Dissemination of libRoadRunner and CompuCell3D

项目摘要/摘要 这一提议将使虚拟组织建模从亚细胞生物学的尺度 从细胞到组织、整个生物体和种群的网络，更容易获得和 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)。两者都有 工具旨在通过将出于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)不熟悉；2)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如果 用户需要在不同平台之间迁移。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体系结构，以强化和 集成Tellurium和CompuCell3D，通过简化开放的 源代码开发。2)简化模型规范、执行和管理的学习过程 分析以减少采用障碍；3)简化和协调安装和使用 桌面、HPC和网络(云/群集)安装，以及4)分发升级的工具和 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。

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.