http://www.dayel.com/comet/cometwiki/api.php?action=feedcontributions&feedformat=atom&user=Markdayel CometWiki - User contributions [en] 2026-04-29T05:15:16Z User contributions MediaWiki 1.22.3 http://www.dayel.com/comet/cometwiki/index.php/3D_Reconstructions_of_in_vitro_Unconstrained_Shells 3D Reconstructions of in vitro Unconstrained Shells 2010-05-04T15:25:39Z <p>Markdayel: </p> <hr /> <div>View the [http://www.dayel.com/comet/Paper/SupportingInformation/SupportingInformation.pdf pdf file version of the supplementary materials] ''in Acrobat'' for 3D interactive versions of these reconstructions. <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx4-01.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx4-01.mov.png]<br /> <br /> Constrained Shell #1<br /> <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-04_2.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx5-04_2.mov.png]<br /> <br /> Constrained Shell #2 (3-lobed split)<br /> <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-05_3.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx5-05_3.mov.png]<br /> <br /> Constrained Shell #3<br /> <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx5-06.mov.png]<br /> <br /> Constrained Shell #4<br /> <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06_1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx5-06_1.mov.png]<br /> <br /> Constrained Shell #5</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/3D_Reconstructions_of_in_vitro_Unconstrained_Shells 3D Reconstructions of in vitro Unconstrained Shells 2010-05-04T15:24:47Z <p>Markdayel: </p> <hr /> <div>See the [http://www.dayel.com/comet/Paper/SupportingInformation/SupportingInformation.pdf pdf file version of the supplementary materials] for 3D interactive versions of these reconstructions. <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx4-01.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx4-01.mov.png]<br /> <br /> Constrained Shell #1<br /> <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-04_2.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx5-04_2.mov.png]<br /> <br /> Constrained Shell #2 (3-lobed split)<br /> <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-05_3.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx5-05_3.mov.png]<br /> <br /> Constrained Shell #3<br /> <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx5-06.mov.png]<br /> <br /> Constrained Shell #4<br /> <br /> <br /> [http://www.dayel.com/comet/supmat/movies/FigS9_MM2-Rx5-06_1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS9_MM2-Rx5-06_1.mov.png]<br /> <br /> Constrained Shell #5</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Implementation_in_C%2B%2B Implementation in C++ 2009-11-22T01:02:31Z <p>Markdayel: </p> <hr /> <div>You can browse the source code here [http://github.com/markdayel/comet here]. The code is written in C++ for speed. We attempt to use an somewhat object-based approach, but a good many of the member variables are declared as static global to allow their access across threads.<br /> <br /> Here is a breakdown of the main classes and functions in the program. There are numerous other functions but this is the core of the program:<br /> <br /> * Main()<br /> ** Spawns threads: &lt;code&gt;collisiondetectionthread&lt;/code&gt; , &lt;code&gt;linkforcesthread&lt;/code&gt; and &lt;code&gt;applyforcesthread&lt;/code&gt; depending on the &lt;code&gt;USETHREAD_COLLISION&lt;/code&gt; , &lt;code&gt;USETHREAD_LINKFORCES&lt;/code&gt; and &lt;code&gt;USETHREAD_APPLYFORCES&lt;/code&gt; parameters.<br /> ** Parses the &lt;code&gt;comet_params.ini&lt;/code&gt; file to read parameters. All of the parameters are implemented as globals (should fix at some point)<br /> ** Creates the main &lt;code&gt;theactin&lt;/code&gt; and &lt;code&gt;nuc_object&lt;/code&gt; objects.<br /> ** Runs through the main iteration loop, calling &lt;code&gt;theactin.iterate()&lt;/code&gt; and saving snapshots every so often.<br /> * Actin class<br /> ** There is only one actin object, &lt;code&gt;theactin&lt;/code&gt; , which constitutes the network, i.e.~contains the nodes and the functions that deal with them.<br /> ** The &lt;code&gt;iterate()&lt;/code&gt; function does one iteration pass, calling: <br /> ***&lt;code&gt;nucleator_node_interactions()&lt;/code&gt; displaces any nodes out of the nucleator object along a normal to the nucleator surface<br /> ***&lt;code&gt;nucleate()&lt;/code&gt; adds new harbinger nodes to the surface of the nucleator<br /> ***&lt;code&gt;crosslinknewnodes()&lt;/code&gt; crosslinks harbingers once they are ready<br /> ***&lt;code&gt;sortnodesbygridpoint()&lt;/code&gt; orders nodes by gridpoint. The {\it only} reason for this is for the division of labor when using threads: We do repulsion by gridpoint to save re-calculating nearby nodes if there are multiple nodes on one gridpoint, and we do not want to divide nodes on one gridpoint across multiple threads.<br /> ***&lt;code&gt;collisiondetection()&lt;/code&gt; detects whether nodes are within &lt;code&gt;NODE_REPULSIVE_RANGE&lt;/code&gt; of one another and adds the repulsive force to &lt;code&gt;rep_force_vec[]&lt;/code&gt; .<br /> ***&lt;code&gt;linkforces()&lt;/code&gt; Calculates the forces between nodes due to links and puts into &lt;code&gt;link_force_vec[]&lt;/code&gt; . If a link goes above a certain threshold force, marks it as broken and removes next time (again to prevent thread problems---since a link is removed both ways and we can't guarantee that both nodes are being processed by same thread)<br /> ***&lt;code&gt;applyforces()&lt;/code&gt; updates the positions of all the nodes. Sums over the threads for &lt;code&gt;rep_force_vec[]&lt;/code&gt; , &lt;code&gt;link_force_vec[]&lt;/code&gt; and &lt;code&gt;repulsion_displacement_vec[]&lt;/code&gt; . <br /> ***Numerous other functions for things like saving bmps, vrml etc. <br /> **Nucleator class<br /> *** There is only one nucleator object at the moment, &lt;code&gt;nuc_object&lt;/code&gt; , which is closely linked to the actin object<br /> *** The nucleator is either a sphere, a capsule (i.e.~a sphere with a cylindrical segment stuck in the middle) or ellipsoid <br /> *** &lt;code&gt;addnodes()&lt;/code&gt; adds harbingers to the surface of the nucleator. The probablility of addition of nodes is normalized by surface area and is symmetric if &lt;code&gt;ASYMMETRIC_NUCLEATION&lt;/code&gt; is zero, or asymmetric if 1 or 2 (stepped or linear bias)<br /> *** &lt;code&gt;definenucleatorgrid()&lt;/code&gt; sets a list of gridpoints to check in case of nodes entering the nucleator. Called once at the beginning.<br /> *** &lt;code&gt;iswithinnucleator()&lt;/code&gt; returns true if the node is within the nucleator<br /> *** &lt;code&gt;collision()&lt;/code&gt; moves a node out of the nucleator along a normal vector <br /> ** Nodes class<br /> *** Nodes exist only as members of the actin object<br /> *** &lt;code&gt;nodegrid&lt;/code&gt; is a 3 dimensional C++ vector of node pointers. Each nodegrid entry starts a circularly linked list of nodes representing the nodes within that gridpoint voxel.