CometWiki - Revision history

Markdayel at 01:35, 16 November 2009

2009-11-16T01:35:57Z

← Older revision		Revision as of 01:35, 16 November 2009
Line 59:		Line 59:
	*[[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]]

Markdayel at 01:35, 16 November 2009

2009-11-16T01:35:43Z

← Older revision		Revision as of 01:35, 16 November 2009
Line 70:		Line 70:
	==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/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]		*[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]

Markdayel at 15:04, 22 September 2009

2009-09-22T15:04:05Z

← Older revision		Revision as of 15:04, 22 September 2009
Line 6:		Line 6:
	\|width="700" valign="top"\|		\|width="700" valign="top"\|

	You can read [http://www.dayel.com/research/comet/ an introduction to the comet project here.]		This wiki describes how to set up and use the `comet' program.

			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).

	~~This wiki describes how to set up and use the `comet' program.~~
	\|valign="top"\|		\|valign="top"\|
	\|}		\|}

Markdayel at 22:17, 9 September 2009

2009-09-09T22:17:47Z

← Older revision		Revision as of 22:17, 9 September 2009
Line 14:		Line 14:
	\|width=300px valign="top"\|		\|width=300px valign="top"\|
	==Essential Information==		==Essential Information==
			===How the Program Works===
			*[[Description of the Model]]
			*[[Program Flow\|Overview of Program Flow]]

	===Video Tutorials===		===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-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-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).		<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]]		*[[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.

Markdayel at 19:45, 7 September 2009

2009-09-07T19:45:55Z

← Older revision		Revision as of 19:45, 7 September 2009
Line 6:		Line 6:
	\|width="700" valign="top"\|		\|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"\|		\|valign="top"\|
	\|}		\|}
Line 23:		Line 15:
	==Essential Information==		==Essential Information==
	===Video Tutorials===		===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]
			*[http://www.dayel.com/research/comet/comet-tutorial-2/ How to make 3D isosurfaces].

	===How the program works===		===How the program works===

Markdayel at 19:18, 7 September 2009

2009-09-07T19:18:24Z

← Older revision		Revision as of 19:18, 7 September 2009
Line 13:		Line 13:

	=====Bead Motility=====		=====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. This bead motility simulator ~~help~~ us understand how this process works, by recreating the process ''in silico''.		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"\|		\|valign="top"\|
	\|}		\|}
Line 19:		Line 22:
	\|width=300px valign="top"\|		\|width=300px valign="top"\|
	==Essential Information==		==Essential Information==
	[http://www.dayel.com/research/comet/comet-tutorial-1/ ~~Here is a video tutorial on how~~ to run the program] [http://www.dayel.com/research/comet/comet-tutorial-2/ ~~and another on how~~ to make 3D isosurfaces].		===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===		===How the program works===

	*[[Description of the Model]]		*[[Description of the Model]]
	*[[Program Flow\|Overview of Program Flow]]		*[[Program Flow\|Overview of Program Flow]]

Markdayel at 04:59, 7 September 2009

2009-09-07T04:59:35Z

← Older revision		Revision as of 04:59, 7 September 2009
Line 19:		Line 19:
	\|width=300px valign="top"\|		\|width=300px valign="top"\|
	==Essential Information==		==Essential Information==
	[http://www.dayel.com/~~cometwiki~~/~~?linkurl=~~/comet-~~tutorials~~/ Here is a video tutorial on how to run the program].		[http://www.dayel.com/research/comet/comet-tutorial-1/ Here is a video tutorial on how to run the program] [http://www.dayel.com/research/comet/comet-tutorial-2/ and another on how to make 3D isosurfaces].

	===How the program works===		===How the program works===

Markdayel at 02:40, 6 September 2009

2009-09-06T02:40:48Z

← Older revision		Revision as of 02:40, 6 September 2009
Line 19:		Line 19:
	\|width=300px valign="top"\|		\|width=300px valign="top"\|
	==Essential Information==		==Essential Information==
	[http://www.dayel.com/comet-tutorials/ Here is a video tutorial on how to run the program].		[http://www.dayel.com/cometwiki/?linkurl=/comet-tutorials/ Here is a video tutorial on how to run the program].

	===How the program works===		===How the program works===

Markdayel at 02:28, 6 September 2009

2009-09-06T02:28:08Z

← Older revision		Revision as of 02:28, 6 September 2009
Line 14:		Line 14:
	=====Bead Motility=====		=====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. This bead motility simulator help us understand how this process works, by recreating the process ''in silico''.		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. This bead motility simulator help us understand how this process works, by recreating the process ''in silico''.

	~~[http://www.dayel.com/comet-tutorials/ Here is a video tutorial on how to run the program].~~
	\|valign="top"\|		\|valign="top"\|
	\|}		\|}
Line 21:		Line 19:
	\|width=300px valign="top"\|		\|width=300px valign="top"\|
	==Essential Information==		==Essential Information==
			[http://www.dayel.com/comet-tutorials/ Here is a video tutorial on how to run the program].

	===How the program works===		===How the program works===

Markdayel at 02:27, 6 September 2009

2009-09-06T02:27:41Z

← Older revision		Revision as of 02:27, 6 September 2009
Line 6:		Line 6:
	\|width="700" valign="top"\|		\|width="700" valign="top"\|

	This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. ~~[http://www.dayel.com/comet-tutorials/ Here is a video tutorial on how to run the program].~~		This wiki describes the set up and usage of `comet', an actin-based bead motility simulator.

	==Introduction==		==Introduction==
Line 14:		Line 14:
	=====Bead Motility=====		=====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. This bead motility simulator help us understand how this process works, by recreating the process ''in silico''.		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. This bead motility simulator help us understand how this process works, by recreating the process ''in silico''.

			[http://www.dayel.com/comet-tutorials/ Here is a video tutorial on how to run the program].
	\|valign="top"\|		\|valign="top"\|
	\|}		\|}