CometWiki - New pages [en]

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2009-10-30T00:15:54Z

Markdayel: Created page with '$1'

Radial Force Movies

2009-05-08T01:34:46Z

Markdayel: Created page with 'To make the radial force movies, use the makeradialmovie script (which uses the gplot.sc gplot script). The syntax is makeradialmovie <startframe> <endframe> You currently nee...'

To make the radial force movies, use the makeradialmovie script (which uses the gplot.sc gplot script). The syntax is
makeradialmovie <startframe> <endframe>

You currently need to edit the script and edit the section:
bmpfilename=`printf "bitmaps_links/x_proj_%05d.jpeg" ${thisframe}`
bmpfilename3=`printf "bitmaps_greenstripe2/x_proj_%05d.jpeg" ${thisframe}`
bmpfilename2=`printf "bitmaps_transverse3/x_proj_%05d.jpeg" ${thisframe}`
to specify which bitmaps to put into the left hand panes

Description of the Model

2009-04-27T00:53:36Z

Markdayel:

==Overview==
[[file:mymodel.png|right|thumb|200px|Figure 1: Schematic of node and link arrangement]]

The <code>comet</code> program is a Monte-Carlo/Lagrangian model that calculates the 3 dimensional positions of a large number of `nodes' representing material in an actin network. For each time step <code>DELTA_T</code>, nodes move a displacement proportional to the force acting upon them. There is no inertia, since this is a low Reynolds number regime. The forces acting on each node are as follows: [[file:mymodel_forces.png|right|thumb|400px|Figure 1: Forces acting on bead]]

*Repulsive forces between nodes
*Link forces between nodes
*Link forces between node and nucleator

[[file:Links_crosssection_inset.jpg|right|thumb|400px|Figure 1: 3D Cross section of part of shell showing links around bead]]

==Details==

The nucleator object is treated as incompressible i.e. if during an iteration a node enters the nucleator, then in the next iteration it is simply moved out of the nucleator along a normal to the nucleator surface.

Nodes are nucleated at a constant rate, proportional to <code>P_NUC</code> , at the nucleator surface. To allow it to find an equilibrium position before being crosslinked into the network, a new node has its <code>harbinger</code> flag set when created, it experiences only repulsive forces for <code>CROSSLINKDELAY</code> iterations. Crosslinks are then formed as follows: All nodes with within <code>XLINK_NODE_RANGE</code> are counted, and links are either formed in random order, or if <code>XLINK_NEAREST</code> nearest first, until the number of crosslinks reaches <code>MAX_LINKS_PER_NODE</code>. Once a link is formed, its original distance is stored and used to calculate link forces. If the link is stretched or compressed away from its original length it behaves as a Hooke's Law spring and excerts a force proportional to, and opposing, the displacement. The scale multiple for this force is <code>LINK_FORCE</code> . This is to simulate an actin filament acting as an entropic spring by flexing motions. If the link force exceeds <code>LINK_BREAKAGE_FORCE</code> then the link breaks.

The nucleator is allowed to move and rotate, subject to displacement and torque vectors from the summed node repulsion from the nucleator, and the nucleator-node link forces. A full treatment of nucleator inertia (viscous drag) is beyond the scope of the current model, and drag is simply scaled by a supplied parameter <code>NUCLEATOR_INERTIA</code> multiplied by the node inertia, and similarly the nucleator moment of inertia is scaled by the supplied parameter <code>MofI</code> . As a first approximation of how this should change with nucleator size, we scale the inertia and moment of inertia by the radius (or radius and length for long axes of the ellipsoids and capsules) if the <code>VARY_INERT_W_RAD</code> parameter is set. Given that this is not drag through a Newtonian fluid, but largely a product of complex fluid and network drag forces, this may not be very accurate. On the other hand the behavior is not very sensitive to the <code>NUCLEATOR_INERTIA</code> parameter anyway.

Output files are saved as jpgs for the x,y and z projections (convolved with a Gaussian to make it look like a microscope image). Post processing routines can produce 3D rendering jpgs, or interactive 3D renderings on-screen. Also, post-processing 3D rendering of a single image will trigger the program to also write a vrml file to allow the 3D view to be imported into other software (e.g. Acrobat 3D etc.). Note: the program calls the Imagemagick <code>convert</code> program to add text to the images and save as jpgs and calls <code>bzip2</code> to compress the data files.

