Dissemination of libRoadRunner and CompuCell3D

libRoadRunner 和 CompuCell3D 的传播

• 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
• 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

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/摘要 该建议将使虚拟组织建模，它跨越从亚细胞生物学尺度 网络通过细胞到组织和整个生物体和人口，更容易获得， 通过改进和整合两个开源计算， 建模环境、亚细胞碲和多细胞CompuCell 3D（CC 3D）。两 工具旨在通过将生物动机的模型规范与 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，2）学习设计，构建， 执行和应用模型，3）如果软件工具消失或 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 基于文档化和测试的可重用软件组件的体系结构， 集成Tellurium和CompuCell 3D，通过简化开放式 源开发。2)简化模型规范、执行和 分析，以减少采用障碍; 3）简化和协调跨 桌面、HPC和Web（云/群集）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。