SimCells: multicellular simulator

I am an associate professor, teaching computer science and biocomputing. You're my student : please go to Moodle Sciences - UBO.

My researches focus on simulating multicellular systems. Read some of my papers or explore my youtube channel

Checkout the software I'm implied in by clicking the upper tabs, and go explore the living at cellular level.

Centyllion is an online multiagents simulator.

You can create numerous complex systems playing on a grid by adding agents and their behaviors.

Take a look at the hundred of examples made by teachers and students (then create your own simulations) :

• stalagmit formation,
• blood coagulation,
• angiogenesis,
• traffic jam,
• water cycle,
• Read the tutorial and try to make the exercice

Matrix Studio is an integrated development environment for OpenCL (GPU + CPU multicore programming).

You can directly code in OpenCL, without the difficulty of programming the host.

Here are the different parts of the software :

• kernel editing,
• matrices definition and visualisation (1, 2 or 3D),
• graphical task diagram,
• multiple libraries writing.

Some usefull resources :

• Code your first OpenCL program in 2 minutes
• Try the different tutorials and exercices
• Want to dive inside? Read the paper explaining how it works.

Net-BioDyn is a desktop application for creating multicellular systems.

An agent is a cell or a molecule, a membrane or a filament, etc.

For example, you can add behaviours to a cell-agent imitating :

• migration,
• division,
• death,
• differentiation, etc.

Some usefull resources :

• Youtube channel with examples (in french)
• How teachers use NetBioDyn? Simply search NetBioDyn with Google
• Try the different exercices made by teachers
• Examples from the Institut français de l'éducation (Ifé)
• Want to dive inside? Read the paper explaining how it works.

Download SimCells, a desktop application for simulating multicellular systems.

An agent represents a cell with :

• a deformable membrane,
• a membrane adhesion,
• complex behaviours made using a visual scripting language,

Simulator possibilities :

• display 2D or 3D environments,
• add upto millions of cells,
• show or export data for excel treatments,
• import 3D images to contextualise your simulations, etc.

Some usefull resources :

• Youtube videos.
• UBO Tube videos
• Read the booklet explaining the basis of SimCells.
• Want to go further? Read the paper about SimCells.

NB : source code not available.

Go to GitHub to see some of my projects and their source code.

Go to CodePen.io to see more of my projects and their source code.

Try my Game Of Life made in shaders.