SciDAP: Scientific Data Analysis Platform

SciDAP：科学数据分析平台

基本信息

批准号：
10622562
负责人：
Artem Barski
金额：
$ 77.96万
依托单位：
DATIRIUM, LLC
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-14 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10622562
关键词：
ATAC-seq Acceleration Adopted Biology ChIP-seq Chromatin Chromatin Structure Code Collaborations Communities Computer Analysis Computer software Coupling DNA-Protein Interaction Data Data Analyses Data Sources Development Disease Ensure Environment Friends Gene Expression Profiling Health Human Resources Individual Innovation Corps Institution Instruction Interview Language Learning Life Linux Maps Marketing Methods MicroRNAs Mutation Detection Output Phase Privatization Process Proliferating Pythons Reproducibility Research Research Personnel Respondent Scientist Small Business Technology Transfer Research Somatic Mutation Stream System Techniques United States National Institutes of Health Universities Visualization Work analysis pipeline 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 improved insight multiple omics next generation sequencing novel open source portability programs prototype research and development single-cell RNA sequencing software development tool transcriptome sequencing usability user-friendly web interface whole genome

项目摘要

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.

最近基于下一代测序（NGS）的表达分析方法的激增，染色质和蛋白质-DNA 相互作用为深入了解生物学创造了巨大的机会，健康和疾病。然而，数据分析需要计算专业知识，而许多生物学家并不具备这些知识具有。因此，在处理基因组数据时，大多数生物学家需要生物信息学家的帮助即使是简单的任务。这使得这些令人兴奋的方法超出了大多数生命科学家的能力范围。 DATIRIUM, LLC（一家来自俄亥俄州辛辛那提的初创企业）提出的第二阶段提案遵循第一阶段项目：导致了 SciDAP（科学数据分析平台）原型（MVP）的开发，这是一种新颖的多 omics 用户友好的数据分析平台，允许生物学家分析数据并实现协作与生物信息学家。当前的第二阶段提案描述了继续 SciDAP 开发的计划。创建用户友好的数据分析包的关键问题是添加新的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，这需要在各个级别进行更改软件的。不幸的是，所有用户友好的生物信息学工具都存在同样的限制。鉴于有超过 150 种基于 NGS 的方法和多种数据处理方法，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通用且用户友好的数据分析平台将接口指令包含到计算管道中。平台将使用这些指令来创建图形界面。具体来说，我们正在使用使用 Common Workflow 开发的容器化管道语言（CWL）使我们的管道既可移植又可复制。在 CWL 之上，Datirium 开发了 CWL 扩展系统，允许描述 CWL 内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）进行分析来提高计算分析的严谨性由于 CWL 管道的可移植性和记录的每个步骤，生物信息学家可以重现和审核作为研究对象进行分析； (ii) 促进实验学家和计算生物学家之间的合作为生物信息学家提供一种指导分析流程的方法，为生物学家提供方便的 GUI； (三) 包括具有优化参数和标记可能问题的可操作质量控制指标的开箱即用管道。在本提案的第一个目标中，我们将开发一个 SciDAP 版本，用于学术集群和商业云。在第二个目标中，我们将与 CCHMC 的 Salomonis 博士合作，采用管道 miRNA、WGS/WXS 和 scMultiome 数据分析。第三，我们将对 SciDAP 进行改进界面将提高生物信息学家和实验学家的 SciDAP 灵活性和可用性。该项目的成功完成将为研究界提供前沿、灵活和生物学家友好的数据分析平台。