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===Introduction===


This site describes the set up and usage of `comet', an actin-based bead motility simulator.  
This wiki describes how to set up and use the `comet' program.


Cells in our body use [http://en.wikipedia.org/wiki/Actin actin] to move.  Unlike the actin-myosin interaction that produces muscle movement, this kind of movement is on a much smaller scale---the scale of individual cells---and allows, for example, neurons to migrate and wire up to the right part of the brain, and cells in our immune system to track down and engulf bacteria.  To achieve this movement, cells lay down actin polymer networks that produce force.  One way to study how our cells use actin to produce force and move is to study a simplified system which still recreates actin-based motility ''in vitro'', such as 'actin-based bead motility'. 
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).
 
In actin-based bead motility, we coat a bead with proteins that normally tell the cell to polymerize actin, then put the bead a solution similar to that inside of the cell, which causes an actin network to build around the bead.  Surprisingly, even when the bead is spherically symmetric, rather than just building a symmetric shell that gets bigger and bigger, it moves off in 'comet tail' of actin.  This bead motility simulator aims to help us understand how this process works.


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==Essential Information==
==Essential Information==
 
===How the Program Works===
===How the program works===
 
*[[Description of the Model]]
*[[Description of the Model]]
*[[Program Flow|Overview of Program Flow]]
*[[Program Flow|Overview of Program Flow]]


===Installing the program===
===Video Tutorials===
*[http://www.dayel.com/research/comet/comet-tutorial-1/  How to run the comet  program on OS X]
*[http://www.dayel.com/research/comet/comet-tutorial-2/  How to make 3D isosurfaces].
 
===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]]


===Running the program===
===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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*[[Implementation in C++]]
*[[Implementation in C++]]


===Making Measurments===
===Making Measurements===


*[[Node Tracks|Tracking network movement and making measurements]]
*[[Node Tracks|Tracking network movement and making measurements]]
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==Code Status==
==Code Status==


*[http://www.dayel.com/git/comet.git Source Repository]
*[http://github.com/markdayel/comet Source Repository]
*[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]
*[http://github.com/markdayel/comet/archives/master Latest Source]
*[http://www.dayel.com/comet/bin Download Binaries]
*[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]


*[[Known Issues]]
*[[Known Issues]]

Latest revision as of 01:35, 16 November 2009

http://www.dayel.com/comet/supmat/movies/thumbnails/FigS2_Fig1_x_proj.mov.png http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png http://www.dayel.com/comet/supmat/movies/thumbnails/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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