ABI Development: systemPipeR - automated NGS workflow and report generation environment

下一代测序(NGS)使研究人员能够常规地对基因组和转录本进行测序，从而彻底改变了生物学许多领域的研究方式。然而，NGS数据的分析仍然是有效利用该技术的主要障碍。虽然在开发专门用于NGS实验各个分析步骤的软件方面投入了大量精力，但目前没有足够的资源将各个软件组成部分整合到能够以省时和可重复的方式从头到尾对大多数类型的NGS应用程序进行分析的自动化工作流程中。该开发项目将通过增强System PipeR来满足这一需求，这是一种流行的R/BioConductor软件包。该项目将能够以省时和可重复的方式将NGS数据转化为具有生物学意义的知识，从而对广泛的科学界和整个社会产生重大影响。这将加速学术界和工业界的许多研究和发现项目，在这些项目中，NGS技术发挥着重要作用。将提供广泛的教育资源，用于基因组和计算生物学交叉学科的培训。将为科学家、博士后研究人员、研究生和本科生提供培训。代表不足群体的成员将参与这一项目的所有方面，同时支持多样性。将提供广泛的在线教程，以最大限度地扩大活动的教育范围。本项目的具体目标是：(目标1)改进系统PipeR？S用户界面和工作流设计框架，将大大简化工作流运行、自动生成报告和设计新工作流的过程。它还将改善用户友好性，使system PipeR对R和非R用户以及没有任何生物信息学专业知识的生物学家同样有用。这一目标的执行计划包括设计一个中央工作流程控制用户界面和采用新的社区标准，以进一步提高分析工作流程的可重复性。(目标2)将为更多的NGS应用程序开发自动化分析工作流程。其中大部分工作流程将与相应NGS应用领域的专家合作设计。我们亦会吸纳社会人士的建议。将为受支持的NGS应用程序提供样本模板，以使用完全填充了所有输入数据和环境设置的单个命令创建工作流实例。(目标3)该项目还将把重点放在当前和未来用户提供的社区融合和绩效评估上。这包括让用户贡献代码或整个工作流程的选项，以及对目标受众进行广泛的培训，让他们使用system PipeR和相关资源分析NGS数据。System PipeR项目网站的网址是：http://girke.bioinformatics.ucr.edu/systemPipeR.

Next-generation sequencing (NGS) has revolutionized how research is carried out in many areas of biology by allowing researchers to sequence genomes and transcriptomes on a routine basis. However, the analysis of NGS data remains a major obstacle to the efficient utilization of the technology. While substantial effort has been invested on the development of software dedicated to the individual analysis steps of NGS experiments, insufficient resources are currently available for integrating the individual software components into automated workflows capable of running the analysis of most types of NGS applications from start-to-finish in a time-efficient and reproducible manner. This Development project will address this need by enhancing systemPipeR, a popular R/Bioconductor software package. The project will have significant impact on a wide range of scientific communities and our society at large by allowing to translate NGS data into biologically relevant knowledge in a time-efficient and reproducible manner. This will accelerate many research and discovery projects in academia and industry, where NGS technologies play an important role. Extensive educational resources for interdisciplinary training at the intersect of genome and computational biology will be provided. Training will be offered to scientists, postdoctoral researchers, graduate and undergraduate students. Members of underrepresented groups will participate in all aspects of this project while supporting diversity. Extensive online tutorials will be provided to maximize the educational outreach of the activities. The specific aims of this project are: (AIM 1) Enhancements to systemPipeR?s user interface and the workflow design framework will greatly simplify the process of running workflows, generating automated reports and designing new workflows. It will also improve user-friendliness to make systemPipeR equally useful for R and non-R users, as well as biologists without any expert knowledge in bioinformatics. The execution plan of this aim includes the design of a central workflow control user interface and the adaptation of new community standards to further increase the reproducibility of analysis workflows. (AIM 2) Automated analysis workflows will be developed for a wide range of additional NGS applications. Most of these workflows will be designed in collaboration with experts of the corresponding NGS application areas. Suggestions from the community will be incorporated as well. Sample templates will be provided for the supported NGS applications to create workflow instances with a single command fully populated with all input data and environment settings. (AIM 3) The project will also have a strong focus on community integration and performance evaluations provided by its current and future users. This includes options for users to contribute code or entire workflows, and extensive training of the target audience to analyze NGS data with systemPipeR and related resources. The URL of the systemPipeR project website is: http://girke.bioinformatics.ucr.edu/systemPipeR.