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Dissemination of libRoadRunner and CompuCell3D

libRoadRunner 和 CompuCell3D 的传播

基本信息

批准号：
10706425
负责人：
James Alexander Glazier
金额：
$ 29.91万
依托单位：
UNIVERSITY OF WASHINGTON
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-30 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10706425
关键词：
3-Dimensional Address Adoption Architecture Biological Cells Collaborations Communities Computer Models Computer software Computers Coupling Data Development Differential Equation Disease model Ecosystem Educational process of instructing Educational workshop Elements Ensure Environment Event Familiarity Future Genes Hormones Infrastructure Institution Internet Joints Learning Libraries Metabolic Modeling Nutrient Organ Output Performance Population Process Pythons Research Personnel Running Signal Transduction Software Design Software Tools Specific qualifier value Tellurium Testing Tissue Model Tissues Training Uncertainty Visual Whole Organism Work base computational platform computer code computing resources cost data visualization design experience flexibility improved interoperability large scale simulation migration model building model design model development multi-scale modeling network models online tutorial open source physiologically based pharmacokinetics predictive modeling simulation simulation environment software development tool two-dimensional virtual web services

项目摘要

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.

项目总结/文摘