The Smoldyn software simulates the reactions and diffusion dynamics of molecules in cellular systems. It simulates each molecule of interest individually to accurately capture natural stochasticity and to yield spatial resolution on the order of nanometers. Smoldyn is efficient enough to conveniently simulate hundreds of thousands of molecules. Simulated molecules diffuse, react, and interact with membranes much as they would in a real biological system. Smoldyn is reasonably widely used, such as for simulating cell signaling systems, the implications of macromolecular crowding, and the diffusive dynamics of transcription factors. Smoldyn is easy to use and easy to install. Please see http://www.smoldyn.org for more information. In this course, I will present and demonstrate the software, and then help students develop their own simulations. Students are encouraged to bring their own project ideas.
The course does not require any previous programming experience. We will need to bring your personal machine and install the software from the following website: smoldyn.org Please do not hesitate in contacting Karin Sasaki if you require assistance.
The course is free for all members of EMBL.
Tutors: Dr. Steve Andrews (Fred Hutchinson Cancer Research Center) and Dr. Karin Sasaki (EMBL-CBM)