<br /> *** The actin class contains a vector of nodes. Each node has an associated &lt;code&gt;nodenum&lt;/code&gt; , &lt;code&gt;x&lt;/code&gt; &lt;code&gt;y&lt;/code&gt; and &lt;code&gt;z&lt;/code&gt; position, &lt;code&gt;nextnode&lt;/code&gt; and &lt;code&gt;prevnode&lt;/code&gt; node pointers for the nodegrid linked list, &lt;code&gt;rep_force_vec[]&lt;/code&gt; , &lt;code&gt;link_force_vec[]&lt;/code&gt; and &lt;code&gt;repulsion_displacement_vec[]&lt;/code&gt; as described above, the grid position of the node, &lt;code&gt;harbinger&lt;/code&gt; and &lt;code&gt;polymer&lt;/code&gt; flags and a &lt;code&gt;listoflinks&lt;/code&gt; i.e. a vector of link object which attach this node to other nodes.<br /> *** &lt;code&gt;polymerize()&lt;/code&gt; Creates a node as a harbinger. Adds its pointer to the gridpoint linked list.<br /> *** &lt;code&gt;depolymerize()&lt;/code&gt; Removes a node, deletes all links and removes from grid.<br /> *** &lt;code&gt;setgridcoords()&lt;/code&gt; Calculates new grid co-ordinates based on x,y,z position<br /> *** &lt;code&gt;addtogrid()&lt;/code&gt; adds the node to the current gridpoint<br /> *** &lt;code&gt;removefromgrid()&lt;/code&gt; removes node from the grid<br /> *** &lt;code&gt;updategrid()&lt;/code&gt; checks to see if node has moved gridpoints, and updates grid is needs to<br /> *** &lt;code&gt;removelink()&lt;/code&gt; removes the specified node from the list of links<br /> ** Links class<br /> *** Links exist only as members of the node objects<br /> *** Each link has an associated &lt;code&gt;linkednodeptr&lt;/code&gt; which points to the target node that the link is to and a &lt;code&gt;broken&lt;/code&gt; flag which is read by &lt;code&gt;actin::linkforces()&lt;/code&gt; and tells it to delete the link if it broke.<br /> *** &lt;code&gt;orig_dist&lt;/code&gt; and &lt;code&gt;orig_distsqr&lt;/code&gt; store the original distance of the link<br /> *** &lt;code&gt;breakcount&lt;/code&gt; stores the number of consecutive iterations the link force has been above &lt;code&gt;LINK_BREAKAGE_FORCE&lt;/code&gt; and is used to increase the probability of breakage<br /> *** &lt;code&gt;getlinkforces()&lt;/code&gt; returns the force acting on the link. Also sets the &lt;code&gt;broken&lt;/code&gt; flag and increments &lt;code&gt;breakcount&lt;/code&gt; if appropriate</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-11-16T01:35:57Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes how to set up and use the `comet' program. <br /> <br /> 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).<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> ===How the Program Works===<br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Video Tutorials===<br /> *[http://www.dayel.com/research/comet/comet-tutorial-1/ How to run the comet program on OS X] <br /> *[http://www.dayel.com/research/comet/comet-tutorial-2/ How to make 3D isosurfaces].<br /> <br /> ===Installing the Program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the Program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurements===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://github.com/markdayel/comet Source Repository]<br /> *[http://github.com/markdayel/comet/archives/master Latest Source]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-11-16T01:35:43Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes how to set up and use the `comet' program. <br /> <br /> 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).<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> ===How the Program Works===<br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Video Tutorials===<br /> *[http://www.dayel.com/research/comet/comet-tutorial-1/ How to run the comet program on OS X] <br /> *[http://www.dayel.com/research/comet/comet-tutorial-2/ How to make 3D isosurfaces].<br /> <br /> ===Installing the Program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the Program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://github.com/markdayel/comet Source Repository]<br /> *[http://github.com/markdayel/comet/archives/master Latest Source]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Desc-0-Description_of_the_Model MediaWiki:Desc-0-Description of the Model 2009-11-07T18:58:22Z <p>Markdayel: Created page with 'Detailed description of the simulation used to computationally model actin-based symmetry breaking and motility'</p> <hr /> <div>Detailed description of the simulation used to computationally model actin-based symmetry breaking and motility</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Desc-0-Ellipsoid_and_Capsule_symmetry_breaking MediaWiki:Desc-0-Ellipsoid and Capsule symmetry breaking 2009-11-07T18:57:16Z <p>Markdayel: Created page with 'Sideways actin-based symmetry breaking motion for simulated ellipsoidal and capsule (listeria-shaped) beads'</p> <hr /> <div>Sideways actin-based symmetry breaking motion for simulated ellipsoidal and capsule (listeria-shaped) beads</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Desc-0-Forces_during_Symmetry_Breaking MediaWiki:Desc-0-Forces during Symmetry Breaking 2009-11-07T18:56:14Z <p>Markdayel: Created page with 'Forces during actin-based symmetry breaking and motility, calculated from the simulation'</p> <hr /> <div>Forces during actin-based symmetry breaking and motility, calculated from the simulation</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Desc-0-Symmetry_Breaking_and_Motility MediaWiki:Desc-0-Symmetry Breaking and Motility 2009-11-07T18:55:36Z <p>Markdayel: Created page with 'Simulations of actin-based symmetry breaking and motility'</p> <hr /> <div>Simulations of actin-based symmetry breaking and motility</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Desc-0-CometWiki MediaWiki:Desc-0-CometWiki 2009-11-07T18:46:52Z <p>Markdayel: Created page with 'Project page for comet, the actin-based bead motility simulator'</p> <hr /> <div>Project page for comet, the actin-based bead motility simulator</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Installing Installing 2009-11-07T18:19:39Z <p>Markdayel: /* Downloading the source */</p> <hr /> <div>==Installing the program==<br /> <br /> '''The program requires ImageMagick for writing images and bzip2 for compressing data files.''' We recommenced using [http://macports.org macports] to install ImageMagick on OS X, and [http://cygwin.org cygwin] to install ImageMagick and bzip2 on windows ([[Installing#Platform_Specific_Information|see 'Platform Specific Information' below]]).<br /> <br /> ===Precompiled binary for OS X===<br /> <br /> We provide a [http://www.dayel.com/comet/bin/ precompiled binary for Mac OS X], and instructions for compiling from source for OS X, Linux and Windows. The precompiled OS X binary includes the VTK 3D visualization and GSL random number generator, but still requires ImageMagick for the bitmap conversion.