Simulating the Cytoskeleton Using Cytosim

Cytosim is an accessible simulation software – developed by EMBL scientists – to simulate realistic individual elements of the cytoskeletal network.

Cytosim can simulate systems at different time and length scales, from single units of cytoskeletal elements, such as molecular motors, up to a few cells.

In this course we will show you how you can use Cytosim tools for any cytoskeletal system and how to run your simulations.

Pre-requisites

We recommend that you have some basic scripting skills for this course to be able to analyse your data generated from Cytosim. 

Learning objectives

• Describe how Cytosim can help you simulate a realistic cytoskeletal system
• Evaluate the basic building blocks that you can use to create your cytoskeletal system
• Run your own simulations and generate valuable data

Module 1: Introduction to Cytosim

Julio Belmonte from the research group of Francois Nedelec explains what Cytosim is, what it can be used for and how you can use it to simulate cytoskeletal networks.

Get Started (Duration 10 mins)

This module is best viewed using Firefox or Internet Explorer on desktops or Safari or Chrome on tablets.

Module 2: Installing and Running Cytosim

We’ll take you through the steps of how to install Cytosim, run your first simulation and show you how to navigate the documentation.

Get Started (Duration: 10 mins)

This module is best viewed using Firefox or Internet Explorer on desktops or Safari or Chrome on tablets.

Module 3: Creating a Configuration File

This module will introduce you to the most common objects, parameters and executables in Cytosim. We will also teach you how to write your first configuration files.  

Get Started (Duration: 20 mins)

This module is best viewed using Firefox or Internet Explorer on desktops or Safari or Chrome on tablets.

Cytosim Help Sheet (PDF)

Module 4 : Cytosim Case Study and Tips

Aastha Mathur from the research group of Francois Nedelec discusses how she used Cytosim to assess the role of actin and microtubules in blood clotting, whilst also giving some handy tips for using Cytosim.

Duration: 5 mins

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