Implementation in C++

2009-04-27T00:39:20Z

Markdayel:

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.

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:

* Main()
** Spawns threads: <code>collisiondetectionthread</code> , <code>linkforcesthread</code> and <code>applyforcesthread</code> depending on the <code>USETHREAD_COLLISION</code> , <code>USETHREAD_LINKFORCES</code> and <code>USETHREAD_APPLYFORCES</code> parameters.
** Parses the <code>comet_params.ini</code> file to read parameters. All of the parameters are implemented as globals (should fix at some point)
** Creates the main <code>theactin</code> and <code>nuc_object</code> objects.
** Runs through the main iteration loop, calling <code>theactin.iterate()</code> and saving snapshots every so often.
* Actin class
** There is only one actin object, <code>theactin</code> , which constitutes the network, i.e.~contains the nodes and the functions that deal with them.
** The <code>iterate()</code> function does one iteration pass, calling:
***<code>nucleator_node_interactions()</code> displaces any nodes out of the nucleator object along a normal to the nucleator surface
***<code>nucleate()</code> adds new harbinger nodes to the surface of the nucleator
***<code>crosslinknewnodes()</code> crosslinks harbingers once they are ready
***<code>sortnodesbygridpoint()</code> 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.
***<code>collisiondetection()</code> detects whether nodes are within <code>NODE_REPULSIVE_RANGE</code> of one another and adds the repulsive force to <code>rep_force_vec[]</code> .
***<code>linkforces()</code> Calculates the forces between nodes due to links and puts into <code>link_force_vec[]</code> . 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)
***<code>applyforces()</code> updates the positions of all the nodes. Sums over the threads for <code>rep_force_vec[]</code> , <code>link_force_vec[]</code> and <code>repulsion_displacement_vec[]</code> .
***Numerous other functions for things like saving bmps, vrml etc.
**Nucleator class
*** There is only one nucleator object at the moment, <code>nuc_object</code> , which is closely linked to the actin object
*** The nucleator is either a sphere, a capsule (i.e.~a sphere with a cylindrical segment stuck in the middle) or ellipsoid
*** <code>addnodes()</code> adds harbingers to the surface of the nucleator. The probablility of addition of nodes is normalized by surface area and is symmetric if <code>ASYMMETRIC_NUCLEATION</code> is zero, or asymmetric if 1 or 2 (stepped or linear bias)
*** <code>definenucleatorgrid()</code> sets a list of gridpoints to check in case of nodes entering the nucleator. Called once at the beginning.
*** <code>iswithinnucleator()</code> returns true if the node is within the nucleator
*** <code>collision()</code> moves a node out of the nucleator along a normal vector
** Nodes class
*** Nodes exist only as members of the actin object
*** <code>nodegrid</code> 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.
*** The actin class contains a vector of nodes. Each node has an associated <code>nodenum</code> , <code>x</code> <code>y</code> and <code>z</code> position, <code>nextnode</code> and <code>prevnode</code> node pointers for the nodegrid linked list, <code>rep_force_vec[]</code> , <code>link_force_vec[]</code> and <code>repulsion_displacement_vec[]</code> as described above, the grid position of the node, <code>harbinger</code> and <code>polymer</code> flags and a <code>listoflinks</code> i.e. a vector of link object which attach this node to other nodes.
*** <code>polymerize()</code> Creates a node as a harbinger. Adds its pointer to the gridpoint linked list.
*** <code>depolymerize()</code> Removes a node, deletes all links and removes from grid.
*** <code>setgridcoords()</code> Calculates new grid co-ordinates based on x,y,z position
*** <code>addtogrid()</code> adds the node to the current gridpoint
*** <code>removefromgrid()</code> removes node from the grid
*** <code>updategrid()</code> checks to see if node has moved gridpoints, and updates grid is needs to
*** <code>removelink()</code> removes the specified node from the list of links
** Links class
*** Links exist only as members of the node objects
*** Each link has an associated <code>linkednodeptr</code> which points to the target node that the link is to and a <code>broken</code> flag which is read by <code>actin::linkforces()</code> and tells it to delete the link if it broke.
*** <code>orig_dist</code> and <code>orig_distsqr</code> store the original distance of the link
*** <code>breakcount</code> stores the number of consecutive iterations the link force has been above <code>LINK_BREAKAGE_FORCE</code> and is used to increase the probability of breakage
*** <code>getlinkforces()</code> returns the force acting on the link. Also sets the <code>broken</code> flag and increments <code>breakcount</code> if appropriate

3D Reconstructions of in vitro Unconstrained Shells

2009-04-17T01:22:13Z

Markdayel:

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.