<br /> <br /> ===Compiling from source===<br /> <br /> ====Downloading the source====<br /> <br /> The source is freely available via [http://git-scm.com/ git] under the open source GNU General Public License. You can download a [http://github.com/markdayel/comet/archives/master zipped copy of the latest source here]. You can [http://github.com/markdayel/comet/ browse the source repository at github] or to create your own local git repository of the source, by installing git then typing:<br /> git clone git://github.com/markdayel/comet.git<br /> <br /> ====Compiling====<br /> <br /> Makefiles are included for building with GCC on linux, OS X, windows, and DEC Alpha, and an Xcode project file is also included for OS X. If you are unfamiliar with git, there is a lot if information online---I found [http://www.gitready.com/ this website] a useful place to start.<br /> <br /> ====VTK and GSL Dependencies====<br /> <br /> The code has two optional dependencies, the [http://www.gnu.org/software/gsl/ Gnu Scientific Library (GSL)] which provides the Mersenne Twister random number generator (more statistically valid than the standard rand() function), and [http://vtk.org The Visualization Toolkit (VTK)] which provides the 3D visualization routines. I have posted precompiled binary versions of the [http://www.dayel.com/2009/09/installing-vtk-on-os-x/ VTK] and [http://www.dayel.com/2009/09/building-gsl-universal-binary/ GSL] libraries for OS X, which you should be able to use directly just by unzipping the files and setting the paths in Xcode or the makefile to point to the include files and libraries. <br /> <br /> =====Compiling without GSL or VTK=====<br /> If the libraries are not available, you can compile without them by changing the #define's USE_GSL_RANDOM and LINK_VTK in the file stdafx.h from 1 to 0 respectively. <br /> <br /> ==Platform Specific Information==<br /> <br /> The code has been developed on OS X 10.5 and Linux, but should run fine in windows. <br /> <br /> ====OS X====<br /> First install the [http://developer.apple.com/tools/ Apple Developer Tools], then open the Xcode project file included in the source. Include the GSL and VTK libraries in the search path, or disable before compiling (see above).<br /> <br /> ====Linux====<br /> A makefile is included for compilation with GNU Make. This should be edited to point to the GSL and VTK libraries, or disable them before compiling (see above). To install GSL on ubuntu type<br /> sudo apt-get install libgsl0-dev<br /> <br /> ====Windows====<br /> First install [http://cygwin.org cygwin], then use cygwin to install ImageMagick, bzip2 and gcc, then compile as for Linux. If compiling with Visual Studio instead of gcc, you will also need a pthreads library.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Installing Installing 2009-11-07T18:18:20Z <p>Markdayel: /* Compiling */</p> <hr /> <div>==Installing the program==<br /> <br /> '''The program requires ImageMagick for writing images and bzip2 for compressing data files.''' We recommenced using [http://macports.org macports] to install ImageMagick on OS X, and [http://cygwin.org cygwin] to install ImageMagick and bzip2 on windows ([[Installing#Platform_Specific_Information|see 'Platform Specific Information' below]]).<br /> <br /> ===Precompiled binary for OS X===<br /> <br /> We provide a [http://www.dayel.com/comet/bin/ precompiled binary for Mac OS X], and instructions for compiling from source for OS X, Linux and Windows. The precompiled OS X binary includes the VTK 3D visualization and GSL random number generator, but still requires ImageMagick for the bitmap conversion.<br /> <br /> ===Compiling from source===<br /> <br /> ====Downloading the source====<br /> <br /> The source is freely available via [http://git-scm.com/ git] under the open source GNU General Public License. You can download a [http://github.com/markdayel/comet/archives/master zipped copy of the latest source here]. You can [http://github.com/markdayel/comet/ browse the source repository at github] or to create your own local git repository of the source in a directory called 'comet', install git then type:<br /> git clone git://github.com/markdayel/comet.git<br /> <br /> ====Compiling====<br /> <br /> Makefiles are included for building with GCC on linux, OS X, windows, and DEC Alpha, and an Xcode project file is also included for OS X. If you are unfamiliar with git, there is a lot if information online---I found [http://www.gitready.com/ this website] a useful place to start.<br /> <br /> ====VTK and GSL Dependencies====<br /> <br /> The code has two optional dependencies, the [http://www.gnu.org/software/gsl/ Gnu Scientific Library (GSL)] which provides the Mersenne Twister random number generator (more statistically valid than the standard rand() function), and [http://vtk.org The Visualization Toolkit (VTK)] which provides the 3D visualization routines. I have posted precompiled binary versions of the [http://www.dayel.com/2009/09/installing-vtk-on-os-x/ VTK] and [http://www.dayel.com/2009/09/building-gsl-universal-binary/ GSL] libraries for OS X, which you should be able to use directly just by unzipping the files and setting the paths in Xcode or the makefile to point to the include files and libraries. <br /> <br /> =====Compiling without GSL or VTK=====<br /> If the libraries are not available, you can compile without them by changing the #define's USE_GSL_RANDOM and LINK_VTK in the file stdafx.h from 1 to 0 respectively. <br /> <br /> ==Platform Specific Information==<br /> <br /> The code has been developed on OS X 10.5 and Linux, but should run fine in windows. <br /> <br /> ====OS X====<br /> First install the [http://developer.apple.com/tools/ Apple Developer Tools], then open the Xcode project file included in the source. Include the GSL and VTK libraries in the search path, or disable before compiling (see above).<br /> <br /> ====Linux====<br /> A makefile is included for compilation with GNU Make. This should be edited to point to the GSL and VTK libraries, or disable them before compiling (see above). To install GSL on ubuntu type<br /> sudo apt-get install libgsl0-dev<br /> <br /> ====Windows====<br /> First install [http://cygwin.org cygwin], then use cygwin to install ImageMagick, bzip2 and gcc, then compile as for Linux. If compiling with Visual Studio instead of gcc, you will also need a pthreads library.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Installing Installing 2009-11-07T18:18:00Z <p>Markdayel: /* Downloading the source */</p> <hr /> <div>==Installing the program==<br /> <br /> '''The program requires ImageMagick for writing images and bzip2 for compressing data files.''' We recommenced using [http://macports.org macports] to install ImageMagick on OS X, and [http://cygwin.org cygwin] to install ImageMagick and bzip2 on windows ([[Installing#Platform_Specific_Information|see 'Platform Specific Information' below]]).<br /> <br /> ===Precompiled binary for OS X===<br /> <br /> We provide a [http://www.dayel.com/comet/bin/ precompiled binary for Mac OS X], and instructions for compiling from source for OS X, Linux and Windows. The precompiled OS X binary includes the VTK 3D visualization and GSL random number generator, but still requires ImageMagick for the bitmap conversion.