Mechanistic Modeling of Cellular Systems

蜂窝系统的机械建模

• 批准号: 10839683
• 负责人: LESLIE M LOEW
• 金额: $ 23.94万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10839683
• 关键词: Address; Adoption; Architecture; Award; Biophysical Process; Cell model; Cell physiology; Cells; Client; Communities; Computer Models; Computer software; Connecticut; Databases; Development; Disease; Education and Outreach; Funding; Goals; High Performance Computing; Infrastructure; Maintenance; Modeling; Modernization; Paper; Parents; Provider; R24; Reproducibility; Research; Resources; Secure; Security; Services; Software Engineering; System; Technology; Trust; Universities; Update; Visualization; biophysical model; cell community; computerized tools; falls; insight; medical schools; migration; models and simulation; parent grant; portability; simulation; software development; software infrastructure; software systems; virtual

PROJECT SUMMARY This parent R24 award establishes a National Resource for Mechanistic Modeling of Cellular Systems to serve the large community of cell and systems biologists. The Resource encompasses COPASI and Virtual Cell (VCell) software platforms, which are arguably the most comprehensive and widely used tools for computational modeling of the biophysical mechanisms controlling cell function. VCell and COPASI each boast thousands of active users. Collectively, their users produce >100 papers per year relying on these software systems. Both VCell and COPASI are hosted at the University of Connecticut School of Medicine and the Resource benefits from a common High Performance Computing (HPC) facility that serves the computationally intensive needs of users and a coordinated training and outreach to the user community. It actively engages with the software standards community to assure the reproducibility and reusability of both the software and the models it generates. A key component is the continuous enhancement of HPC support for increased portability, scalability and cloud compatibility (Specific Aim 2 of the parent grant). As stated in this aim, we strive to maintain and update the software infrastructure to meet this goal. Nevertheless, modern software engineering technologies are changing at breath-taking pace in this domain and some recent paradigm-shifting advances could not be foreseen and cannot be addressed within the limitations of the current funding. This supplement proposal focuses on three such emerging needs for the VCell framework that can be properly addressed only with additional resources and expertise: (i) transition the HPC/cloud architecture from Docker Swarm to Kubernetes, (ii) implement identity and access management using third-party authentication providers, and (iii) port and update the Restlet-based API to OpenAPI.

项目概要 该母 R24 奖项建立了国家蜂窝系统机械建模资源，以服务 细胞和系统生物学家的大社区。该资源包括 COPASI 和虚拟单元 (VCell) 软件平台，可以说是最全面、使用最广泛的工具 控制细胞功能的生物物理机制的计算模型。 VCell 和 COPASI 各有所长 数以千计的活跃用户。总的来说，他们的用户每年依靠这些软件发表超过 100 篇论文 系统。 VCell 和 COPASI 均由康涅狄格大学医学院和 资源受益于为计算提供服务的通用高性能计算 (HPC) 设施 用户的强烈需求以及对用户社区的协调培训和推广。它积极参与 与软件标准社区合作，确保软件和软件的可重复性和可重用性 它生成的模型。一个关键组成部分是不断增强 HPC 对增加的支持 可移植性、可扩展性和云兼容性（母基金的具体目标 2）。正如这个目标所指出的，我们 努力维护和更新软件基础设施以实现这一目标。尽管如此，现代软件 工程技术在这个领域正在以惊人的速度发生变化，并且最近发生了一些范式转变 无法预见预付款，也无法在现有资金的限制内解决预付款问题。这 补充提案重点关注 VCell 框架的三个新兴需求，这些需求可以适当地 仅通过额外的资源和专业知识即可解决：(i) 从 Docker 过渡 HPC/云架构 Swarm 到 Kubernetes，(ii) 使用第三方身份验证实现身份和访问管理 提供商，以及 (iii) 将基于 Restlet 的 API 移植并更新为 OpenAPI。

项目成果

RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.

• DOI: 10.1093/nar/gkab411
• 发表时间: 2021-07-02
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Shaikh B;Marupilla G;Wilson M;Blinov ML;Moraru II;Karr JR
• 通讯作者: Karr JR

The release of inhibition model reproduces kinetics and plasticity of neurotransmitter release in central synapses.

抑制模型的释放再现了中枢突触中神经递质释放的动力学和可塑性。

• DOI: 10.21203/rs.3.rs-2700789/v1
• 发表时间: 2023
• 期刊: Research square
• 作者: Norman,ChristopherA;Krishnakumar,ShyamS;Timofeeva,Yulia;Volynski,KirillE
• 通讯作者: Volynski,KirillE

Optimization of Media Change Intervals through Hydrogels Using Mathematical Models.

• DOI: 10.1021/acs.biomac.2c00961
• 发表时间: 2023-02-13
• 期刊: BIOMACROMOLECULES
• 影响因子: 6.2
• 作者: Ruiter, Floor A. A.;King, Jasia;Swapnasrita, Sangita;Giselbrecht, Stefan;Truckenmuller, Roman;LaPointe, Vanessa L. S.;Baker, Matthew B.;Carlier, Aurelie
• 通讯作者: Carlier, Aurelie

Phosphatidylinositol 4,5-bisphosphate is regenerated by speeding of the PI 4-kinase pathway during long PLC activation.

• DOI: 10.1085/jgp.202012627
• 发表时间: 2020-12-07
• 期刊: The Journal of general physiology
• 作者: Myeong J;de la Cruz L;Jung SR;Yeon JH;Suh BC;Koh DS;Hille B
• 通讯作者: Hille B

Measurement of solubility product in a model condensate reveals the interplay of small oligomerization and self-association.

模型冷凝物中溶度积的测量揭示了小寡聚和自缔合的相互作用。

• DOI: 10.1101/2024.01.23.576869
• 发表时间: 2024
• 期刊: bioRxiv : the preprint server for biology
• 作者: Chattaraj,Aniruddha;Baltaci,Zeynep;Mayer,BruceJ;Loew,LeslieM;Ditlev,JonathonA
• 通讯作者: Ditlev,JonathonA