CometWiki - Revision history

Markdayel at 01:35, 16 November 2009

2009-11-16T01:35:57Z

Markdayel at 01:35, 16 November 2009

2009-11-16T01:35:43Z

Markdayel at 15:04, 22 September 2009

2009-09-22T15:04:05Z

Markdayel at 22:17, 9 September 2009

2009-09-09T22:17:47Z

Markdayel at 19:45, 7 September 2009

2009-09-07T19:45:55Z

Markdayel at 19:18, 7 September 2009

2009-09-07T19:18:24Z

Markdayel at 04:59, 7 September 2009

2009-09-07T04:59:35Z

Markdayel at 02:40, 6 September 2009

2009-09-06T02:40:48Z

Markdayel at 02:28, 6 September 2009

2009-09-06T02:28:08Z

Markdayel at 02:27, 6 September 2009

2009-09-06T02:27:41Z

@@ Line 59: / Line 59: @@
 *[[Implementation in C++]]
-===Making Measurments===
+===Making Measurements===
 *[[Node Tracks|Tracking network movement and making measurements]]

@@ Line 70: / Line 70: @@
 ==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/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]

@@ Line 5: / Line 5: @@
 {|cellpadding="10"
 |width="700" valign="top"|
 This wiki describes how to set up and use the `comet' program.
 |valign="top"|
 |}

@@ Line 14: / Line 14: @@
 |width=300px valign="top"|
 ==Essential Information==
 ===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].
-===How the program works===
+===Installing the Program===
-*[[Description of the Model]]
-*[[Program Flow|Overview of Program Flow]]
-−
-===Installing the program===
 <code>comet</code> runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).
@@ Line 28: / Line 28: @@
 *[[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.

@@ Line 6: / Line 6: @@
 |width="700" valign="top"|
-This wiki describes the set up and usage of `comet', an actin-based bead motility simulator.
+You can read [http://www.dayel.com/research/comet/ an introduction to the comet project here.]
-==Introduction==
+This wiki describes how to set up and use the `comet' program.
-=====Cell Movement=====
-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.
-−
-=====Bead Motility=====
-One popular way to study how our cells use actin networks to produce force and move is using a simplified system---''actin-based bead motility''---which recreates motility ''in vitro''.  To do this, 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, the bead moves off in 'comet tail' of actin.
-−
-====The Comet Bead-Motility Simulator====
-This bead motility simulator (named 'Comet') helps us understand how this process works, by recreating the process in silico.  It's a top-down model, based on idea that the large-scale elastic behavior of the network is the key to motility, rather than small-scale filament effects.  Because it's able, by simulating the elastic behavior alone, not only to reproduce the experimental observations, but also to make new predictions that turn out to hold in the experimental system, it shows how the elastic behavior of the actin network works to produce motility.
 |valign="top"|
 |}
@@ Line 23: / Line 15: @@
 ==Essential Information==
 ===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/research/comet/comet-tutorial-1/  How to run the comet  program on OS X]
 ===How the program works===