Dissemination of libRoadRunner and CompuCell3D

NIH RePORTER · NIH · U24 · $306,959 · view on reporter.nih.gov ↗

Abstract

Project Summary/Abstract 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.

Key facts

NIH application ID
10020978
Project number
5U24EB028887-02
Recipient
UNIVERSITY OF WASHINGTON
Principal Investigator
James Alexander Glazier
Activity code
U24
Funding institute
NIH
Fiscal year
2020
Award amount
$306,959
Award type
5
Project period
2019-09-30 → 2024-06-30