Difference between revisions of "CometWiki"

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__NOTOC__
 
__NOTOC__
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[http://www.dayel.com/comet/supmat/movies/FigS2_Fig1_x_proj.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS2_Fig1_x_proj.mov.png]
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[http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]
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[http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]
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{|cellpadding="10"
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|width="700" valign="top"|
  
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==CometWiki==
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This wiki describes how to set up and use the `comet' program. 
  
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Welcome to CometWiki. This site describes the set up and usage of `comet' the actin-based motility simulator.
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You can read [http://www.dayel.com/research/comet/ an introduction to the comet project here](to return here, click on 'cometwiki' rather than using the browser back button).
  
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==Examples==
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|valign="top"|
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|}
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{|cellpadding="10"
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|width=300px valign="top"|
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==Essential Information==
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===How the Program Works===
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*[[Description of the Model]]
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*[[Program Flow|Overview of Program Flow]]
  
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*[http://www.dayel.com/comet/supmat/movies/FigS2_Fig1_x_proj.mov Example simulation run 2D (from Figure 1 in paper)]
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===Video Tutorials===
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*[http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov 3D links view of above example]
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*[http://www.dayel.com/research/comet/comet-tutorial-1/ How to run the comet  program on OS X]  
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*[http://www.dayel.com/comet/supmat/movies/FigS5a_radial_report_force.mov Forces and link breaks during symmetry breaking]
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*[http://www.dayel.com/research/comet/comet-tutorial-2/ How to make 3D isosurfaces].
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*[http://www.dayel.com/comet/supmat/movies/FigS5bSmoothMotilityLink_breaks.mov Link breaks during smooth motility]
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*[http://www.dayel.com/comet/supmat/movies/FigS4a_circ_measure_vtk_.mov Circumferential measurements during symmetry breaking]
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===Installing the Program===
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*[http://www.dayel.com/comet/supmat/movies/FigS4b_radial_measure_vtk_.mov Radial measurements during symmetry breaking]
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*[http://www.dayel.com/comet/supmat/movies/FigS6a_vtk_smooth_circ_trimmed.mov Circumferential measurements during smooth motilty]
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*[http://www.dayel.com/comet/supmat/movies/FigS6b_vtk_radial_trimmed.mov Radial measurements during smooth motilty]
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*[http://www.dayel.com/comet/supmat/movies/FigS7a_Ellipsoid_vtk_.mov Sideways symmetry breaking of ellipsoid (3D)]
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<code>comet</code> runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).
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*[http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov Sideways symmetry breaking of capsule (2D)]
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*[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-01.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #1]
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*[[Installing|Instructions for downloading and installing comet]]
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*[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-03.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #2]
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*[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell1.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #3]
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*[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell2.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #4]
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx4-01.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #1]
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===Running the Program===
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-04_2.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #2]
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-05_3.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #3]
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #4]
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06_1.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #5]
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The program is called from the command line.  The command line parameters tell the program what to do (calculate a new run, re-process existing data, interactive 3D view etc.).  A <code>cometparams.ini</code> file in the working directory tells the program detailed information about the model parameters to use for calculation and display.
  
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*[[Running the program|Command line parameters for the <code>comet</code> program]]
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*[[cometparams.ini parameter file|Model settings in the <code>cometparams.ini</code> file]]
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*[[Display settings|Display settings in the <code>cometparams.ini</code> file]]
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*[[Running comet on a cluster|Running <code>comet</code> on a cluster]]
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| valign="top"|
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==Simulator Output==
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===Example Results===
  
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*[[Symmetry Breaking and Motility]]
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*[[Forces during Symmetry Breaking]]
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*[[Circumferential and Radial measurements]]
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*[[Ellipsoid and Capsule symmetry breaking]]
  
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===Model Robustness===
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*[[Model Robustness|The effect of changing the main parameters]]
  
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==Usage==
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===In Vitro===
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*[[3D Reconstructions of in vitro Constrained Shells]]
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*[[3D Reconstructions of in vitro Unconstrained Shells]]
  
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{|cellpadding="5"
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==In Depth Information==
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|width="45%"|
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===Installing===
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*[[Installing]]
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You can download
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===Inner workings of the code===
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*[[Detailed Program Flow]]
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*[[Implementation in C++]]
  
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===Running the program===
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===Making Measurements===
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*[[Running the program]]
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===Settings===
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*[[Node Tracks|Tracking network movement and making measurements]]
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*[[Radial Force Movies]]
  
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*[[cometparams.ini parameter file]]
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|valign="top"|
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|}
  
  
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|width="45%" valign="top"|
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==Code Status==
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===Scripts===
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|valign="top"|
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*[http://github.com/markdayel/comet Source Repository]
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|}
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*[http://github.com/markdayel/comet/archives/master Latest Source]
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*[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]
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*[[Known Issues]]
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*[[To Do]]
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*[[Using Git]]

Latest revision as of 17:35, 15 November 2009

FigS2_Fig1_x_proj.mov.png FigS3_Fig1vtkx1.mov.png FigS7b_Symmetric_Capsule.mov.png

This wiki describes how to set up and use the `comet' program.

You can read an introduction to the comet project here(to return here, click on 'cometwiki' rather than using the browser back button).

Essential Information

How the Program Works

Video Tutorials

Installing the Program

comet runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).

Running the Program

The program is called from the command line. The command line parameters tell the program what to do (calculate a new run, re-process existing data, interactive 3D view etc.). A cometparams.ini file in the working directory tells the program detailed information about the model parameters to use for calculation and display.

Simulator Output

Example Results

Model Robustness

In Vitro

In Depth Information

Inner workings of the code

Making Measurements


Code Status

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