<br /> <br /> ===Compiling from source===<br /> <br /> ====Downloading the source====<br /> <br /> The source is freely available via [http://git-scm.com/ git] under the open source GNU General Public License. You can download a [http://github.com/markdayel/comet/archives/master zipped copy of the latest source here]. You can [http://github.com/markdayel/comet/ browse the source repository at github] or to create your own local git repository of the source in a directory called 'comet', install git then type:<br /> git clone git://github.com/markdayel/comet.git<br /> <br /> ====Compiling====<br /> <br /> Makefiles are included for building with GCC on linux, OS X, windows, and DEC Alpha, and an Xcode project file is also included for OS X. You can browse the source at http://www.dayel.com/git/comet.git . If you are unfamiliar with git, there is a lot if information online---I found [http://www.gitready.com/ this website] a useful place to start.<br /> <br /> ====VTK and GSL Dependencies====<br /> <br /> The code has two optional dependencies, the [http://www.gnu.org/software/gsl/ Gnu Scientific Library (GSL)] which provides the Mersenne Twister random number generator (more statistically valid than the standard rand() function), and [http://vtk.org The Visualization Toolkit (VTK)] which provides the 3D visualization routines. I have posted precompiled binary versions of the [http://www.dayel.com/2009/09/installing-vtk-on-os-x/ VTK] and [http://www.dayel.com/2009/09/building-gsl-universal-binary/ GSL] libraries for OS X, which you should be able to use directly just by unzipping the files and setting the paths in Xcode or the makefile to point to the include files and libraries. <br /> <br /> =====Compiling without GSL or VTK=====<br /> If the libraries are not available, you can compile without them by changing the #define's USE_GSL_RANDOM and LINK_VTK in the file stdafx.h from 1 to 0 respectively. <br /> <br /> ==Platform Specific Information==<br /> <br /> The code has been developed on OS X 10.5 and Linux, but should run fine in windows. <br /> <br /> ====OS X====<br /> First install the [http://developer.apple.com/tools/ Apple Developer Tools], then open the Xcode project file included in the source. Include the GSL and VTK libraries in the search path, or disable before compiling (see above).<br /> <br /> ====Linux====<br /> A makefile is included for compilation with GNU Make. This should be edited to point to the GSL and VTK libraries, or disable them before compiling (see above). To install GSL on ubuntu type<br /> sudo apt-get install libgsl0-dev<br /> <br /> ====Windows====<br /> First install [http://cygwin.org cygwin], then use cygwin to install ImageMagick, bzip2 and gcc, then compile as for Linux. If compiling with Visual Studio instead of gcc, you will also need a pthreads library.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Sidebar MediaWiki:Sidebar 2009-11-01T19:27:42Z <p>Markdayel: </p> <hr /> <div>* navigation<br /> ** mainpage|mainpage-description<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help<br /> * SEARCH<br /> * Supporting Information<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/|Supporting Information for PLoS Biology paper<br /> * Code<br /> **http://github.com/markdayel/comet/archives/master|Download Lastest Source<br /> **http://github.com/markdayel/comet|Source Repository<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg|Download OS X Binary<br /> **Known Issues|Known Issues<br /> * TOOLBOX<br /> * LANGUAGES</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Sidebar MediaWiki:Sidebar 2009-11-01T19:10:39Z <p>Markdayel: </p> <hr /> <div>* navigation<br /> ** mainpage|mainpage-description<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help<br /> * SEARCH<br /> * Supporting Information<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/|Supporting Information for PLoS Biology paper<br /> * Code<br /> **http://github.com/markdayel/comet/archives/master|Lastest Source (zip)<br /> **http://github.com/markdayel/comet|Source Repository<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg|Download OS X Binary<br /> **Known Issues|Known Issues<br /> * TOOLBOX<br /> * LANGUAGES</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Help:Contents Help:Contents 2009-10-30T00:24:39Z <p>Markdayel: /* Wikitext Formatting */</p> <hr /> <div>Here are some instructions on using CometWiki. The syntax is essentially the same as wikipedia. Another good way to learn is to use existing pages as examples---click the 'edit' link at the top of a page to see the source.<br /> If you have any problems with the wiki, you can email me at: markdayel@gmail.com<br /> <br /> =Wikitext Formatting=<br /> <br /> You can find info on how to format wikitext [http://meta.wikimedia.org/wiki/Help:Wikitext_examples here].<br /> <br /> =Uploading Files=<br /> <br /> Upload files with the 'Upload file' link on the left. You can upload image files, pdfs, movies etc. Avoid uploading images as tif format if possible since it is not natively supported by most browsers and produces huge files (png is a good lossless format if you want the image to have perfect accuracy, otherwise jpeg with quality of 95% works very well and produces relatively small files)<br /> <br /> There is a limit on the upload file size. If you want to upload something really big, email me: markdayel@gmail.com<br /> <br /> <br /> Media files can be linked to in the text with e.g.<br /> <br /> &lt;tt&gt;&lt;nowiki&gt;[[:media:mypaper.pdf | here's my paper]]&lt;/nowiki&gt;&lt;/tt&gt;<br /> <br /> <br /> Images can be typeset with thumbnails automatically, e.g.<br /> <br /> &lt;tt&gt;&lt;nowiki&gt;[[Image:Choanodiagram3.1.jpg|thumb|250px|right|Choanoflagellate]] &lt;/nowiki&gt;&lt;/tt&gt;<br /> <br /> will produce a 250 pixel wide thumbnail of the image on the right of the page, with the caption 'Choanoflagellate'<br /> <br /> Wiki table formatting is a bit byzantine---to quickly convert tables from excel to wikitext, you can use [http://people.fas.harvard.edu/~sdouglas/table.cgi this online form] but please also upload the xls file to make it easier for others to update the table.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Help:Contents Help:Contents 2009-10-30T00:24:22Z <p>Markdayel: Created page with 'Here are some instructions on using CometWiki. The syntax is essentially the same as wikipedia. Another good way to learn is to use existing pages as examples---click the 'edit…'</p> <hr /> <div>Here are some instructions on using CometWiki. The syntax is essentially the same as wikipedia. Another good way to learn is to use existing pages as examples---click the 'edit' link at the top of a page to see the source.<br /> If you have any problems with the wiki, you can email me at: markdayel@gmail.com<br /> <br /> =Wikitext Formatting=<br /> <br /> You can find info on how to format wikitext [http://meta.wikimedia.org/wiki/Help:Wikitext_examples here]. Below are some commonly used examples with their wiki code.