[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]

Constrained Shell #1

[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]

Constrained Shell #2 (3-lobed split)

[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]

Constrained Shell #3

[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]

Constrained Shell #4

[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]

Constrained Shell #5

3D Reconstructions of in vitro Constrained Shells

2009-04-17T01:21:53Z

Markdayel:

See the [http://www.dayel.com/comet/SupplementaryMaterials/Dayel_Supplementary_Materials_(no_movies)_10_05_09.pdf pdf file version of the supplementary materials] for 3D interactive versions of these reconstructions.

[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-01.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS8_MM2-Rx6-01.mov.png]

Constrained Shell #1

[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-03.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS8_MM2-Rx6-03.mov.png]

Constrained Shell #2

[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS8_SquashedShell1.mov.png]

Constrained Shell #3

[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell2.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS8_SquashedShell2.mov.png]

Constrained Shell #4

Ellipsoid and Capsule symmetry breaking

2009-04-17T01:21:34Z

Markdayel: Created page with '[http://www.dayel.com/comet/supmat/movies/FigS7a_Ellipsoid_vtk_.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7a_Ellipsoid_vtk_.mov.png] Sideways symmetry breaking...'

[http://www.dayel.com/comet/supmat/movies/FigS7a_Ellipsoid_vtk_.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7a_Ellipsoid_vtk_.mov.png]

Sideways symmetry breaking of ellipsoid (3D)

[http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]

Sideways symmetry breaking of capsule (2D)

Circumferential and Radial measurements

2009-04-17T01:19:22Z

Markdayel:

[http://www.dayel.com/comet/supmat/movies/FigS4a_circ_measure_vtk_.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS4a_circ_measure_vtk_.mov.png]

Circumferential measurements during symmetry breaking

[http://www.dayel.com/comet/supmat/movies/FigS4b_radial_measure_vtk_.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS4b_radial_measure_vtk_.mov.png]

Radial measurements during symmetry breaking

[http://www.dayel.com/comet/supmat/movies/FigS6a_vtk_smooth_circ_trimmed.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS6a_vtk_smooth_circ_trimmed.mov.png]

Circumferential measurements during smooth motilty

[http://www.dayel.com/comet/supmat/movies/FigS6b_vtk_radial_trimmed.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS6b_vtk_radial_trimmed.mov.png]

Radial measurements during smooth motilty

Forces during Symmetry Breaking

2009-04-17T01:19:00Z

Markdayel:

[http://www.dayel.com/comet/supmat/movies/FigS5a_radial_report_force.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS5a_radial_report_force.mov.png]

Forces and link breaks during symmetry breaking

[http://www.dayel.com/comet/supmat/movies/FigS5bSmoothMotilityLink_breaks.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS5bSmoothMotilityLink_breaks.mov.png]

Link breaks during smooth motility

Symmetry Breaking and Motility

2009-04-17T01:18:43Z

Markdayel: Created page with 'Click on the thumbnails below to play example movies. ==Symmetry Breaking and Motility== [http://www.dayel.com/comet/supmat/movies/FigS1_Data09_roi_frame_.mov http://www.dayel...'

Using Git

2009-04-16T21:48:32Z

Markdayel:

[http://git-scm.com/documentation The main git website] is a good place to start learning how to use git, and Github also has a [http://github.com/guides/home nice collection of guides]. I also found [http://zrusin.blogspot.com/2007/09/git-cheat-sheet.html this cheat sheet] to be a particularly good one-page summary of useful git commands.

