Maintenance and Development of the IMa Program

IMa 程序的维护和发展

• 批准号: 8539501
• 负责人: Emanuel Hey
• 金额: $ 22.46万
• 依托单位: TEMPLE UNIV OF THE COMMONWEALTH
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8539501
• 关键词: Alleles; Charts and Tables; Code; Complex; Computational Biology; Computers; DNA Sequence; Data; Data Files; Data Set; Development; Disease; Extensible Markup Language; Gene Exchanges; Generations; Genes; Goals; Haplotypes; Human; Individual; Investigation; Joints; Knowledge; Learning; Maintenance; Methods; Modeling; Names; Occupations; Output; Population; Population Sizes; Population Study; Process; Research Personnel; Running; Sample Size; Scientist; Services; Single Nucleotide Polymorphism; Source Code; Specific qualifier value; Speed; Structure; Technology; Time; Universities; Work; Writing; acronyms; base; computer program; data modeling; design; file format; migration; next generation; programs; vector

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.

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差异，包括差异是物种内人群结构的正常部分，以及在物种形成过程中发生的差异。该计划对差异过程的丰富模型进行了统计分析，该模型包括人口分离，基因交换和人口规模的参数；对于多个人群的模型和数据集，它确实如此。 但是，该程序在单个处理器上运行，对于具有大量基因座的较新数据集来说太慢了。该程序也很难让研究人员学习，并且由于已添加了新功能，因此该程序的源代码变得难以修改，或者对于多个研究人员而言，该计划的源代码也很难一起工作。最后，当数据集很大并且分析很复杂时，当前的输入和输出文件格式很笨拙且难以使用。 在拟议的项目下，IMA程序将被重写，以包括大型数据集和在多个处理器上运行的新方法。源代码还将重新设计为面向对象，然后将其在C ++中重写。将编写一个新的图形前端程序，以简化：数据检查的任务；输入文件组件；模型规范；开始工作；和查看运行时状态。为了促进组装和检查数据文件，并简化了启动作业的过程，将重写用于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该程序，以在遵循SVG（可扩展矢量图形）XML标准的文件中生成所有图表和表。