TIMOTHY

TISSUE MODELLING FRAMEWORK

• About Timothy
• Downloads
• Publications
• Examples
• Acknowledgements
• Contact Us

License

Timothy is licensed under the GNU General Public License, version 2 or later. That means you are free to download, reuse, modify, and distribute any Timothy's files under the terms of either the GPL version 2 or version 3, and to run Timothy in combination with any code with any license that is compatible with either versions 2 or 3.

If you use Timothy in your scientific work, please cite as:

• "Large Scale Parallel Simulations of 3-D Cell Colony Dynamics" , M.Cytowski, Z.Szymanska, IEEE Computing in Science and Engineering, vo l.16, no.5, pp.86,95, Sept.-Oct. 2014, doi: 10.1109/MCSE.2014.2 [pdf]
• "Large-Scale Parallel Simulations of 3D Cell Colony Dynamics: The Cellular Environment", M.Cytowski, Z.Szymanska, IEEE Computing in Science and Engineering , vol.17, no.5, pp.44-48, Sept.-Oct. 2015, doi: 10.1109/MCSE.2015.66

Downloads

Latest version of Timothy can be downloaded here:
timothy-0.9.tgz

Octree benchmark can be downloaded here:
octree-walk.tar.gz

Dependencies

There are few prerequisites needed for the successful installation of Timothy:

• C compiler supporting OpenMP (tested compilers: GNU gcc, IBM xlc),
• MPI library (tested implementations: OpenMPI, IBM POE for Power7 AIX, IBM MPI library for Blue Gene/Q),
• Zoltan v.3.8 library (available at http://www.cs.sandia.gov/zoltan/),
• Hypre v.2.9.0b library (available at http://acts.nersc.gov/hypre/),
• SPRNG v.2.0 library (available at http://www.sprng.org/).

Documentation

Timothy source code was documented with Doxygen.
Click here to browse the documentation.