<br /> <br /> To create a new page, first make a link to it in an existing page, by enclosing text in double square brackets, e.g.:<br /> <br /> <br /> =Uploading Files=<br /> <br /> Upload files with the 'Upload file' link on the left. You can upload image files, pdfs, movies etc. Avoid uploading images as tif format if possible since it is not natively supported by most browsers and produces huge files (png is a good lossless format if you want the image to have perfect accuracy, otherwise jpeg with quality of 95% works very well and produces relatively small files)<br /> <br /> There is a limit on the upload file size. If you want to upload something really big, email me: markdayel@gmail.com<br /> <br /> <br /> Media files can be linked to in the text with e.g.<br /> <br /> &lt;tt&gt;&lt;nowiki&gt;[[:media:mypaper.pdf | here's my paper]]&lt;/nowiki&gt;&lt;/tt&gt;<br /> <br /> <br /> Images can be typeset with thumbnails automatically, e.g.<br /> <br /> &lt;tt&gt;&lt;nowiki&gt;[[Image:Choanodiagram3.1.jpg|thumb|250px|right|Choanoflagellate]] &lt;/nowiki&gt;&lt;/tt&gt;<br /> <br /> will produce a 250 pixel wide thumbnail of the image on the right of the page, with the caption 'Choanoflagellate'<br /> <br /> Wiki table formatting is a bit byzantine---to quickly convert tables from excel to wikitext, you can use [http://people.fas.harvard.edu/~sdouglas/table.cgi this online form] but please also upload the xls file to make it easier for others to update the table.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki:Privacy_policy CometWiki:Privacy policy 2009-10-30T00:20:04Z <p>Markdayel: </p> <hr /> <div>== Real names ==<br /> While serious contributors are encouraged to use their real names, this is not required; a user account may be created using a pseudonym. <br /> <br /> == E-mail ==<br /> You may optionally provide your e-mail address when [[Special:Userlogin|creating a user account]], or update it in your [[Special:preferences|preferences]]. This is ''not'' required, but if you do choose to submit your e-mail address:<br /> *Other signed-in contributors may send you direct e-mail via your user page and vice-versa; your address will be revealed only if you respond<br /> *If you lose your password, you can have it reassigned through the [[Special:Userlogin|login page]] and a temporary password sent to you.<br /> <br /> <br /> == IP addresses ==<br /> Depending on how you are connected to the Internet, your IP address may generally identify your Internet service provider, or uniquely identify the computer from which you are connecting.<br /> <br /> The IP addresses of anonymous contributors are permanently recorded in the publicly viewable page histories. If you do not wish to publicly reveal your IP address, you should [[Special:Userlogin|create a user account]]; your user name (which may be a pseudonym) will then be recorded in place of the IP address.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki:General_disclaimer CometWiki:General disclaimer 2009-10-30T00:17:39Z <p>Markdayel: Created page with 'The content of this site is being provided freely, and no kind of agreement or contract is created between you and the owners or users of this site, the owners of the servers upo…'</p> <hr /> <div>The content of this site is being provided freely, and no kind of agreement or contract is created between you and the owners or users of this site, the owners of the servers upon which it is housed, individual contributors to these pages, or project administrators, sysops or anyone else connected with this project subject to your claims against them directly. You are granted a limited license to copy anything from this site; it does not create or imply any contractual or extracontractual liability on the part of Wikimedia or any of its agents, members, organizers or other users.<br /> <br /> Any of the trademarks, service marks, collective marks, design rights, personality rights or similar rights that are mentioned, used or cited on this site are the property of their respective owners. Unless otherwise stated, Wikimedia sites are neither endorsed by nor affiliated with any of the holders of such rights, nor can Wikimedia grant rights to use otherwise protected materials. Your use of any such incorporeal property is at your own risk.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki:Privacy_policy CometWiki:Privacy policy 2009-10-30T00:17:29Z <p>Markdayel: Created page with 'The content of this site is being provided freely, and no kind of agreement or contract is created between you and the owners or users of this site, the owners of the servers upo…'</p> <hr /> <div>The content of this site is being provided freely, and no kind of agreement or contract is created between you and the owners or users of this site, the owners of the servers upon which it is housed, individual contributors to these pages, or project administrators, sysops or anyone else connected with this project subject to your claims against them directly. You are granted a limited license to copy anything from this site; it does not create or imply any contractual or extracontractual liability on the part of Wikimedia or any of its agents, members, organizers or other users.<br /> <br /> Any of the trademarks, service marks, collective marks, design rights, personality rights or similar rights that are mentioned, used or cited on this site are the property of their respective owners. Unless otherwise stated, Wikimedia sites are neither endorsed by nor affiliated with any of the holders of such rights, nor can Wikimedia grant rights to use otherwise protected materials. Your use of any such incorporeal property is at your own risk.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/$1 $1 2009-10-30T00:15:54Z <p>Markdayel: Created page with '$1'</p> <hr /> <div>$1</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-22T15:04:05Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes how to set up and use the `comet' program. <br /> <br /> 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).<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> ===How the Program Works===<br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Video Tutorials===<br /> *[http://www.dayel.com/research/comet/comet-tutorial-1/ How to run the comet program on OS X] <br /> *[http://www.dayel.com/research/comet/comet-tutorial-2/ How to make 3D isosurfaces].<br /> <br /> ===Installing the Program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the Program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Installing Installing 2009-09-09T22:29:02Z <p>Markdayel: </p> <hr /> <div>==Installing the program==<br /> <br /> '''The program requires ImageMagick for writing images and bzip2 for compressing data files.''' We recommenced using [http://macports.org macports] to install ImageMagick on OS X, and [http://cygwin.org cygwin] to install ImageMagick and bzip2 on windows ([[Installing#Platform_Specific_Information|see 'Platform Specific Information' below]]).