RepServer: Antigen Receptor Repertoire Analysis Pipelines via the WWW

描述（由申请人提供）：生物体在感染或接种疫苗后产生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。这组分子在自身免疫性疾病、淋巴瘤和白血病等多种疾病的发病机制中也起着重要作用。因此，对个体这些分子的分析广泛应用于各种基础研究、研究和开发以及临床环境中。尽管保留表分析的重要性和复杂性，目前还没有一套软件工具来分析保留表数据。工具只存在于分析任务的子集，而那些存在的工具是由单个研究小组开发用于单个项目的。这些工具不能一起工作，如果不进行需要生物信息学专业知识的修改，就不能在新的研究中使用，这使得研究人员不得不手工执行重复和容易出错的任务，开发内部的、不容易推广或系统应用的特殊算法，并花费大量的手工劳动来重新格式化主要和派生数据，以便在工具之间传递。这种方法不仅容易出错，耗费时间和人力，而且在研究小组内部和小组之间的重复性也会受到影响。我们建议通过开发RepServer来解决这一关键障碍，RepServer是一套可互操作的曲目分析工具和一个接口，允许用户上传一组曲目序列，并通过一个无缝的工作流来执行分析中的所有步骤，并生成一份分析报告，其中包括数据汇总表、统计分析、图表和工作流日志。RepServer的影响将是显著的。RepServer将通过减少重复工作和消除对数据进行大量手动操作的需要来提高库分析的效率。后者反过来又会通过减少错误来提高分析的准确性和可靠性。RepServer将为工作台生物学家和临床医生提供复杂的计算分析。RepServer将提供可重复性的基础设施，这是将曲目分析转化为临床环境的关键一步。RepServer将对所有依赖剧目分析的研究、开发和临床实践领域产生影响。

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.