Commercialization of SciDAP, a next generation universal platform for collaborative data analysis

SciDAP 的商业化，下一代协作数据分析通用平台

• 批准号: 10338010
• 负责人: Artem Barski
• 金额: $ 5.2万
• 依托单位: DATIRIUM, LLC
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-05-01 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10338010
• 关键词: Biology; Businesses; Collaborations; Computer Analysis; DNA Methylation; DNA-Protein Interaction; Data; Data Analyses; Disease; Ensure; Environment; Gene Expression Profiling; Health; Instruction; Language; Life; Methods; Methylation; Modeling; Output; Reproducibility; Research; SPT6 Protein; Scientist; System; Testing; Visualization; Work; base; bioinformatics tool; biomedical scientist; bisulfite sequencing; commercialization; computational pipelines; flexibility; genomic data; graphical user interface; insight; multiple omics; next generation; next generation sequencing; novel; portability; prototype; recruit; single-cell RNA sequencing; skills; tool; usability; user-friendly

Summary The recent proliferation of next-generation sequencing (NGS) - based methods for the analysis of gene expression, 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. We hypothesize that we can create a data analysis platform that is both universal and user-friendly by including 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 Workflow 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 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 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- methylation and scRNA-Seq; then we will work with biologists to ensure that the resulting interface is both user- friendly and enables collaboration with bioinformaticians. In this iCorps supplement, Datirium recruited Amy Duncan, MBA, a commercialization expert specializing in launch of research products to work with us on developing a a comprehensive, effective, and multi-faceted commercialization and launch plan. Specifically, we hope to gain the skills and information necessary to thoroughly understand our varied groups of potential customers and partners and to validate (or modify) our business model and technical solutions. To this end, we will embark on extensive research about how the interviewees will receive our product and test our initial plans for commercialization.

总结 近年来，基于下一代测序（NGS）的基因分析方法的激增， 表达，染色质结构和蛋白质-DNA相互作用创造了巨大的机会， 对基础生物学、健康和疾病的新见解。然而，分析结果数据需要 许多传统生物学家不具备的计算专业知识。因此，在处理基因组学时， 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。这些令人兴奋的地方 这是大多数生命科学家无法企及的方法。 来自俄亥俄州辛辛那提的一家初创公司DATIRIUM，LLC的这份提案描述了创建SciDAP的计划 （科学数据分析平台），一个新颖的多组学用户友好的数据分析平台，让生物学家 分析数据本身，并使生物学家和生物信息学家之间的合作成为可能。 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 将指令接口到计算流水线本身。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 工作流语言（CWL）。CWL允许描述工具，管道和计算环境， 这些流水线既可移植又可再现。在CWL之上，Datirium开发了一个CWL扩展系统 它允许描述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（i）使分析可重现和可审计， 由于CWL管道的可移植性，生物信息学家将分析的每个步骤记录为研究对象; (ii)使实验学家和计算生物学家之间的合作， 生物信息学家的方式来指导分析流程和生物学家与GUI的便利;（iii）包括 开箱即用的管道，具有优化的参数和可操作的QC指标，可以标记可能的问题。 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多种类型的分析。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- 甲基化和scRNA-Seq;然后，我们将与生物学家合作，以确保最终的界面是用户- 友好，并能够与生物信息学家合作。 在这个iCorps补充中，Datirium招募了Amy邓肯，MBA，一位商业化专家，专门从事 推出研究产品，与我们合作开发一个全面、有效和多方面的 商业化和启动计划。具体而言，我们希望获得必要的技能和信息， 彻底了解我们的潜在客户和合作伙伴的各种群体，并验证（或修改）我们的 商业模式和技术解决方案。为此，我们将着手进行广泛的研究， 受访者将收到我们的产品，并测试我们的初步商业化计划。

项目成果

Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

• DOI: 10.1016/j.xpro.2021.100989
• 发表时间: 2021-12-17
• 期刊: STAR protocols
• 作者: Surumbayeva A;Kotliar M;Gabitova-Cornell L;Kartashov A;Peri S;Salomonis N;Barski A;Astsaturov I
• 通讯作者: Astsaturov I