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.

概括 最近，基于下一代测序 (NGS) 的基因分析方法不断涌现 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、健康和疾病的新颖见解。然而，对结果数据的分析需要 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 根据数据，大多数生物学家即使是简单的任务也需要生物信息学家的帮助。这使这些令人兴奋的 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 的这项提案描述了创建 SciDAP 的计划 （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，使生物学家能够 分析数据本身并促进生物学家和生物信息学家之间的合作。 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，包括 将指令连接到计算管道本身。平台将使用这些指令来创建 用户的图形界面。具体来说，我们正在使用使用 Common 开发的容器化管道 工作流语言（CWL）。 CWL 允许描述工具、管道和计算环境 这些管道既可移植又可重复。在 CWL 之上，Datirium 开发了 CWL 扩展系统 允许描述 CWL 工作流程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提高计算分析的严谨性：(i) 使分析具有可重复性和可审计性 由生物信息学家由于 CWL 管道的可移植性并将分析的每个步骤记录为研究对象； (ii) 通过提供以下内容来促进实验学家和计算生物学家之间的合作 生物信息学家可以直接分析流程，而生物学家则可以使用 GUI 的便利； (三) 包括 开箱即用的管道具有优化的参数和可操作的质量控制指标，可标记可能的问题。 在本提案的第一个目标中，我们将创建该平台的原型。在第二个目标中，我们将进行 与生物信息学家和实验学家进行可用性测试，以测试我们的平台是否可以适应 以用户友好的方式进行多种类型的分析。具体来说，与 Salomonis 博士合作 CCHMC，我们将测试将两个现有分析例程集成到 SciDAP 中是多么容易：BS-Seq DNA- 甲基化和 scRNA 测序；然后我们将与生物学家合作，确保最终的界面既适合用户 友好并能够与生物信息学家合作。 在这份 iCorps 增刊中，Datirium 聘请了工商管理硕士 Amy Duncan，她是一位专门从事以下领域的商业化专家： 推出研究产品，与我们合作开发全面、有效、多方面的 商业化和推出计划。具体来说，我们希望获得必要的技能和信息 彻底了解我们不同的潜在客户和合作伙伴群体，并验证（或修改）我们的 商业模式和技术解决方案。为此，我们将开展广泛的研究，探讨如何 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