SciDAP: Scientific Data Analysis Platform

SciDAP：科学数据分析平台

• 批准号: 10484046
• 负责人: Artem Barski
• 金额: $ 80.25万
• 依托单位: DATIRIUM, LLC
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-14 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10484046
• 关键词: ATAC-seq; Adopted; Biology; ChIP-seq; Chromatin Structure; Code; Collaborations; Communities; Computer Analysis; Computer software; Coupling; DNA-Protein Interaction; Data; Data Analyses; Data Sources; Data Store; Development; Disease; Ensure; Environment; Gene Expression Profiling; Health; Human Resources; Individual; Innovation Corps; Institution; Instruction; Interview; Language; Learning; Life; Linux; Methods; MicroRNAs; Mutation Detection; Output; Phase; Privatization; Process; Pythons; Reproducibility; Research; Research Personnel; Respondent; Scientist; Small Business Technology Transfer Research; Somatic Mutation; System; Techniques; United States National Institutes of Health; Universities; Visualization; Work; XCL1 gene; analysis pipeline; base; bioinformatics tool; biomedical scientist; bisulfite sequencing; chromatin protein; commercialization; computational pipelines; computerized data processing; cost; exome; experimental study; flexibility; genome browser; genomic data; graphical user interface; human disease; insight; multiple omics; next generation sequencing; novel; open source; portability; programs; prototype; research and development; software development; tool; transcriptome sequencing; usability; user-friendly; web interface; whole genome

The recent proliferation of next-generation sequencing (NGS) - based methods for the analysis of expression, chromatin and protein-DNA interactions has created tremendous opportunities for gaining insights into biology, health, and disease. However, analysis of the data requires computational expertise that many biologists do not possess. Hence, when dealing with genomics data, majority of biologists require the help of bioinformaticians even for simple tasks. This places these exciting methods beyond the reach of the majority of life scientists. This phase II proposal from DATIRIUM, LLC, a start-up from Cincinnati, OH follows phase I project that resulted in the development of a prototype (MVP) of SciDAP (Scientific Data Analysis Platform), a novel multi- omics user-friendly data analysis platform that allows biologists to analyze the data and enables collaboration with bioinformaticians. The current phase II proposal describes a plan to continue SciDAP development. The key problem for creating user-friendly data analysis packages is the difficulty in adding new or modifying existing pipelines: due to the tight coupling between pipeline and user interface this required changes at all levels of software. Unfortunately, the same limitation exists for all user-friendly bioinformatics tools. Given that there are more than 150 NGS-based methods and many ways to process the data, this explains why a universal and user-friendly data analysis platform does not yet exist. We hypothesized that we can create a data analysis platform that is both universal and user-friendly by including interface instructions into computational pipelines. Platform will use these instructions to create a graphical interface. Specifically, we are using containerized pipelines developed using Common Workflow Language (CWL) making our pipelines both portable and reproducible. On top of CWL, Datirium developed a system of CWL extensions that allows to describe the inputs and outputs visualizations within the CWL workflows. Importantly, our platform will increase the rigor of computational analysis by (i) making the analysis reproducible and auditable by bioinformaticians due to CWL pipeline portability and recording each step of the analysis as Research Objects; (ii) enabling collaboration between experimentalists and computational biologists by providing bioinformaticians with a way to direct analysis flow and biologists with the convenience of GUI; (iii) Including out of the box pipelines with optimized parameters and actionable QC metrics that flag possible issues. In the first aim of this proposal we will develop a version of SciDAP for use on academic clusters and commercial clouds. In the second aim, in collaboration with Dr. Salomonis at CCHMC, we will adopt pipelines miRNA, WGS/WXS and scMultiome data analysis. In the third, we will develop improvements to SciDAP interface that will increase SciDAP flexibility and usability for bioinformaticians and experimentalists. Successful completion of this project will provide the research community with a cutting edge, flexible and biologist-friendly data analysis platform.

下一代测序（NGS）的最新扩散基于表达分析的方法， 染色质和蛋白质-DNA相互作用为获得生物学的见解带来了巨大的机会， 健康和疾病。但是，对数据的分析需要许多生物学家没有的计算专业知识 具有。因此，在处理基因组学数据时，大多数生物学家都需要生物信息学家的帮助 即使是简单的任务。这将这些令人兴奋的方法超出了大多数生活科学家的影响力。 该阶段的II阶段提案来自Datirium，LLC，俄亥俄州辛辛那提的一家初创公司，遵循第一阶段项目 导致了SCIDAP（科学数据分析平台）的原型（MVP）的发展，这是一种新颖 OMICS用户友好的数据分析平台，允许生物学家分析数据并启用协作 与生物信息学家。当前的II阶段提案描述了继续开发SCIDAP的计划。 创建用户友好的数据分析软件包的关键问题是添加新或修改的困难 现有管道：由于管道和用户界面之间的紧密耦合，此必需的所有级别都会发生变化 软件。不幸的是，所有用户友好的生物信息学工具都存在相同的限制。鉴于那里 是150多种基于NGS的方法以及处理数据的许多方法，这解释了为什么通用和 用户友好的数据分析平台尚不存在。 我们假设我们可以创建一个数据分析平台，该平台既通用又可以用户友好 在计算管道中包括界面说明。平台将使用这些说明来创建 图形接口。具体而言，我们使用的是使用通用工作流开发的容器化管道 语言（CWL）使我们的管道既便携式又可再现。在CWL之上，Datirium开发了 CWL扩展的系统，允许描述CWL中的输入和输出可视化 工作流程。重要的是，我们的平台将通过（i）进行分析来增加计算分析的严格性 由于CWL管道可移植性，生物信息学家可重现和可审核 分析作为研究对象； （ii）实现实验者与计算生物学家之间的合作 通过为生物信息学者提供一种直接分析和生物学家的方式，以方便GUI； （iii） 包括包含优化参数和可行的QC指标的盒子管道，以标记可能的问题。 在本提案的第一个目的中，我们将开发一个版本的SCIDAP，以用于学术群集和 商业云。在第二个目标中，与CCHMC的Salomonis博士合作，我们将采用管道 miRNA，WGS/WXS和SCMULTIOME数据分析。在第三个中，我们将对SCIDAP进行改进 界面将增加生物信息学家和实验家的SCIDAP灵活性和可用性。 该项目的成功完成将为研究社区提供尖端，灵活和 生物学家友好的数据分析平台。