Difference between revisions of "CometWiki"

Introduction

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

Cells in our body use 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'.

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.

Code Status

• Source Repository
• Source Files
• Download Binaries

• Known Issues
• To Do

• Using Git

Supplementary Materials

• Supplementary Materials

Essential Information

How the program works

• Description of the Model
• Overview of Program Flow
• Detailed Program Flow
• Implementation in C++

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

In Depth Information

Making Measurments

• Tracking network movement and making measurements
• Radial Force Movies

Simulator Output

Example Results

• 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