This proposal will make Virtual Tissue modeling, which spans scales from subcellular biological networks through cells to tissues and whole organisms and populations, more accessible and useful to biomedical researchers by improving and integrating two open-source computational modeling environments, subcellular Tellurium, and multicellular CompuCell3D (CC3D). Both tools aim to simplify model design by separating biologically-motivated model specification from the computer code which runs the simulation. Impediments to adoption of Virtual Tissue modeling include: 1) lack of familiarity, 2) substantial effort required to learn to design, build, execute and apply models and 3) concern over sustainability if software tools disappear or if users need to migrate between platforms. To address these concerns, we will: 1) Apply a design architecture based on documented and tested reusable software components to harden and integrate Tellurium and CompuCell3D, improving long term sustainability by simplifying open- source development. 2) Streamline the learning process for model specification, execution, and analysis to reduce barriers to adoption; 3) Simplify and harmonize installation and use across desktop, HPC and web (cloud/cluster) installations, and 4) Disseminate upgraded tools and expand the user and developer base via workshops, support infrastructure and online tutorials.
The proposed work will allow biomedical researchers to more easily create predictive models of disease in cells, tissues, and organs. Two computational platforms, CompuCell3D and Tellurium will be combined to form a seamless modeling application. The design of the software will be modular to ensure that components within the combined application can be easily reused by other software developers thus saving considerable costs in future development.