To have changes you've made merged into the main repository, prepare them as a patch (<code>git format-patch</code>) then submit them by email to markdayel@gmail.com

==Tips==

If using windows, be careful with line endings. Windows tends to change LF into CRLF. They can be changed back using the <code>dos2unix</code> command in cygwin. Also, make sure the permissions are not messed up (they should be 664)

Display settings

2009-04-15T19:37:00Z

Markdayel:

These settings in the <code>cometparams.ini</code> affect the way data is displayed. There are two display outputs, bitmaps (2D) and VTK (3D). Bitmaps are automatically created during the initial calculation run, but usually start only after the symmetry breaking direction is determined (since this determines the observer position). Bitmaps can also be produced after the initial calculation run is complete with <code>comet post</code>, and VTK output is produced only after the initial calculation run with <code>comet view</code> or <code>comet vtk</code>:

===Producing Bitmaps===
You can call the bitmap processing with
comet post 0:0

where <code>0:0</code> processes all frames, or a range of frames if specified.

===Producing VTK output===
You can call the VTK processing either interactively with
comet view 300:300
Note only a single frame can be specified for the interactive view.

or in batch mode with
comet vtk 0:0

VTK can also produce vrml files to import the 3D models into other software (e.g. Acrobat 3D) by calling with one frame only
comet vtk 300:300

==Bitmap display settings==

===Basic settings===
X_BMP true # whether to write a bitmap for x axis (default for symmetry breaking plane)
Y_BMP true # whether to write a bitmap for y axis
Z_BMP true # whether to write a bitmap for z axis
WRITE_BMPS_PRE_SYMBREAK false # whether to write images before symmetry breaks. (mainly useful to see what is going on for conditions when symmetry doesn't break!)
BMP_WIDTH 800 # width of bitmap in pixels
BMP_HEIGHT 800 # height of bitmap in pixels
VIEW_HEIGHT 30 # bitmap scale (height of image in um)
BMP_OUTPUT_FILETYPE jpeg # graphic type for bitmap save (must be recognized ImageMagick type)
BMP_COMPRESSION 100 # bitmap quality setting (ImageMagick)
DRAW_CAGE false # whether to draw the nucleator on the bitmaps (as a 2D projection of cage of points)
CAGE_ON_SIDE false # whether to draw the cage on the side of the image
GAUSSFWHM 0.70 # width of the gaussian used to blur the node points to make the pseudo microscope image
INIT_R_GAIN 80 # initial gain for red bitmap channel (rescaled at symmetry breaking)
INIT_G_GAIN 30 # initial gain for green bitmap channel (rescaled at symmetry breaking)
INIT_B_GAIN 200 # initial gain for blue bitmap channel (rescaled at symmetry breaking)
BMP_AA_FACTOR 1 # antialiasing factor (produces bigger image and resizes)

===Plotting forces on bead===
SEGMENT_BINS false # whether to plot radial segments
RADIAL_SEGMENTS 12 # number of radial segments
PLOTFORCES false # whether to plot forces
PLOTFORCES_INCLUDEIMPACTS true # whether to include surface impacts in force display vectors
PLOTFORCES_INCLUDELINKFORCES true # whether to include link tension in force display vectors
FORCE_BAR_SCALE 10 # scale factor for force plotting

===Plotting speckle in shell and tail===
SPECKLE true # whether to color actin with speckles
SPECKLEGRID true # specles as grid?
SPECKLEGRIDPERIOD 1000 # grid period (time)
SPECKLEGRIDTIMEWIDTH 0 # grid stripe pulse width (time)
SPECKLEGRIDSTRIPEWIDTH 0.3 # grid bar width (distance)
SPECKLE_FACTOR 0.3 # density of speckles if no grid

==VTK settings (3D)==

===Basic Settings===
VTK_WIDTH 800 # VTK image width
VTK_HEIGHT 800 # VTK image height
VIS_PROJECTION z # position of camera: x,y,z or rip ; x,y,z correspond to the bitmap images, rip puts the camera ahead of and slightly above bead to view the rip
VTK_AA_FACTOR 2 # antialias factor
COLOUR_GAMMA 1.6 # color scale gamma

===What to display===
VIS_NUCLEATOR true # whether to display nucleator
VTK_NUC_WIREFRAME true # whether to display wireframe nucleator in addition (helps show rotation)
VIS_NODES false # whether to display individual nodes as balls
VIS_LINKS false # whether to display links as lines
VIS_SHADELINKS true # whether to color links by strain
VIS_ISONODES false # whether to display isosurfaces of node density
VIS_NUCOPACITY 1.0 # opacity of nucleator
VIS_TRACKS true # whether to display node tracks
VIS_USENUCTEXMAP false # whether to put texture on nucleator

