Difference between revisions of "CometWiki"

This site describes the set up and usage of `comet', an actin-based bead motility simulator.

Actin is a polymer built by cells that allows them to move. Actin-based bead motility is an in vitro model system used to study how our cells produce force and move, carried out by coating a bead with proteins that tell the cell to polymerize actin, and putting the bead a solution that mimics the material inside cells. This causes an actin network to build around the bead. Surprisingly even when the bead is spherically symmetric, rather than just buiding a symmetric shell that gets bigger and bigger, it moves off in 'comet tail' of actin. This bead motility simulater aims to help us understand how this process works.

Simulator Output

Examples

• Symmetry Breaking and Motility
• Forces during Symmetry Breaking
• Circumferential and Radial measurements
• Ellipsoid and Capsule symmetry breaking

Model Robustness

• The effect of changing the main parameters

In Vitro

• 3D Reconstructions of in vitro Constrained Shells
• 3D Reconstructions of in vitro Unconstrained Shells

Essential Information

Installing the program

comet runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).

• Instructions for downloading and installing comet

Running the program

The program is called from the command line. The command line parameters tell the program what to do (calculate a new run, re-process existing data, interactive 3D view etc.). A cometparams.ini file in the working directory tells the program detailed information about the model parameters to use for calculation and display.

• Command line parameters for the comet program
• Model settings in the cometparams.ini file
• Display settings in the cometparams.ini file
• Running comet on a cluster

How the program works

• Overview of How the comet program works
• Implementation

In Depth

• Tracking network movement and making measurements

Code Status

• Source Repository
• Source Files
• Download Binaries

• Known Issues
• To Do

• Using Git