ABI Development: Improved Tools for Population Genomics

该项目的目标是开发计算机软件，使科学家能够比较自然种群的生物体基因组。群体基因组学（研究群体而非个体基因组DNA的多样性）在农业、人类学、自然资源保护、医学和其他几个生物学领域有着重要的应用。最近的技术进步大大降低了DNA测序的成本，因此可以获得大量的数据。与此同时，统计学家已经开发出新的方法来分析大量基因组大小的数据。将这些数据与新的分析方法相结合，可以让科学家们回答有关物种生物学的基本问题，这些问题以前从未得到过。然而，大多数群体基因组学研究未能利用最新的群体基因组学统计方法。这是因为基因组数据需要大量的处理来为分析步骤做准备，而这些操作并不容易学习。生物信息学知识的缺乏导致了结论的错误、结果的不可复制、分析的不完整以及群体基因组学项目周转时间的缓慢。该项目旨在提供能够以一致和正确的方式处理这些任务的软件，并允许直接访问统计工具，从而为人口生物学带来新的见解。该项目将通过建立一个用户友好且直观的管道平台“Pop-gen管道平台”（PPP）来解决基于模型的种群基因组学的最大障碍。这个平台将帮助研究人员避免重新发明数据处理脚本以将数据输入到他们的人口基因组学分析中所固有的问题，并大大减少时间和精力。PPP将包括用于数据准备的测试脚本和管道，以及构建进化模型、执行数据分析和通过Python中的Ruffus计算管道库创建结果可视化所需的工具。PPP也将作为一个具有图形用户界面（GUI）的独立应用程序，在流行和强大的银河项目（www.galaxyproject.org）下开发，用于生物信息学分析。部署Galaxy/PPP的在线服务器将在费城坦普尔大学（www.dev3.cst.temple.edu）开发和维护，供用户以先到先得的方式交互式提交工作。将建立网上论坛以提供支持，并收集有关PPP进一步发展的建议。关于PPP示例应用的教程和视频将被添加到银河计划维基百科培训频道中。此外，这项工作的一个重要部分将包括通过夏季研讨会教育天普大学的高年级学生、费城地区的高中教师和他们的学生，让他们了解现代生物学中生物信息学的力量。有关PPP和相关发展的信息可访问https://bio.cst.temple.edu/~hey/software/software.htm。

The goal of this project is to develop computer software that allows scientists to compare the genomes of natural populations of organisms. Population genomics (the study of diversity in the genomic DNA of populations instead of individuals) has important applications in agriculture, anthropology, conservation, medicine, and several other fields of biology. Recent technology advances have greatly lowered the cost of DNA sequencing so large amounts of data are available. At the same time statisticians have developed new methods for analyzing large collections of genome-sized data. Combining the data with the new analysis approaches can let scientists answer fundamental questions about the biology of species that have never before been accessible. However, most population genomics studies fail to take advantage of the latest population genomics statistical methods. This is because the genomic data requires a lot of processing to prepare it for the analysis steps, and these operations are not easy to learn. Lack of bioinformatics knowledge has led to erroneous conclusions, irreproducible results, incomplete analyses, and slow turnaround time of population genomics projects. This project aims to provide software that can handle those tasks in a consistent and correct way and allow direct access to the statistical tools, to bring about new insights in population biology. This project will address the largest impediments to model-based population genomics by building a user-friendly and intuitive pipeline platform, the "Pop-gen Pipeline Platform" (PPP). This platform will help researchers avoid the problems inherent in re-inventing data processing scripts to feed data into their population genomics analyses, and considerably reduce time and effort. PPP will include tested scripts and pipelines for data preparation, and in addition the tools needed to build evolutionary models, carry out analyses of data, and create visualization of results via the Ruffus Computation Pipeline Library in Python. PPP will also be developed as a stand-alone application with a graphical user interface (GUI) under the popular and robust Galaxy Project (www.galaxyproject.org) for bioinformatics analyses. An online server deploying Galaxy/PPP will be developed and maintained at Temple University, Philadelphia (www.dev3.cst.temple.edu) for users to interactively submit jobs on a first-come-first-served basis. Online forums will be established for support, and to collect suggestions regarding what is desired for further development under PPP. Tutorials and videos about example applications of the PPP will be added to the Galaxy Project Wikipedia training channels. Additionally, a significant part of this work will involve educating Temple University seniors, Philadelphia area high school teachers, and their students about the power of bioinformatics in modern biology through summer workshops. Information about PPP, and associated developments can be accessed at https://bio.cst.temple.edu/~hey/software/software.htm.