===3D view settings===
VTK_MOVE_WITH_BEAD false # whether to keep bead in center of screen
VIS_LINETHICKNESS 1.2 # line thickness for links
VIS_PSCALE 55 # scaling factor
VTK_VIEWANGLE 50 # camera zoom
VIS_PARALLELPROJECTION true # turns off perspective
VIS_CAMERADISTMULT 5 # how far to put camera (multiple of radius)
VIS_NORMALISEFRAMES false # whether to normalize intensity of node density isosurface

==Misc==
VIS_VTK_HIGHQUAL false # VTK antialiasing
VIS_FILEPREFIX vtk # output file prefix

==Settings that apply to both bitmaps and VTK==

SYM_BREAK_TO_RIGHT true # rotate camera to orient symmetry break direction to the right (else just rotate to be in the y-z plane)
FOCALDEPTH 2.5 # restrict plotting of nodes etc. to slab twice this distance thick centered on bead
BMP_FIX_BEAD_MOVEMENT false # move camera with bead so bead stays in center of screen
BMP_FIX_BEAD_ROTATION false # rotate the camera with the bead

Model Robustness

2009-04-14T17:04:17Z

Markdayel:

==Robustness test: LINK_BREAKAGE_FORCE==
[[file:08-10-07_1138_imagearray.jpg|600px]]

==Robustness test: LINK_FORCE==
[[file:08-10-07_1139_imagearray.jpg|600px]]

==Robustness test: NODE_REPLUSIVE_MAG==
[[file:08-10-07_1140_imagearray.jpg|600px]]

==Robustness test: NUC_LINK_FORCE==
[[file:08-10-07_1141_imagearray.jpg|600px]]

==Robustness test: NUC_LINK_BREAKAGE_DIST==
[[file:08-10-07_1142_imagearray.jpg|600px]]

==Robustness test: NUCLEATOR_INERTIA==
[[file:08-10-07_1143_imagearray.jpg|600px]]

==Robustness test: P_NUC==
[[file:08-10-07_1144_imagearray.jpg|600px]]

==Robustness test: RADIUS==
[[file:08-10-07_1145_imagearray.jpg|600px]]

==Robustness test: P_XLINK==
[[file:08-10-07_1146_imagearray.jpg|600px]]

==Robustness test: FORCE_SCALE_FACT==
[[file:08-10-07_1148_imagearray.jpg|600px]]

Implementation

2009-04-13T20:07:18Z

Markdayel: moved Implementation to Detailed Program Flow

The flowchart below shows a detailed view of the how the program works.

[[file:Overview_complex.png|800px|Figure 2: Comet program flow (detailed)]]

How comet works

2009-04-13T18:48:18Z

Markdayel: moved How comet works to Program Flow

The core of the program is essentially the following iteration loop. Nodes are added, forces calculated, and node positions updated as shown:

[[file:Overview_simple.png|800px|Figure 2: Comet program flow (simple)]]

To Do

2009-04-13T18:25:10Z

Markdayel:

*XML import/export format.
**At the moment, if we change the load/save code to add a variable etc, the save file format changes so we can't load old datasets. Current workaround is to check the date of the old data and temporarily revert to that version of the code in the git repository. A proper fix would be to have a separate XML save format that also contains the names of the variables, so that future changes don't break the load/save.
*Xgrid
**Given the importance of running the program on a cluster, it would be nice to use [http://www.apple.com/server/macosx/technology/xgrid.html Apple's Xgrid]

Known Issues

2009-04-13T18:19:44Z

Markdayel:

* Resuming from a saved data point wipes the old velocities.txt file

Recommendations for running comet

2009-04-13T17:56:14Z

Markdayel:

We highly recommend running 'comet' on a cluster of machines, rather than just one. The program takes some time to run (an hour or two for early events like symmetry breaking; overnight if you want to look at the later motility, pulsatile motion etc.) Running the program concurrently on at least 5 machines (I used 9) lets you efficiently test the effect of changing one parameter through a range of values. You can set it going then come back the following day and have the whole thing laid out for you. I've found this very useful, and have included a set of scripts to automate the process, including automatically generating the montage of images seen in the robustness section so you can quickly scan the effect of varying the parameter.

