Maciek Swat - Using Python to democratize Virtual Tissues modeling

Virtual Tissues is a term that describes a broad category of biophysics-based mechanistic models of living tissues/organs. The primary goal of those models is to study and understand how basic cellular behaviors at a single cell level give rise to biological development, disease initiation, progression etc… The big promise of Virtual Tissues is to allow researchers to run virtual experiments to simulate tissue response to various chemicals, understand, optimize and personalize treatment modalities, search for new therapeutics opportunities etc.
Virtual Tissue models have been developed for several decades but we learned that by adopting and embracing Python we could deliver those models (and the software platforms that implement them) an order of magnitude faster.
In this talk I will introduce basic techniques behind Virtual Tissues, present a few interesting applications of Virtual Tissues (model of Polycystic Kidney Disease and vascular tumor growth) and address how using Python we were able to significantly increase access to Virtual Tissue models. I will discuss challenges and opportunities that Virtual Tissues offer and (time-permitting) I will demo how to build a simple Virtual Tissue model using CompuCell3D (www.compucell3d.org) Virtual Tissue Platform.


Bio: Maciek Swat spent 15 years in academia (Indiana University, University of Pennsylvania) working on a broad range of problems ranging from elementary particle physics, to biophysical tissue modelling, to closed-loop cognitive neuromodulation. Currently he is working as a Staff Scientist at Inscripta - a Digital Genome Engineering company developing mathematical models and bioinformatics algorithms/solutions.