MULTIPOPULATION INFLUENZA A GENOMIC EVOLUTION

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 我们已经调试了A型流感病毒（IVA）遗传进化的随机模拟。该模型的目的是构建一个现实的模型，以在目前作为Pitt MIDAS项目（Burke et al.）的一部分运行的美国范围内的人群模型中接种特定病毒株的引入。该模型考虑了三个遗传物质库（鸟类、猪和人类），所有库中都发生了遗传进化。一些菌株会在不同的池之间传播，从而在人类中引入新的菌株。代码是用Fortran 95编写的。我们目前在工作站上的单次运行时间约为48小时，因为我们希望模拟大约40年的进化。由于我们需要根据数据校准模型，我们希望进行大量（如果可能的话，>10000）较短（5-7年）的运行，以构建现实的参数集。最初，它将独立运行。因此，最初需要的是一个分布式平台，没有共享内存的要求。我们正在为MPI实现开发软件，以支持自适应参数学习-但这还没有准备好。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. 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.