MULTIPOPULATION INFLUENZA A GENOMIC EVOLUTION

多群体流感基因组进化

• 批准号: 8364295
• 负责人: Gilles Clermont
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364295
• 关键词: Biomedical Research; Birds; Code; Data; Evolution; Family suidae; Funding; Genetic Materials; Genomics; Grant; High Performance Computing; Hour; Human; Influenza; Influenza A virus; Learning; Modeling; National Center for Research Resources; Population; Principal Investigator; Research; Research Infrastructure; Resources; Running; Seeds; Simulate; Source; Time; United States National Institutes of Health; Viral; Writing; cost; genetic evolution; shared memory; simulation; software development

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We have debugged a stochastic simulation of genetic evolution of the influenza A virus (IVA). The purpose of the model is to a construct a realistic model to seed the introduction of specific viral strains in US-wide population models currently run as part of the Pitt MIDAS project (Burke et al.). The model considers three pools of genetic material (birds, swine and humans), with genetic evolution occurring in all pools. Some strains will get transmitted between pools, thus introducing new strains in humans. The code is written in Fortran95. Our current single-run time on a workstation is about 48 hours as we wish to simulate evolution over about 40 years. Since we need to calibrate the model to data, we wish to conduct a large number (>10000 if possible) of shorter (5-7 years) runs to construct realistic parameter sets. Runs would initially be run independently. Thus the initial need is for a distributed platform, without shared memory requirement. We are developing the software for an MPI implementation to support adaptive parameter learning- but this is not ready for prime time yet.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 我们已经讨论了流感病毒（IVA）遗传进化的随机模拟。该模型的目的是构造一个现实的模型，以播种目前作为Pitt Midas项目的一部分，在美国范围内的人群模型中引入特定的病毒株（Burke等人）。该模型考虑了三个遗传物质（鸟类，猪和人类）的三个池，遗传进化发生在所有池中。一些菌株将在池之间传播，从而引入人类的新菌株。该代码写在fortran95中。我们目前在工作站上的单次时间时间约为48小时，因为我们希望在40年内模拟演变。由于我们需要将模型校准到数据，因此我们希望进行大量（如果可能的话）短（5 - 7年）运行以构建现实的参数集。运行最初将独立运行。因此，最初的需求是针对分布式平台，而无需共享内存要求。我们正在开发用于支持自适应参数学习的MPI实现的软件 - 但这还没有准备好用于黄金时段。