Sustainable software solutions for two widely used tools in genomic research

适用于基因组研究中两种广泛使用的工具的可持续软件解决方案

• 批准号: 528703105
• 负责人: Professor Dr. Korbinian Schneeberger
• 金额: --
• 依托单位: Institut für Genetik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/528703105?language=en
• 关键词: Sustainable; software; solutions; two; widely

Genomics research is fundamental in medical, breeding, and applied evolutionary studies. Recent technological advances now allow cost-efficient reconstruction of the entire genomic sequence. This has given a significant boost to genomics research as now we can study the genomes and genomic differences between a multitude of whole-genome assemblies for the first time. However, computational tools for genome comparison are still in their infancy. We have developed two widely used software tools, syri and plotsr, to identify and visualise structural differences between genomic sequences. Both tools follow a unique approach where they actually do not start by searching for genomics differences, but instead identify all colinear regions first. By definition, all other regions are rearrangements, which can be identified easily and provide the most accurate results. In this project, we will develop resources to ensure sustainable usage of these tools and create frameworks for further development. Specifically we propose to develop new documentation, to refactor the source code to the current standards, to create best-practices guidelines, to automate source code-checking and quality testing to achieve long-term stability of the software repositories while allowing community developers to update the software. Finally, we will also generate workflows for the use of syri and plotsr on public analysis servers like Galaxy Europe. We believe this project will make both syri and plotsr more accessible to the larger scientific community as well as ensure that they are continuously maintained and further developed.

基因组学研究是医学、育种和应用进化研究的基础。最近的技术进步现在使整个基因组序列的重建具有成本效益。这大大促进了基因组学的研究，因为现在我们可以第一次研究多种全基因组组件之间的基因组和基因组差异。然而，用于基因组比较的计算工具仍处于初级阶段。我们已经开发了两个广泛使用的软件工具，SYRI和PLOTSR，用于识别和可视化基因组序列之间的结构差异。这两种工具都遵循一种独特的方法，实际上它们并不是从搜索基因组学差异开始，而是首先识别所有共线区域。根据定义，所有其他区域都是重新排列，可以很容易地识别并提供最准确的结果。在这个项目中，我们将开发资源，以确保这些工具的可持续使用，并为进一步的发展建立框架。具体地说，我们建议开发新的文档，根据当前标准重构源代码，创建最佳实践指南，自动化源代码检查和质量测试，以实现软件存储库的长期稳定，同时允许社区开发人员更新软件。最后，我们还将生成在Galaxy Europe等公共分析服务器上使用Syri和Plotsr的工作流。我们相信，这一项目将使SYRI和PLOTSR更容易为更大的科学界所接受，并确保它们得到持续维护和进一步发展。