<br /> <br /> ===Precompiled binary for OS X===<br /> <br /> We provide a [http://www.dayel.com/comet/bin/ precompiled binary for Mac OS X], and instructions for compiling from source for OS X, Linux and Windows. The precompiled OS X binary includes the VTK 3D visualization and GSL random number generator, but still requires ImageMagick for the bitmap conversion.<br /> <br /> ===Compiling from source===<br /> <br /> ====Downloading the source====<br /> <br /> The source is freely available via [http://git-scm.com/ git] under the open source GNU General Public License. You can download a [http://www.dayel.com/git/comet.git?a=snapshot;h=refs/heads/master zipped copy of the latest source here], or to create your own local git repository of the source in a directory called 'comet', install git then type:<br /> git clone git://www.dayel.com/comet.git<br /> <br /> ====Compiling====<br /> <br /> Makefiles are included for building with GCC on linux, OS X, windows, and DEC Alpha, and an Xcode project file is also included for OS X. You can browse the source at http://www.dayel.com/git/comet.git . If you are unfamiliar with git, there is a lot if information online---I found [http://www.gitready.com/ this website] a useful place to start.<br /> <br /> ====VTK and GSL Dependencies====<br /> <br /> The code has two optional dependencies, the [http://www.gnu.org/software/gsl/ Gnu Scientific Library (GSL)] which provides the Mersenne Twister random number generator (more statistically valid than the standard rand() function), and [http://vtk.org The Visualization Toolkit (VTK)] which provides the 3D visualization routines. I have posted precompiled binary versions of the [http://www.dayel.com/2009/09/installing-vtk-on-os-x/ VTK] and [http://www.dayel.com/2009/09/building-gsl-universal-binary/ GSL] libraries for OS X, which you should be able to use directly just by unzipping the files and setting the paths in Xcode or the makefile to point to the include files and libraries. <br /> <br /> =====Compiling without GSL or VTK=====<br /> If the libraries are not available, you can compile without them by changing the #define's USE_GSL_RANDOM and LINK_VTK in the file stdafx.h from 1 to 0 respectively. <br /> <br /> ==Platform Specific Information==<br /> <br /> The code has been developed on OS X 10.5 and Linux, but should run fine in windows. <br /> <br /> ====OS X====<br /> First install the [http://developer.apple.com/tools/ Apple Developer Tools], then open the Xcode project file included in the source. Include the GSL and VTK libraries in the search path, or disable before compiling (see above).<br /> <br /> ====Linux====<br /> A makefile is included for compilation with GNU Make. This should be edited to point to the GSL and VTK libraries, or disable them before compiling (see above). To install GSL on ubuntu type<br /> sudo apt-get install libgsl0-dev<br /> <br /> ====Windows====<br /> First install [http://cygwin.org cygwin], then use cygwin to install ImageMagick, bzip2 and gcc, then compile as for Linux. If compiling with Visual Studio instead of gcc, you will also need a pthreads library.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Installing Installing 2009-09-09T22:20:53Z <p>Markdayel: </p> <hr /> <div>==Installing the program==<br /> <br /> '''The program requires ImageMagick for writing images and bzip2 for compressing data files.''' We recommenced using [http://macports.org macports] to install ImageMagick on OS X, and [http://cygwin.org cygwin] to install ImageMagick and bzip2 on windows ([[Installing#Platform_Specific_Information|see 'Platform Specific Information' below]]).<br /> <br /> ===Precompiled binary for OS X===<br /> <br /> We provide a [http://www.dayel.com/comet/bin/ precompiled binary for Mac OS X], and instructions for compiling from source for OS X, Linux and Windows. The precompiled OS X binary includes the VTK 3D visualization and GSL random number generator, but still requires ImageMagick for the bitmap conversion.<br /> <br /> ===Compiling from source===<br /> <br /> ====Downloading the source====<br /> <br /> The source is freely available via [http://git-scm.com/ git] under the open source GNU General Public License. You can download a [http://www.dayel.com/git/comet.git?a=snapshot;h=refs/heads/master zipped copy of the latest source here], or to create your own local git repository of the source in a directory called 'comet', install git then type:<br /> git clone git://www.dayel.com/comet.git<br /> <br /> Makefiles are included for building with GCC on linux, OS X, windows, and DEC Alpha, and an Xcode project file is also included for OS X. You can browse the source at http://www.dayel.com/git/comet.git . If you are unfamiliar with git, there is a lot if information online---I found [http://www.gitready.com/ this website] a useful place to start.<br /> <br /> ====Dependencies====<br /> <br /> The code has two optional dependencies, the [http://www.gnu.org/software/gsl/ Gnu Scientific Library (GSL)] which provides the Mersenne Twister random number generator (more statistically valid than the standard rand() function), and [http://vtk.org The Visualization Toolkit (VTK)] which provides the 3D visualization routines. If these libraries are not available, you can compile without them by changing the #define's USE_GSL_RANDOM and LINK_VTK in the file stdafx.h from 1 to 0 respectively. Follow [[installing VTK on OS X|these instructions]] to install universal VTK libraries under OS X (macports now has a 'vtk5' package that will compile the libraries---I haven't tested it with these yet). I will also upload instructions on how to make OS X universal libraries GSL soon.<br /> <br /> ==Platform Specific Information==<br /> <br /> The code has been developed on OS X 10.5 and Linux, but should run fine in windows. <br /> <br /> ====OS X====<br /> First install the [http://developer.apple.com/tools/ Apple Developer Tools], then open the Xcode project file included in the source. Include the GSL and VTK libraries in the search path, or disable before compiling (see above).<br /> <br /> ====Linux====<br /> A makefile is included for compilation with GNU Make. This should be edited to point to the GSL and VTK libraries, or disable them before compiling (see above). To install GSL on ubuntu type<br /> sudo apt-get install libgsl0-dev<br /> <br /> ====Windows====<br /> First install [http://cygwin.org cygwin], then use cygwin to install ImageMagick, bzip2 and gcc, then compile as for Linux. If compiling with Visual Studio instead of gcc, you will also need a pthreads library.</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-09T22:17:47Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> You can read [http://www.dayel.com/research/comet/ an introduction to the comet project here.]<br /> <br /> This wiki describes how to set up and use the `comet' program. <br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> ===How the Program Works===<br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Video Tutorials===<br /> *[http://www.dayel.com/research/comet/comet-tutorial-1/ How to run the comet program on OS X] <br /> *[http://www.dayel.com/research/comet/comet-tutorial-2/ How to make 3D isosurfaces].