Dissemination of libRoadRunner and CompuCell3D

libRoadRunner 和 CompuCell3D 的传播

基本信息

批准号：
10259719
负责人：
James Alexander Glazier
金额：
$ 30.48万
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/10259719
关键词：
3-Dimensional Address Adoption Architecture Biological Cells Collaborations Communities Computer Models Computer software Computers Coupling Data Development Differential Equation Diffuse 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 Savings 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 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.

项目概要/摘要该提案将进行虚拟组织建模，其范围涵盖亚细胞生物通过细胞到组织以及整个有机体和群体的网络，更容易访问和利用通过改进和集成两个开源计算对生物医学研究人员有用建模环境、亚细胞碲和多细胞 CompuCell3D (CC3D)。两个都这些工具旨在通过将生物学驱动的模型规范与运行模拟的计算机代码。采用虚拟组织的障碍建模包括：1）缺乏熟悉度，2）需要付出大量努力来学习设计、构建、执行和应用模型，以及 3）如果软件工具消失或者如果用户需要在平台之间迁移。为了解决这些问题，我们将：1）应用设计基于记录和测试的可重用软件组件的架构，以强化和集成 Tellurium 和 CompuCell3D，通过简化开放式流程来提高长期可持续性源码开发。 2) 简化模型规范、执行和的学习过程进行分析以减少采用障碍； 3) 简化和协调安装和使用桌面、HPC 和 Web（云/集群）安装，以及 4) 传播升级的工具和通过研讨会、支持基础设施和在线教程扩大用户和开发人员基础。