SciDAP: a next generation universal platform for collaborative data analysis

近年来，基于下一代测序（NGS）的基因表达分析方法不断涌现， 染色质结构和蛋白质-DNA相互作用为获得新的 对基础生物学、健康和疾病的深刻见解。然而，对结果数据的分析需要计算 这是许多传统生物学家所不具备的。因此，在处理基因组学数据时，大多数 即使是简单的任务，生物学家也需要生物信息学家的帮助。这些令人兴奋的方法 大多数生命科学家的研究范围。 来自俄亥俄州辛辛那提的一家初创公司Datirium，LLC的这份提案描述了一项计划， SciDAP（科学数据分析平台），一种新颖的多组学用户友好的数据分析平台， 生物学家自己分析数据，并使生物学家和生物信息学家之间的合作。 Datirium是由该应用程序的PI，阿尔特姆巴斯基博士和安德烈Kartashov创建的，最初是为了帮助用户 与BioWardrobe的安装和支持。BioWardrobe，一个用户友好的开源整合基因组学 分析平台，由辛辛那提儿童医院医学中心的Barski实验室开发 2015年，CCHMC。它已被40多个CCHMC实验室用于处理8000多个实验， 已在40多个出版物中应用。此外，Datirium已经安装并将继续 在几个外部研究中心维护BioWardrobe服务器。 对于Datirium，BioWardrobe作为最小可行产品（MVP），可以确认需求 这类软件的市场定位，但也突出了几个设计上的限制。中的关键 增加新的或修改现有管道的困难：由于管道之间的紧密耦合， 和用户界面，这需要在软件的所有级别上进行更改。不幸的是，同样的限制存在于所有 用户友好的生物信息学工具。鉴于有超过150种基于NGS的方法和许多方法可以 由于数据处理的复杂性，这就解释了为什么还没有一个通用和用户友好的数据分析平台。 我们假设，我们可以创建一个数据分析平台，这是通用的和用户友好的，包括- 将接口指令插入到计算流水线本身中。平台将使用这些说明创建一个 为用户提供图形界面。具体来说，我们使用的是使用Common Work开发的容器化管道- 流语言（CWL）。CWL允许描述工具，管道和计算环境，使这些 管道既便携又可复制。在CWL之上，Datirium开发了一个CWL扩展系统， 允许描述CWL工作流中的输入和输出可视化。重要的是，我们的平台 将通过以下方式增加计算分析的严谨性：（i）使分析可重现并可由生物素- 由于CWL管道的可移植性和记录作为研究对象的分析的每一步，formaticans;（ii） 通过提供生物信息学家， 通过GUI的便利性指导分析流程和生物学家;（iii）包括开箱即用的管道- 具有优化参数和可操作的QC指标的行，可标记可能的问题。 在本提案的第一个目标中，我们将创建平台的原型。在第二个目标中，我们将 与生物信息学家和实验学家一起进行可用性测试，以测试我们的平台是否能够适应 以用户友好的方式进行各种类型的分析。具体而言，与Salomonis博士合作， CCHMC，我们将测试将两个现有的分析程序整合到SciDAP中的容易程度：BS-Seq DNA-甲基- 然后，我们将与生物学家合作，以确保最终的界面既用户友好， 并能与生物信息学家合作。 该项目的成功完成将为研究界提供一个先进的，灵活的， 生物学家友好的数据分析平台。

The recent proliferation of next-generation sequencing (NGS) - based methods for the analysis of gene expres- sion, chromatin structure and protein-DNA interactions has created tremendous opportunities for gaining novel insights into basic biology, health, and disease. However, analysis of the resulting data requires computational expertise that many traditional 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 proposal from DATIRIUM, LLC, a start-up company from Cincinnati, OH describes a plan to create SciDAP (Scientific Data Analysis Platform), a novel multi-omics user-friendly data analysis platform to allow biologists to analyze the data themselves and to enable collaboration between biologists and bioinformaticians. Datirium was founded by this application’s PIs, Artem Barski, PhD and Andrey Kartashov, initially to assist users with installation and support of BioWardrobe. BioWardrobe, a user-friendly open-source integrative genomics analysis platform, was developed by the Barski laboratory at Cincinnati Children’s Hospital Medical Center (CCHMC) in 2015. It has been used by more than 40 CCHMC laboratories to process more than 8000 experi- ments and has been applied in more than 40 publications. In addition, Datirium has installed and continues to maintain BioWardrobe servers at several external research centers. For Datirium, BioWardrobe served as a Minimum Viable Product (MVP) that allowed to confirm the need and existence of market niche for such software, but also highlighted several design limitations. The key among them was 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 hypothesize that we can create a data analysis platform that is both universal and user-friendly by includ- ing interface instructions into computational pipelines itself. Platform will use these instructions to create a graphical interface for users. Specifically, we are using containerized pipelines developed using Common Work- flow Language (CWL). CWL allows to describe tools, pipelines and computational environment making these 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 bioin- formaticians 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 pipe- lines with optimized parameters and actionable QC metrics that flag possible issues. In the first aim of this proposal we will create a prototype of the platform. In the second aim, we will conduct usability testing with bioinformaticians and experimentalists to test whether our platform can accommodate diverse types of the analysis in a user-friendly fashion. Specifically, in collaboration with Dr. Salomonis at CCHMC, we will test how easy it is to integrate two existing analysis routines into SciDAP: BS-Seq DNA-methyl- ation and scRNA-Seq; then we will work with biologists to ensure that the resulting interface is both user-friendly and enables collaboration with bioinformaticians. Successful completion of this project will provide the research community with a cutting edge, flexible and biologist-friendly data analysis platform.