RepServer: Antigen Receptor Repertoire Analysis Pipelines via the WWW

RepServer：通过 WWW 的抗原受体库分析管道

• 批准号: 8636990
• 负责人: LINDSAY G. COWELL
• 金额: $ 64.15万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-04-01 至 2017-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8636990
• 关键词: Address; Algorithms; Antibodies; Antigen Receptors; Archives; Area; Autoimmune Diseases; Autoimmune Responses; Basic Science; Bioinformatics; Cells; Clinical; Computer software; Data; Data Analyses; Development; Diagnosis; Diagnostic; Disease; Event; Fc Receptor; Foundations; Future; Genes; Goals; Hand; Hematologic Neoplasms; High Performance Computing; Immune; Immune response; Immune system; Immunity; Immunologic Deficiency Syndromes; Individual; Infection; Internet; J segment gene; Jaw; Knowledge; Left; Manuals; Metadata; Methods; Modification; Nature; Organism; Output; Pathogenesis; Patient Monitoring; Pattern; Play; Reporting; Reproducibility; Research; Research Infrastructure; Research Personnel; Role; Software Tools; Somatic Mutation; Time; Translational Research; Translations; Vaccination; Vaccine Design; Vertebrates; Work; clinical practice; computer program; data acquisition; data management; design; improved; leukemia/lymphoma; next generation sequencing; novel therapeutics; prognostic; repository; research and development; response; senescence; software development; task analysis; tool; web site

DESCRIPTION (provided by applicant): An organism's ability to mount an effective immune response after infection or vaccination depends on the type of antibodies and antigen receptors produced by its immune system cells. This set of molecules also plays an important role in the pathogenesis of many kinds of disease, such as autoimmune disease, lymphoma, and leukemia. Thus, analysis of an individual's repertoire of such molecules is applied in a wide variety of basic research, research and development, and clinical contexts. Despite the importance and complexity of repertoire analysis, there is currently no suite of software tools for analysis of repertoire data. Tools exist for only a subset of analysis tasks, and those that do exist were developed for use on a single project by a single research group. These tools do not function together and cannot be utilized in new studies without modification that requires bioinformatics expertise, leaving researchers to perform repetitive and error-prone tasks by hand, to develop internal, idiosyncratic algorithms not easily generalizable or systematically applied, and to expend significant manual labor reformatting primary and derived data for passing between tools. This approach is not only error-prone and time- and labor-intensive, but it comes at the expense of reproducibility, both within and between research groups. We propose to address this critical barrier to progress by developing RepServer, a suite of interoperable repertoire analysis tools and an interface that allows users to upload a set of repertoire sequences and pass them through a seamless workflow that executes all steps in the analysis and generates an analysis report complete with data summary tables, statistical analyses, figures, and workflow logs. The impact of RepServer will be significant. RepServer will improve the efficiency of repertoire analysis by reducing duplication of effort and eliminating the need for significant manual manipulation of data. The latter will in turn improve the accuracy and reliability of analyses by reducing errors. RepServer will make sophisticated computational analyses of repertoires accessible to bench biologists and clinicians. RepServer will provide the infrastructure for reproducibility, a critical step towards translation of repertoire analysis into clinical settings. RepServer will have impact in all areas of research, development, and clinical practice that rely on repertoire analysis.

描述（由申请人提供）：生物体在感染或疫苗接种后安装有效免疫反应的能力取决于其免疫系统细胞产生的抗体和抗原受体的类型。这组分子在多种疾病的发病机理中也起着重要作用，例如自身免疫性疾病，淋巴瘤和白血病。因此，对个人对此类分子的曲目的分析应用于各种基础研究，研发以及临床环境中。尽管曲目分析的重要性和复杂性，但目前尚无用于分析曲目数据的软件工具。仅用于一部分分析任务的工具，并且确实存在的工具是由一个研究小组开发用于单个项目的工具。这些工具没有合作的工作，并且不能在不需要生物信息学专业知识的新研究中使用，从而使研究人员手工执行重复性和容易出错的任务，开发内部，特质算法不容易概括或系统地应用，并且可以在工具之间使用大量的手动重新格式化和衍生的主要数据。这种方法不仅容易出错，而且是时间和劳动力密集的，而且在研究小组之间和之间，它都以可重复性为代价。我们建议通过开发Repserver，一套可互操作的曲目分析工具和一个界面来解决这一进步的关键障碍，该工具允许用户上传一组曲目序列，并将其传递通过无缝的工作流程，以在分析中执行所有步骤，并在分析中执行所有步骤，并生成一份分析报告，并与数据摘要报告，统计分析，图形，图形和工作流程和工作流程和工作流程和工作流程和工作流程和工作流程。代表者的影响将很大。 Repserver将通过减少努力重复并消除对数据进行大量手动操纵的需求来提高曲目分析的效率。后者反过来将通过减少错误来提高分析的准确性和可靠性。代表将对基准生物学家和临床医生可以访问的曲目进行复杂的计算分析。 Repserver将为可重复性提供基础设施，这是将曲目分析转化为临床环境的关键一步。 Repserver将在依赖曲目分析的所有研究，开发和临床实践领域产生影响。