I recommend putting a default '''cometparams.ini''' into a main directory for the data e.g. '''~/runs'''. In that directory run the '''varyset''' script (included with the source):
varyset <parameter> <startval> <endval> <number of steps>
This will create a subdirectory within '''runs''' that contains subdirectories numbered 1,2,3,etc. each containing a version of the '''cometparams.ini''' file with the <parameter> value varying in linear steps between <startval> and <endval>. It will also add information to run the individual comet jobs into ~/joblist.

If you have access to a cluster with a working job control system, you might want to use that. I had trouble with the job control system on the cluster I was using, and ended up writing my own:

On the head node, I have the
startnewjobs
script running as a cron job every 15 minutes. This checks to see if the worker nodes are idle (5 min load average below a certain threshold) and starts the next job if they are.

The script jobstat will list the progress, e.g.
mark@biostar01:/cluster/comet$ jobstat

Machine 1mld 5mld ID R Frame
b1 3.69 3.15 05-14-09_0017 1 |T 16|S 109/700 *
b2 3.39 2.93 05-14-09_0017 8 |T 15|S 116/700 *
b3 3.38 2.87 05-14-09_0017 4 |T 15|S 112/700 *
b4 3.55 3.07 05-14-09_0017 6 |T 15|S 114/700 *

0 nodes free
4 jobs waiting

If you don't have access to a cluster, there is a single computer version of startnewjobs
startjobsloop
which will check ~/joblist for new jobs and run them sequentially.

The script
makematrix
pulls together an image matrix (as seen in the robustness section) to summarize the effect of varying the parameter. The directory name, time, computer and main section of the competparams.ini file are converted into an image and included on the left hand side of the summary, to keep track of the details of the run.

Supmat

2009-04-13T04:20:31Z

Markdayel:

Click on the thumbnails below to play example movies.

==Symmetry Breaking and Motility==

[http://www.dayel.com/comet/supmat/movies/FigS1_Data09_roi_frame_.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS1_Data09_roi_frame_.mov.png]

Experimental symmetry breaking run

[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]

Example simulation run 2D (from Figure 1 in paper)

[http://www.dayel.com/comet/supmat/movies/FigS3_Fig1vtkx1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS3_Fig1vtkx1.mov.png]

3D links view of above example

==Forces during Symmetry Breaking==

[http://www.dayel.com/comet/supmat/movies/FigS5a_radial_report_force.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS5a_radial_report_force.mov.png]

Forces and link breaks during symmetry breaking

[http://www.dayel.com/comet/supmat/movies/FigS5bSmoothMotilityLink_breaks.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS5bSmoothMotilityLink_breaks.mov.png]

Link breaks during smooth motility

==Circumferential and Radial measurements==

[http://www.dayel.com/comet/supmat/movies/FigS4a_circ_measure_vtk_.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS4a_circ_measure_vtk_.mov.png]

Circumferential measurements during symmetry breaking

[http://www.dayel.com/comet/supmat/movies/FigS4b_radial_measure_vtk_.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS4b_radial_measure_vtk_.mov.png]

Radial measurements during symmetry breaking

[http://www.dayel.com/comet/supmat/movies/FigS6a_vtk_smooth_circ_trimmed.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS6a_vtk_smooth_circ_trimmed.mov.png]

Circumferential measurements during smooth motilty

[http://www.dayel.com/comet/supmat/movies/FigS6b_vtk_radial_trimmed.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS6b_vtk_radial_trimmed.mov.png]

Radial measurements during smooth motilty

==Ellipsoid and Capsule symmetry breaking==

[http://www.dayel.com/comet/supmat/movies/FigS7a_Ellipsoid_vtk_.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7a_Ellipsoid_vtk_.mov.png]

Sideways symmetry breaking of ellipsoid (3D)

[http://www.dayel.com/comet/supmat/movies/FigS7b_Symmetric_Capsule.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS7b_Symmetric_Capsule.mov.png]

Sideways symmetry breaking of capsule (2D)

==3D Reconstructions of ''in vitro'' Constrained Shells==

[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-01.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS8_MM2-Rx6-01.mov.png]

