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）：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。该程序实现了对分歧过程的丰富模型的统计分析，其中包括种群分离时间，基因交换和种群大小的参数;并且它对多个种群的模型和数据集进行了统计分析。 然而，该程序运行在一个单一的处理器上，它是太慢的新的数据集非常大量的基因座。该程序对研究人员来说也很难学习，随着新功能的加入，程序的源代码变得很难修改，也很难让多个研究人员一起工作。最后，当前的输入和输出文件格式在数据集很大且分析很复杂时难以使用。 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，然后将用C++重写。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;以及查看运行时状态。为方便汇编和检查数据文件，以及简化启动作业的过程，输入文件和模型规格的新格式将被重写，以遵循简单的XML（可扩展标记语言）规格。为了使程序输出更容易访问，该程序将被修改为在遵循SVG（可缩放矢量图形）XML标准的文件中生成所有图表和表格。 公共卫生关系：该项目将支持IMa计算机程序的开发，该程序被许多科学家用于研究人口，包括人类人口以及其他物种的人口如何进化和分化。人类种群如何以及为什么分化的知识被用于识别与适应相关的基因以及携带导致疾病的等位基因的基因。目前的程序运行缓慢，对于使用最新DNA测序技术生成的大型数据集来说是笨拙的。在拟议的项目下，将采用新的方法来处理非常大的数据集和使用多个计算机处理器（并行化）。还将采用新的用户界面和数据文件及结果的新格式。