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cellzilla.info

Cellzilla2D

Or Zipped Mathematica Notebook. Models are compatible with CelleratorML. XML-based file formats for transferring models. Cellzilla models can also be saved to SBML using xlr8r2sbml. Stochastic models can be simulated using xSSA. 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. 2017 June 20 ].

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Cellzilla2D | cellzilla.info Reviews
<META>
DESCRIPTION
Or Zipped Mathematica Notebook. Models are compatible with CelleratorML. XML-based file formats for transferring models. Cellzilla models can also be saved to SBML using xlr8r2sbml. Stochastic models can be simulated using xSSA. 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. 2017 June 20 ].
<META>
KEYWORDS
1 cellzilla
2 cellzilla2d
3 performs xcellerator
4 and cellzillaml
5 cellzilla reference
6 getting started
7 latest file release
8 git repository
9 report a bug
10 feature request
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cellzilla,cellzilla2d,performs xcellerator,and cellzillaml,cellzilla reference,getting started,latest file release,git repository,report a bug,feature request,publications/citations,addcell,addedge,addvertex,areafunction,bellcurve,boundary,boundarycell
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Cellzilla2D | cellzilla.info Reviews

https://cellzilla.info

Or Zipped Mathematica Notebook. Models are compatible with CelleratorML. XML-based file formats for transferring models. Cellzilla models can also be saved to SBML using xlr8r2sbml. Stochastic models can be simulated using xSSA. 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. 2017 June 20 ].

INTERNAL PAGES

cellzilla.info cellzilla.info
1

CellzillaArrows

http://www.cellzilla.info/CellzillaArrows.html

Cellzilla adds several arrow forms to the list of Cellerator Arrow Forms. That may be used in a model; these new arrows allow for interactions between constituents in different Cellzilla compartments. X⟶X, Diffusion[DX,DX']}. X diffuses between cells with permeability constant DX or a function f[i,j,k] where i and j are the from and to cell indices and k is the edge index. The arrow is the LongRightArrow, [LongRightArrow]. Or ␛- ␛. X⟶X, Transport[f]}. Or ␛- ␛. Means the escape key.). In any case the glob...

2

BellCurve

http://www.cellzilla.info/BellCurve.html

Returns a pure function that evaluates a bell-shaped curve (similar to a scaled normal distribution but with maximum value M). BellCurve[M, μ, σ][x]. Evaluates to the function M e. BellCurve[M,{μx,μy},{σx,σy}][x,y]. Evaluates to the function.

3

AddCell

http://www.cellzilla.info/AddCell.html

Adds a cell to a Tissue. AddCell[tissue, {i1, i2, .}]. Are integer indices of edges that already exist in the tissue. Returns the new Tissue object. Download Example as Zipped Mathematica Notebook.

4

CellVertexCoordinates

http://www.cellzilla.info/CellVertexCoordinates.html

Determines the vertex coordinates corresponding to a specific cell in a Tissue. Returns the vertex coordinates for cell i. Returns the vertex coordinates for all cells. CellVertexCoordinates[cell, edges, vertices]. Returns the vertex coordinates for the specified cell. Here edges. Are the lists of edges and vertices from a Tissue. Object; and cell. Is a list of edge numbers corresponding to the desired cell. Download Example as Zipped Mathematica Notebook.

5

AddVertex

http://www.cellzilla.info/AddVertex.html

Adds a Vertex to a Tissue. AddVertex[tissue, {x,y}]. Are the real coordinates of the new vertex. Returns the new Tissue object. Download Example as Zipped Mathematica Notebook.

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xlr8r.info xlr8r.info

xSSAlite

http://www.xlr8r.info/SSA/index.html

Is a Mathematica package that implements Dan Gillespie's Stochastic Simulation Algorithm using Cellerator-arrow notation. The "lite" part of xSSAlite refers to the fact that this version only implements the Cellerator-mass action reactions. Non-mass-action reactions are only implemented in the full version which is currently still in testing. The original Stochastic Simulation Algorithm. Bug Report or Feature Request. Version 2.1 or later.

biomathman.com biomathman.com

bruceware

http://www.biomathman.com/bruceware/index.html

Way back in the dark ages when I was overworked and underpaid by a rather disreputable beltway bandit one of co-workers jestfully asked me one morning, "So what's the latest bruceWare? In other words the term bruceware doesn't mean anything. This website, on the other hand, is a place to post links to some of the software projects that I've worked on, some more disreputable then others. Generally it'll just be a pointer to the appropropriate software repository. XCellerator, AKA xlr8r. The MathSBML packa...

beshapiro.com beshapiro.com

bruceware

http://www.beshapiro.com/bruceware/index.html

Way back in the dark ages when I was overworked and underpaid by a rather disreputable beltway bandit one of co-workers jestfully asked me one morning, "So what's the latest bruceWare? In other words the term bruceware doesn't mean anything. This website, on the other hand, is a place to post links to some of the software projects that I've worked on, some more disreputable then others. Generally it'll just be a pointer to the appropropriate software repository. XCellerator, AKA xlr8r. The MathSBML packa...

bruce-shapiro.net bruce-shapiro.net

bruceware

http://www.bruce-shapiro.net/bruceware/index.html

Way back in the dark ages when I was overworked and underpaid by a rather disreputable beltway bandit one of co-workers jestfully asked me one morning, "So what's the latest bruceWare? In other words the term bruceware doesn't mean anything. This website, on the other hand, is a place to post links to some of the software projects that I've worked on, some more disreputable then others. Generally it'll just be a pointer to the appropropriate software repository. XCellerator, AKA xlr8r. The MathSBML packa...

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Cellzilla2D

Or Zipped Mathematica Notebook. Models are compatible with CelleratorML. XML-based file formats for transferring models. Cellzilla models can also be saved to SBML using xlr8r2sbml. Stochastic models can be simulated using xSSA. 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. 2017 June 20 ].

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