Multiscale Simulation with CompuCell3D and BionetSolver

SOSlibPy, mentioned in previous posts (here, here and here), has now been replaced by BionetSolver. If you want to run multicellular, multiscale simulations with CompuCell3D, you may download a windows installer for BionetSolver. BionetSolver works with CC3D 3.5.0 or newer. Please download CC3D here. First install CC3D 3.5.0 and then run the installer for BionetSolver. When you do, it should default to the installation directory for CC3D. Just double check to make sure the default installation path for BionetSolver is the same as the root CC3D directory on your machine. Once you’ve installed it, there are demo BionetSolver simulations in the ‘\Demos\BionetSolverExamples’ folder. In the same folder, you will also find a quick start document for writing BionetSolver/CC3D simulations. The following is a series of slides that provide an introduction to using BionetSolver with CC3D. It takes you through a simple demo simulation called ‘CellSort_BionetsolverDemo’. As a final note, if you’re interested in using BionetSolver on a platform other than Windows, let me know. I can help you get it built for your machine.

Just some quick notes before you go through the slides below:

1) SBML stands for Systems Biology Markup Language, an XML-based model-description language for reaction kinetic models. BionetSolver can load SBML models which are essentially translated to a system of ordinary differential equations (ODEs) and solved as such. Underneath BionetSolver is SOSlib (SBML ODE Solver library) which, in turn, uses Sundials CVODE to numerically solve systems of ODEs. These can be ‘attached’ to cells in CC3D to represent internal (subcellular) biochemical networks.

2) Note that there is nothing particularly ‘special’ or different about BionetSolver steppables (refer to CC3D documentation to learn about steppables – these are written in Python and they allow one to specify complex biological processes or mechanisms in CC3D). The ‘skeleton’ of the steppable is just like any other CC3D steppable. Importing the BionetSolver API and initializing the Bionetwork Manager object in the steppable (see 3rd slide below) makes the simple BionetSolver API (7 core functions) available within the steppable.

Okay, now you can proceed with the slides…  🙂

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~ by bionetsolver on May 4, 2011.

4 Responses to “Multiscale Simulation with CompuCell3D and BionetSolver”

  1. Hi, I am using CC3D,too. But it got some bug. Could you please help me? How can I contact you?

  2. Hi Jinlong – Thanks for your interest. I just added my email address to my about page. Just look at my pages in my sidebar. There should be an about page listed there (now). Here’s the link to it: https://ryanroper.wordpress.com/about/. Feel free to email me with any questions about CC3D or BionetSolver. Also, you can join the CC3D mailing list. Click this link to find directions for subscribing to the mailing list. There, you can also ask CC3D questions.

  3. Hi Ryan,

    Excellent work!!! It is exciting to see the new version being released, and I will leave some feedback (as well as encountered questions of course) after rebuild my previous work.

    Thanks,

    Ryan (Form UCC, Ireland)

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