Maintenance and Development of the IMa Program

IMa 程序的维护和发展

• 批准号: 8237153
• 负责人: Emanuel Hey
• 金额: $ 23.25万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 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 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8237153
• 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. PUBLIC HEALTH RELEVANCE: This project will support the development of the IMa computer program that is used by many scientists to study how populations, including human populations as well as populations of other species have evolved and diverged. Knowledge of how and why human populations are differentiated is used for the identification of genes that are associated with adaptation and that carry alleles that contributed to disease. The current program runs slowly and is unwieldy for the large data sets that are being generated using the latest DNA sequencing technologies. Under the pro- posed project new methods will be implemented for handling very large data sets and for using multiple computer processors (parallelization). A new user interface and new formats for data files and results will also be implemented.

描述（由申请人提供）：此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化，包括分化作为物种内部种群结构的正常部分，以及物种形成过程中发生的分化。该程序实现了对发散过程的丰富模型的统计分析，该模型包括种群分离，基因交换和种群大小的时间参数；它对多个人群的模型和数据集也是如此。然而，该程序在单个处理器上运行，对于具有大量轨迹的新数据集来说速度太慢。该程序对研究人员来说也很难学习，而且随着新功能的加入，程序的源代码变得难以修改，也很难让多个研究人员一起工作。最后，当数据集很大且分析很复杂时，当前的输入和输出文件格式非常笨拙且难以处理。在提议的项目下，IMa程序将被重写，以包括大型数据集和在多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，然后将用c++重写。将编写一个新的图形前端程序来简化以下任务：数据检查；输入文件汇编；模型规范;开始工作;以及查看运行时状态。为了便于组装和检查数据文件，并简化开始工作的过程，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。为了使程序输出更易于访问，将对程序进行修改，以便在遵循SVG（可缩放矢量图形）XML标准的文件中生成所有图表和表格。