Difference between revisions of "CometWiki"

From CometWiki
Jump to: navigation, search
m
m
 
(101 intermediate revisions by one user not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 +
[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/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]
 +
{|cellpadding="10"
 +
|width="700" valign="top"|
  
−
==CometWiki==
+
This wiki describes how to set up and use the `comet' program. 
  
−
Welcome to CometWiki. This site describes the set up and usage of `comet' the actin-based motility simulator.
+
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).
  
−
==Examples==
+
|valign="top"|
 +
|}
 +
{|cellpadding="10"
 +
|width=300px valign="top"|
 +
==Essential Information==
 +
===How the Program Works===
 +
*[[Description of the Model]]
 +
*[[Program Flow|Overview of Program Flow]]
  
−
====Symmetry Breaking and Motility====
+
===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].
  
−
*[http://www.dayel.com/comet/supmat/movies/FigS2_Fig1_x_proj.mov Example simulation run 2D (from Figure 1 in paper)]
+
===Installing the Program===
−
*[http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov 3D links view of above example]
+
  
−
====Forces during Symmetry Breaking====
+
<code>comet</code> runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).
  
−
*[http://www.dayel.com/comet/supmat/movies/FigS5a_radial_report_force.mov Forces and link breaks during symmetry breaking]
+
*[[Installing|Instructions for downloading and installing comet]]
−
*[http://www.dayel.com/comet/supmat/movies/FigS5bSmoothMotilityLink_breaks.mov Link breaks during smooth motility]
+
  
−
====Circumferential and Radial measurements====
+
===Running the Program===
  
−
*[http://www.dayel.com/comet/supmat/movies/FigS4a_circ_measure_vtk_.mov Circumferential measurements during symmetry breaking]
+
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.
−
*[http://www.dayel.com/comet/supmat/movies/FigS4b_radial_measure_vtk_.mov Radial measurements during symmetry breaking]
+
−
*[http://www.dayel.com/comet/supmat/movies/FigS6a_vtk_smooth_circ_trimmed.mov Circumferential measurements during smooth motilty]
+
−
*[http://www.dayel.com/comet/supmat/movies/FigS6b_vtk_radial_trimmed.mov Radial measurements during smooth motilty]
+
  
−
====Ellipsoid and Capsule symmetry breaking====
+
*[[Running the program|Command line parameters for the <code>comet</code> program]]
 +
*[[cometparams.ini parameter file|Model 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]]
 +
| valign="top"|
 +
==Simulator Output==
 +
===Example Results===
  
−
*[http://www.dayel.com/comet/supmat/movies/FigS7a_Ellipsoid_vtk_.mov Sideways symmetry breaking of ellipsoid (3D)]
+
*[[Symmetry Breaking and Motility]]
−
*[http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov Sideways symmetry breaking of capsule (2D)]
+
*[[Forces during Symmetry Breaking]]
 +
*[[Circumferential and Radial measurements]]
 +
*[[Ellipsoid and Capsule symmetry breaking]]
  
−
====Reconstructions of ''in vitro'' Constrained Shells====
+
===Model Robustness===
 +
*[[Model Robustness|The effect of changing the main parameters]]
  
−
*[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-01.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #1]
+
===In Vitro===
−
*[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-03.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #2]
+
*[[3D Reconstructions of in vitro Constrained Shells]]
−
*[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell1.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #3]
+
*[[3D Reconstructions of in vitro Unconstrained Shells]]
−
*[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell2.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #4]
+
  
−
====Reconstructions of ''in vitro'' Unconstrained Shells====
+
==In Depth Information==
−
*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx4-01.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #1]
+
−
*[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]
+
−
*[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]
+
−
*[http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06.mov 3D reconstruction of in vitro shell constrained between slide and coverslip #4]
+
−
*[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]
+
  
 +
===Inner workings of the code===
 +
*[[Detailed Program Flow]]
 +
*[[Implementation in C++]]
  
 +
===Making Measurements===
  
 +
*[[Node Tracks|Tracking network movement and making measurements]]
 +
*[[Radial Force Movies]]
  
 +
|valign="top"|
 +
|}
  
−
==Usage==
 
  
−
{|cellpadding="5"
+
==Code Status==
−
|width="45%"|
+
−
===Installing===
+
−
*[[Installing]]
+
  
−
You can download
+
*[http://github.com/markdayel/comet Source Repository]
 +
*[http://github.com/markdayel/comet/archives/master Latest Source]
 +
*[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]
  
−
===Running the program===
+
*[[Known Issues]]
−
*[[Running the program]]
+
*[[To Do]]
  
−
===Settings===
+
*[[Using Git]]
−
 
+
−
*[[cometparams.ini parameter file]]
+
−
 
+
−
 
+
−
|width="45%" valign="top"|
+
−
===Scripts===
+
−
 
+
−
|valign="top"|
+
−
|}
+

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"