Maintenance and Development of the IMa Program

描述(由申请人提供)：本申请描述了一个维护和开发计算机程序的项目。IMA计算机程序被研究人员广泛用于研究分歧，包括作为物种内种群结构的正常部分的分歧，以及在物种形成过程中发生的分歧。该程序实现了对分化过程的丰富模型的统计分析，该模型包括种群分离时间、基因交换和种群大小的参数；它对多个种群的模型和数据集也是这样做的。然而，该程序在单个处理器上运行，对于具有大量位置的较新数据集来说，它太慢了。该程序对调查人员来说也很难学习，随着新功能的加入，该程序的源代码变得很难修改，也很难让多名研究人员一起工作。最后，当数据集很大，分析很复杂时，当前的输入和输出文件格式很笨拙，很难处理。根据拟议的项目，IMA程序将被重写，以包括用于大型数据集和在多个处理器上运行的新方法。源代码也将被重新设计为面向对象的，然后它将被重写为C。将编写一个新的图形前端程序，以简化以下任务：数据检查；输入文件汇编；模型规范；启动作业；以及查看运行状态。为了方便数据文件的汇编和检查，并简化启动作业的过程，将重写输入文件和模型规范的新格式，以遵循简单的XML(可扩展标记语言)规范。为了使程序输出更容易访问，程序将被修改为在一个遵循SVG(可伸缩向量图形)XML标准的文件中生成所有图表和表格。

DESCRIPTION (provided by applicant): This application describes a project to maintain and develop a computer program. The IMa computer program is widely used by researchers for the study of divergence, including divergence as the normal part of population structure within species, and the divergence that happens during speciation. The program implements a statistical analysis of a rich model of the divergence process that includes parameters for times of population separation, gene exchange, and population size; and it does so for models and data sets for multiple populations. However the program runs on a single processor and it is too slow for newer data sets with very large numbers of loci. The program is also difficult for investigators to learn, and as new features have been added to it the source code of the program has become difficult to modify or for multiple researchers to work on together. Finally the current input and output file formats are unwieldy and difficult to work with when data sets are large and analyses are complex. Under the proposed project the IMa program will be rewritten to include new methods for large data sets and for running on multiple processors. The source code will also be redesigned to be object oriented, and then it will be rewritten in C++. A new graphical front-end program will be written to simplify the tasks of: data checking; input file assembly; model specification; starting jobs; and viewing runtime status. To facilitate assembly and checking of data files, and to simplify the process of starting jobs, a new format for input files and model specification will be rewritten to follow a simple XML (Extensible Markup Language) specification. To make program output more accessible the program will be revised to generate all charts and tables in a file that follows the SVG (Scalable Vector Graphics) XML standard.