Constrained Shell #1

[http://www.dayel.com/comet/supmat/movies/FigS8_MM2-Rx6-03.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS8_MM2-Rx6-03.mov.png]

Constrained Shell #2

[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell1.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS8_SquashedShell1.mov.png]

Constrained Shell #3

[http://www.dayel.com/comet/supmat/movies/FigS8_SquashedShell2.mov http://www.dayel.com/comet/supmat/movies/thumbnails/FigS8_SquashedShell2.mov.png]

Constrained Shell #4

==3D Reconstructions of ''in vitro'' Unconstrained Shells==

[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]

Constrained Shell #1

[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]

Constrained Shell #2 (3-lobed split)

[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]

Constrained Shell #3

[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]

Constrained Shell #4

[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]

Constrained Shell #5

Node Tracks

2009-04-11T02:02:23Z

Markdayel:

==Following the network motion==

You can use node tracks to see where the network goes. Turn on network tracks with the BMP_TRACKS setting in cometparams.ini. e.g.
BMP_TRACKS true # turns on node tracking
TRACK_MIN_RANGE 300.0 # select nodes created between this time...
TRACK_MAX_RANGE 305.0 # ...and this time (in frames)
TRACKFRAMESTEP 5 # number of frames between each point in the track when plotted
MAX_NODES_TO_TRACK 30 # how many nodes to track

Set BMP_TRACKS to true, and set TRACK_MIN_RANGE and TRACK_MAX_RANGE to bracket the time range for the creation of nodes you want tracked. The program will look for a set of MAX_NODES_TO_TRACK nodes within those created in this time bracket. If you want 2D tracks on the bitmaps, you probably also want to set BMP_FIX_BEAD_MOVEMENT to true so that the bitmap tracks aren't upset by the translation of the image.

==Measuring stretching and compression==

In addition, node tracks can be used to measure stretching of the shell or tail:
TRACKS_LENGTHS true # if false then tracks node movement, if true then tracks pairs and measures the distances between them
TRACK_TARGET_DIST 2.5 # tells code to select node pairs aiming for about this distance between them
SECOND_SHELL false # if SECOND_SHELL is false, tracks circumferential lengths in one shell
# if SECOND_SHELL is true, tracks radial lengths between two shells
TRACK_MIN_RANGE2 10 # select nodes created between this time...
TRACK_MAX_RANGE2 30 # ...and this time for the second shell

Node tracks are added separately after the initial calculation run, e.g. running
comet post 300:500
would track nodes up to frame 500. This creates new node tracks in a file <code>nodetracks.txt</code>, but ''only if this file doesn't already exist'' otherwise it just loads the existing tracks, so make sure to delete or rename this file if you want to calculate new tracks. The node range given to the <code>comet post</code> command must include TRACK_MIN_RANGE, TRACK_MAX_RANGE (and TRACK_MIN_RANGE2 and TRACK_MAX_RANGE2 if they are being used). Note: the program will automatically try to select nodes distributed evenly across the bead, but needs enough nodes within the frame range given.

==Processing the data==

Once this is done the tracks will be rendered onto the bitmaps, and can be viewed in 3d by setting
VIS_TRACKS true
then running
comet view 400:400

Measures will be shown as lines, with associated numbers. Depending on the purpose, you may want to exclude certain lines (e.g. if measuring the expansion and contraction of the shell, you probably want to remove any pairs that span the crack. To remove particular measures, find the numbers using the 3D view, then set the track numbers to remove in the 'comet_remove_nodetracks' script. This will edit the nodetracks.txt and nodedistances.txt files and remove those measurements. Note the numbering changes when you do this, so re-check with comet view nnn:nnn and re-run with the new numbers if you need to remove more. Running the script 'comet_process_distances' processes these into comma delimited (csv) files for raw, normalized and averaged summaries which can be loaded into Gnuplot, Excel etc. to easily plot the distances as they change over time.

==Other Parameters==

If you want to restrict the choice of nodes to the symmetry breaking plane, set

NODE_TRACK_SELECT_Z_RANGE 1.5

which restricts the nodes selected to +/- this distance from the bead center in the z direction

TRACK_TARGET_DIST 2.5 # aim for this initial length when picking node pairs to track