Difference between revisions of "CometWiki"

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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]
 
[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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==CometWiki==
 
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{|cellpadding="10"
 
{|cellpadding="10"
 
|width="700" valign="top"|
 
|width="700" valign="top"|
  
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===Introduction===
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This wiki describes how to set up and use the `comet' program. 
  
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This site describes the set up and usage of `comet', an actin-based bead 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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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'. 
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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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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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===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===
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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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*[[Installing|Instructions for downloading and installing comet]]
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===Running the Program===
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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"|
 
==Simulator Output==
 
==Simulator Output==
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===Example Results===
 
===Example Results===
  
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*[[3D Reconstructions of in vitro Unconstrained Shells]]
 
*[[3D Reconstructions of in vitro Unconstrained Shells]]
  
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==In Depth Information==
  
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==Essential Information==
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===Inner workings of the code===
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===Installing the program===
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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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*[[Installing|Instructions for downloading and installing comet]]
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===Running the program===
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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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===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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*[[Detailed Program Flow]]
 
*[[Detailed Program Flow]]
 
*[[Implementation in C++]]
 
*[[Implementation in C++]]
  
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===Making Measurements===
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==In Depth Information==
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===Making Measurments===
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*[[Node Tracks|Tracking network movement and making measurements]]
 
*[[Node Tracks|Tracking network movement and making measurements]]
 
*[[Radial Force Movies]]
 
*[[Radial Force Movies]]
  
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|width="200" valign="top"|
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|valign="top"|
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|}
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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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==Supplementary Materials==
 
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*[http://www.dayel.com/comet/SupplementaryMaterials/ Supplementary Materials]
 
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|valign="top"|
 
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|}
 

Latest revision as of 18:35, 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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