Comprehensive, Flexible and FAIR Tools for the HuBMAP HIVE

适用于 HuBMAP HIVE 的全面、灵活且公平的工具

• 批准号: 10397722
• 负责人: Benedict Paten
• 金额: $ 130.46万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-21 至 2022-06-20
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10397722
• 关键词: Address; Anatomy; Biological Availability; Communities; Community Developments; Computer software; Computing Methodologies; Data; Development; Ensure; FAIR principles; Histologic; Human BioMolecular Atlas Program; Human body; Image Analysis; International; Lead; Libraries; Measurement; Methods; Modeling; Molecular; Participant; Process; Research; Research Personnel; Resolution; Technology; Tissues; Validation; Vision; Work; community involvement; computerized tools; data integration; data privacy; experience; flexibility; improved; innovation; method development; open source; query tools; repository; software development; tool; tool development

Abstract The Human BioMolecular Atlas Program (HuBMAP) will redefine our understanding of the human body by recovering multi-scale tissue organization -- anatomical, histological, and molecular, at unprecedented resolution, through computational integration of diverse experimental measurements. We propose to develop computational methods and tools to enable the use of HuBMAP collected data by consortium participants, the international research community and the large software and method development community. Our proposal is focused on three key directions for the Tools Component: (1) Community involvement: Development of repositories, APIs, interfaces and schemas to enable the hosting, discovery and integration of tools and libraries developed by us and others. We would put specific emphasis on making sure that this process is efficient, reduces duplicated efforts and transparent enabling involvement of the general developer community. All tools would be developed as open source software. (2) Innovative tool development: While we intend to rely and use existing tools as much as possible, we also propose to develop a comprehensive set of innovative tools for the specific challenges presented by the HuBMAP long term vision and data. These include tools for querying and retrieving data collected by the HUBMAP, expression and image analysis methods and libraries, tools for the analysis of spatial and temporal data from the MAP and tools for modeling and data integration which would enable the integration of HuBMAP data with the vast amounts of other publicly available biological data. (3) Flexibility: We expect that improved technology and variance in the specific plans of the Tissue Mapping Centers would lead to additional types of data that we have not designed tools for in the past. We have thus assembled an experienced and diverse group of investigators, all with significant experience in tool development that, together, span the spectrum of potential types of data. Our proposal includes detailed plans for ensuring that the tools we develop and implement are findable, accessible, interoperable and reusable (FAIR) and addresses issues related to validation of tool accuracy and usefulness, data privacy and reproducibly. The Tools component would work very closely with other HIVE components to disseminate the tools and to connect with both the developers and the international research communities.

摘要 人类生物分子图谱计划（HuBMAP）将重新定义我们对人类的理解。 通过恢复多尺度组织组织--解剖学、组织学和分子学， 前所未有的分辨率，通过计算集成不同的实验， 测量.我们建议开发计算方法和工具，使使用 HuBMAP收集了联盟参与者、国际研究界和 大型软件和方法开发社区。我们的建议集中在三个关键方面 工具组件的方向：（1）社区参与：开发存储库， API、接口和模式，用于托管、发现和集成工具， 我们和其他人开发的图书馆。我们会特别强调， 流程高效，减少重复工作，透明， 一般开发人员社区。所有工具都将作为开放源码软件开发。（二） 创新工具开发：虽然我们打算尽可能多地依赖和使用现有工具， 如果可能，我们还建议开发一套全面的创新工具， HuBMAP长期愿景和数据所带来的挑战。其中包括查询工具 以及检索由HUBMAP、表达和图像分析方法收集的数据， 库，用于分析MAP中的空间和时间数据的工具以及建模工具 和数据集成，这将使HuBMAP数据与大量 其他公开的生物数据。(3)灵活性：我们希望改进的技术 组织绘图中心的具体计划的差异将导致额外的类型 我们过去没有为之设计工具的数据。因此，我们召集了一位经验丰富的 和不同的调查小组，都具有丰富的经验，在工具开发， 一起，跨越了潜在数据类型的范围。 我们的提案包括详细的计划，以确保我们开发和实施的工具是 可查找、可访问、可互操作和可重用（FAIR），并解决与验证相关的问题 工具的准确性和实用性、数据隐私性和可重复性。工具组件将工作 非常密切地与其他HIVE组件，以传播工具，并与 开发人员和国际研究界。

项目成果

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads.

• DOI: 10.1038/s41592-021-01299-w
• 发表时间: 2021-11
• 期刊: Nature methods
• 影响因子: 48
• 作者: Shafin K;Pesout T;Chang PC;Nattestad M;Kolesnikov A;Goel S;Baid G;Kolmogorov M;Eizenga JM;Miga KH;Carnevali P;Jain M;Carroll A;Paten B
• 通讯作者: Paten B

Interactive single-cell data analysis using Cellar.

• DOI: 10.1038/s41467-022-29744-0
• 发表时间: 2022-04-14
• 期刊: Nature communications
• 影响因子: 16.6

scSTEM: clustering pseudotime ordered single-cell data.

• DOI: 10.1186/s13059-022-02716-9
• 发表时间: 2022-07-07
• 期刊: Genome biology
• 影响因子: 12.3

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation.

• DOI: 10.1038/s41592-022-01445-y
• 发表时间: 2022-06
• 期刊: NATURE METHODS
• 影响因子: 48
• 作者: Formenti, Giulio;Rhie, Arang;Walenz, Brian P.;Thibaud-Nissen, Francoise;Shafin, Kishwar;Koren, Sergey;Myers, Eugene W.;Jarvis, Erich D.;Phillippy, Adam M.
• 通讯作者: Phillippy, Adam M.

scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics.

scResolve：从多细胞空间转录组学中恢复单细胞表达谱。

• DOI: 10.1101/2023.12.18.572269
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Chen,Hao;Lee,YoungJe;Ovando,JoseA;Rosas,Lorena;Rojas,Mauricio;Mora,AnaL;Bar-Joseph,Ziv;Lugo-Martinez,Jose
• 通讯作者: Lugo-Martinez,Jose