<br /> <br /> ===Installing the Program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the Program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-07T19:45:55Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> You can read [http://www.dayel.com/research/comet/ an introduction to the comet project here.]<br /> <br /> This wiki describes how to set up and use the `comet' program. <br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> ===Video Tutorials===<br /> *[http://www.dayel.com/research/comet/comet-tutorial-1/ How to run the comet program on OS X] <br /> *[http://www.dayel.com/research/comet/comet-tutorial-2/ How to make 3D isosurfaces].<br /> <br /> ===How the program works===<br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-07T19:18:24Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ==Introduction==<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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. <br /> <br /> ====The Comet Bead-Motility Simulator====<br /> 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.<br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> ===Video Tutorials===<br /> [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].<br /> <br /> ===How the program works===<br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-07T04:59:35Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ==Introduction==<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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''.<br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> [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].<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-06T02:40:48Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ==Introduction==<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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''.<br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> [http://www.dayel.com/cometwiki/?linkurl=/comet-tutorials/ Here is a video tutorial on how to run the program].<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-06T02:28:08Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ==Introduction==<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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''.<br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> [http://www.dayel.com/comet-tutorials/ Here is a video tutorial on how to run the program].<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-06T02:27:41Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ==Introduction==<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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''.<br /> <br /> [http://www.dayel.com/comet-tutorials/ Here is a video tutorial on how to run the program].<br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-09-04T17:08:43Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> 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].<br /> <br /> ==Introduction==<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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''.<br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-08-03T02:33:24Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ==Introduction==<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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''.<br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg Download OS X Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Sidebar MediaWiki:Sidebar 2009-07-30T16:54:02Z <p>Markdayel: </p> <hr /> <div>* navigation<br /> ** mainpage|mainpage-description<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help<br /> * SEARCH<br /> * Supporting Information<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/|Supporting Information for PLoS Biology paper<br /> * Code<br /> **http://www.dayel.com/git/comet.git?a=snapshot;h=refs/heads/master|Lastest Source (zip)<br /> **http://www.dayel.com/git/comet.git|Source Repository<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/code/comet_osx_binary_v0.2.dmg|Download OS X Binary<br /> **Known Issues|Known Issues<br /> * TOOLBOX<br /> * LANGUAGES</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T03:24:31Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ==Introduction==<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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''.<br /> |valign=&quot;top&quot;|<br /> |}<br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T01:00:12Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ===Introduction===<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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''.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:59:12Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ===Introduction===<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> 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, it moves off in 'comet tail' of actin. This bead motility simulator help us understand how this process works, by recreating the process ''in silico''.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:49:47Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ===Introduction===<br /> =====Cell Movement=====<br /> 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. <br /> <br /> =====Bead Motility=====<br /> One popular way to study how our cells use actin to produce force and move is using a simplified system---actin-based bead motility---which recreates motility ''in vitro''. In this system, 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 help us understand how this process works, by recreating the process ''in silico''.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:47:37Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ===Introduction===<br /> <br /> 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. <br /> <br /> One popular way to study how our cells use actin to produce force and move is using a simplified system---actin-based bead motility---which recreates motility ''in vitro''. In this system, 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.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:47:25Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ===Introduction===<br /> <br /> 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. <br /> <br /> One popular way to study how our cells use actin to produce force and move is using a simplified system ---actin-based bead motility---which recreates motility ''in vitro''. In this system, 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.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:46:54Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ===Introduction===<br /> <br /> 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. <br /> <br /> One popular way to study how our cells use actin to produce force and move is to study a simplified system ---actin-based bead motility---which recreates actin-based force generation and motility ''in vitro''. In this system, 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.