Paul Macklin's Math Cancer Lab Website

MathCancer on Twitter

Recent news

Friday, Feb 20th, 2015
Banner and Logo Contest : MultiCellDS Project: As the MultiCellDS (multicellular data standards) project continues to ramp up, we could use some artistic skill.Right now, we don't have a banner (aside from a ... [read more]

Thursday, Dec 11th, 2014
2015 Speaking Schedule: Here is my current speaking schedule for 2015. Please join me if you can! Feb. 13, 2015: Seminar at the Institute for Scientific Computing Research, ... [read more]

Welcome to Dr. Macklin's Lab!

Paul Macklin is a mathematician and an assistant professor at the Center for Applied Molecular Medicine at the University of Southern California. Our lab works to develop and validate sophisticated models of cancer in individual patients. We work in tightly-integrated teams of clinicians, modelers, and biologists to develop computational tools that will one day help improve clinical planning.

Macklin is leading development of standardizations for computational and experimental model data, which will help computational modelers to share, extend, refine, and recombine cancer models into sophisticated cancer simulators. A novel component of this work is the digital cell line: an extensible, standardized representation of a cell line, its physical and behavioral characteristics (phenotype), and necessary microenvironmental conditions. A library of digital cell lines will allow modelers and experimentalists to more easily share insights and measurements on cancer and other cells, and incorporate these into simulations.

Macklin is also leading development of two open source 3-D simulation packages: BioFVM (finite volume method for biological problems) simulates diffusive transport of dozens of substrates in large 3-D tissues. PhysiCell (physics-based cell simulator) simulates multicellular systems of 5×106 or more cells in 3-D tissues. Both simulators make heavy use of vectorization and OpenMP for parallelization. They can efficiently simulate millions of mechanics-based cells in 3-D tissues with 5-10 diffusing substrates using quad-core desktop workstations, and more with single supercomputer compute nodes.