Difference between revisions of "CometWiki"

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==CometWiki==
 
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This site describes the set up and usage of `comet', an actin-based bead motility simulator. 
 
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[http://en.wikipedia.org/wiki/Actin Actin] is a polymer built by cells that allows them to move.  Actin-based bead motility is an ''in vitro'' model system used to study how our cells produce force and move, carried out by coating a bead with proteins that tell the cell to polymerize actin, and putting the bead a solution that mimics the material inside cells.  This causes an actin network to build around the bead.  Surprisingly even when the bead is spherically symmetric, rather than just buiding a symmetric shell that gets bigger and bigger, it moves off in 'comet tail' of actin.  This bead motility simulater aims to help us understand how this process works.
 
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Here are some examples of the simulator output:
 
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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]
 
[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]
 
[http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]
 
[http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]
 
[http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]
 
[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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This wiki describes how to set up and use the `comet' program. 
  
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*[[Examples|More examples]]
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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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==Essential Information==
 
==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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===Installing the program===
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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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===Installing the Program===
  
 
<code>comet</code> runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).
 
<code>comet</code> runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).
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*[[Installing|Instructions for downloading and installing comet]]
 
*[[Installing|Instructions for downloading and installing comet]]
  
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===Running the program===
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===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 <code>cometparams.ini</code> file in the working directory tells the program detailed information about the model parameters to use for calculation and display.
 
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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*[[Display settings|Display settings in the <code>cometparams.ini</code> file]]
 
*[[Display settings|Display settings in the <code>cometparams.ini</code> file]]
 
*[[Running comet on a cluster|Running <code>comet</code> on a cluster]]
 
*[[Running comet on a cluster|Running <code>comet</code> on a cluster]]
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==Simulator Output==
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===Example Results===
  
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===How the program works===
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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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*[[How comet works|Overview of How the comet program works]]
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===Model Robustness===
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*[[Implementation]]
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*[[Model Robustness|The effect of changing the main parameters]]
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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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==In Depth Information==
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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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===Making Measurements===
  
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===In Depth===
 
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*[[Model Robustness]]
 
 
*[[Node Tracks|Tracking network movement and making measurements]]
 
*[[Node Tracks|Tracking network movement and making measurements]]
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*[[Radial Force Movies]]
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==Code Status==
 
==Code Status==
  
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*[http://www.dayel.com/git/comet.git Source Repository]
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*[http://github.com/markdayel/comet Source Repository]
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*[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]
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*[http://github.com/markdayel/comet/archives/master Latest Source]
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*[http://www.dayel.com/comet/bin Download Binaries]
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*[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]
  
 
*[[Known Issues]]
 
*[[Known Issues]]
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*[[Using Git]]
 
*[[Using Git]]
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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"