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Sidebar MediaWiki:Sidebar 2009-07-27T00:34:50Z <p>Markdayel: </p> <hr /> <div>* navigation<br /> ** mainpage|mainpage-description<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help<br /> * SEARCH<br /> * Supporting Information<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/|Supporting Information for PLoS Biology paper<br /> * Code<br /> **http://www.dayel.com/git/comet.git?a=snapshot;h=refs/heads/master|Lastest Source (zip)<br /> **http://www.dayel.com/git/comet.git|Source Repository<br /> **http://www.dayel.com/comet/bin|Download OS X Binary<br /> **Known Issues|Known Issues<br /> * TOOLBOX<br /> * LANGUAGES</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:04:25Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> ===Introduction===<br /> <br /> 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'. <br /> <br /> 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.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:04:01Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> ===Introduction===<br /> <br /> This wiki describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> 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'. <br /> <br /> 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.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Mainpage MediaWiki:Mainpage 2009-07-27T00:02:52Z <p>Markdayel: Created page with 'CometWiki'</p> <hr /> <div>CometWiki</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:01:28Z <p>Markdayel: /* CometWiki */</p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> ===Introduction===<br /> <br /> This site describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> 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'. <br /> <br /> 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.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> <br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-27T00:01:01Z <p>Markdayel: moved Main Page to CometWiki</p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> ==CometWiki==<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> ===Introduction===<br /> <br /> This site describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> 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'. <br /> <br /> 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.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/Main_Page Main Page 2009-07-27T00:01:01Z <p>Markdayel: moved Main Page to CometWiki</p> <hr /> <div>#REDIRECT [[CometWiki]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/CometWiki CometWiki 2009-07-26T04:26:36Z <p>Markdayel: </p> <hr /> <div>__NOTOC__<br /> [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]<br /> [http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]<br /> [http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]<br /> ==CometWiki==<br /> {|cellpadding=&quot;10&quot;<br /> |width=&quot;700&quot; valign=&quot;top&quot;|<br /> ===Introduction===<br /> <br /> This site describes the set up and usage of `comet', an actin-based bead motility simulator. <br /> <br /> 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'. <br /> <br /> 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.<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> {|cellpadding=&quot;10&quot;<br /> |width=300px valign=&quot;top&quot;|<br /> ==Essential Information==<br /> <br /> ===How the program works===<br /> <br /> *[[Description of the Model]]<br /> *[[Program Flow|Overview of Program Flow]]<br /> <br /> ===Installing the program===<br /> <br /> &lt;code&gt;comet&lt;/code&gt; runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).<br /> <br /> *[[Installing|Instructions for downloading and installing comet]]<br /> <br /> ===Running the program===<br /> <br /> 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 &lt;code&gt;cometparams.ini&lt;/code&gt; file in the working directory tells the program detailed information about the model parameters to use for calculation and display.<br /> <br /> *[[Running the program|Command line parameters for the &lt;code&gt;comet&lt;/code&gt; program]]<br /> *[[cometparams.ini parameter file|Model settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Display settings|Display settings in the &lt;code&gt;cometparams.ini&lt;/code&gt; file]]<br /> *[[Running comet on a cluster|Running &lt;code&gt;comet&lt;/code&gt; on a cluster]]<br /> | valign=&quot;top&quot;|<br /> ==Simulator Output==<br /> ===Example Results===<br /> <br /> *[[Symmetry Breaking and Motility]]<br /> *[[Forces during Symmetry Breaking]]<br /> *[[Circumferential and Radial measurements]]<br /> *[[Ellipsoid and Capsule symmetry breaking]]<br /> <br /> ===Model Robustness===<br /> *[[Model Robustness|The effect of changing the main parameters]]<br /> <br /> ===In Vitro===<br /> *[[3D Reconstructions of in vitro Constrained Shells]]<br /> *[[3D Reconstructions of in vitro Unconstrained Shells]]<br /> <br /> ==In Depth Information==<br /> <br /> ===Inner workings of the code===<br /> *[[Detailed Program Flow]]<br /> *[[Implementation in C++]]<br /> <br /> ===Making Measurments===<br /> <br /> *[[Node Tracks|Tracking network movement and making measurements]]<br /> *[[Radial Force Movies]]<br /> <br /> |valign=&quot;top&quot;|<br /> |}<br /> <br /> <br /> ==Code Status==<br /> <br /> *[http://www.dayel.com/git/comet.git Source Repository]<br /> *[http://www.dayel.com/git/comet.git?a=tree;h=refs/heads/master;hb=master Source Files]<br /> *[http://www.dayel.com/comet/bin Download Binaries]<br /> <br /> *[[Known Issues]]<br /> *[[To Do]]<br /> <br /> *[[Using Git]]</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Sidebar MediaWiki:Sidebar 2009-07-25T05:27:56Z <p>Markdayel: </p> <hr /> <div>* navigation<br /> ** http://www.dayel.com| Return to dayel.com<br /> ** mainpage|mainpage-description<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help<br /> * SEARCH<br /> * Supporting Information<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/|Supporting Information for PLoS Biology paper<br /> * Code<br /> **http://www.dayel.com/git/comet.git?a=snapshot;h=refs/heads/master|Lastest Source (zip)<br /> **http://www.dayel.com/git/comet.git|Source Repository<br /> **http://www.dayel.com/comet/bin|Download OS X Binary<br /> **Known Issues|Known Issues<br /> * TOOLBOX<br /> * LANGUAGES</div> Markdayel http://www.dayel.com/comet/cometwiki/index.php/MediaWiki:Sidebar MediaWiki:Sidebar 2009-07-20T21:10:55Z <p>Markdayel: </p> <hr /> <div>* navigation<br /> ** http://www.dayel.com| Return to dayel.com<br /> ** mainpage|mainpage-description<br /> ** recentchanges-url|recentchanges<br /> ** helppage|help<br /> * SEARCH<br /> * Supporting Information<br /> **http://www.dayel.com/comet/Paper/SupportingInformation/|Supporting Information for PLoS Biology paper<br /> * Code<br /> **http://www.dayel.com/git/comet.git|Source Repository<br /> **http://www.dayel.com/git/comet.git?a=snapshot;h=refs/heads/master|Lastest Source (zip)<br /> **http://www.dayel.com/comet/bin|Download Binaries<br /> **Known Issues|Known Issues<br /> * TOOLBOX<br /> * LANGUAGES</div> Markdayel