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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|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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===Video Tutorials===
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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/research/comet/comet-tutorial-2/  How to make 3D isosurfaces].
  
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==Usage==
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===Installing the Program===
  
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{|cellpadding="5"
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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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|width="45%"|
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==Examples==
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*[[Installing|Instructions for downloading and installing comet]]
  
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====Symmetry Breaking and Motility====
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===Running the Program===
  
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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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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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*[http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov 3D links view of above example]
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====Forces during Symmetry Breaking====
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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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*[http://www.dayel.com/comet/supmat/movies/FigS5a_radial_report_force.mov Forces and link breaks during symmetry breaking]
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*[[Symmetry Breaking and Motility]]
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*[http://www.dayel.com/comet/supmat/movies/FigS5bSmoothMotilityLink_breaks.mov Link breaks during smooth 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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====Circumferential and Radial measurements====
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===Model Robustness===
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*[[Model Robustness|The effect of changing the main parameters]]
  
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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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===In Vitro===
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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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*[[3D Reconstructions of in vitro Constrained Shells]]
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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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*[[3D Reconstructions of in vitro Unconstrained Shells]]
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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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====Ellipsoid and Capsule symmetry breaking====
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==In Depth Information==
  
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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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===Inner workings of the code===
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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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*[[Detailed Program Flow]]
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*[[Implementation in C++]]
  
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====3D Reconstructions of ''in vitro'' Constrained Shells====
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===Making Measurements===
  
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*[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-01.mov Shell #1]
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*[[Node Tracks|Tracking network movement and making measurements]]
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*[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-03.mov Shell #2]
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*[[Radial Force Movies]]
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*[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell1.mov Shell #3]
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*[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell2.mov Shell #4]
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====3D Reconstructions of ''in vitro'' Unconstrained Shells====
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|valign="top"|
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx4-01.mov Shell #1]
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|}
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-04_2.mov Shell #2 (3-lobed split)]
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-05_3.mov Shell #3]
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06.mov Shell #4]
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*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06_1.mov Shell #5]
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|width="45%" valign="top"|
 
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===Installing===
 
  
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Detailed instructions for downloading and installing comet on OS X, Linux or Windows can be found [[Installing|here]]
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==Code Status==
  
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===Running the program===
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*[http://github.com/markdayel/comet Source Repository]
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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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Simple instructions for running the program from the command line can be found [[Running the program|here]]
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*[[Known Issues]]
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*[[To Do]]
  
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===Settings===
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*[[Using Git]]
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The program reads its settings from a file called cometparams.ini. [[cometparams.ini parameter file|Here]] is an overview of the main parameters.
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===Scripts===
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|valign="top"|
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|}
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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

Retrieved from "http://www.dayel.com/comet/cometwiki/index.php?title=CometWiki&oldid=310"