SimPlot
SimRange
SimShow
SimShowAt
SimShowFinal
SmootheCell
SmootheCells
SSANetwork
SolutionVariables
StaticSimulation
Template Gallery
TemplateCircular-
 HoneycombCover

TemplateHoneycombCover
TemplateParabolic
TemplatePolygon
TemplateRandom
TemplateRing
TemplateRandom-
 CircularGrid

TemplateRandomOvalish
TemplateRandom-
 SemicircularGrid

TemplateRandomSquareGrid
TemplateRectangular
Tissue
TissueCells
TissueCheck
TissueEdges
TissueQ
TissueVertices
ToAVI
ToMOV
Torus
TorusQ
ToTorus
TorusTissue
UndangleEdge
UndangleEdges
UndangleVertex
UndangleVertices
VertexNeighbors
VerticesNotOnBoundary
VerticesOnBoundary
VerticesOnTop,Bottom,
  Left,Right

VertexOutwardVector
VerticesUsed
VoronoiToTissue
WTAAnimate
WTAShow
X2SSANetwork
  

The contents of this web page and its subsidiary web pages are licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License. Unless otherwise specified, all software posted on this and its subsidiary web pages are released under the GNU General Public License.

xCellerator, Cellerator, xlr8r, cellzilla, growzilla and arrowzilla are trademarks of the authors and may not be used without permission. Cellerator and Cellerator based technology is protected under United States Patent Number 7,319,945.

[ 2013-07-05 ]