Zhou Yeqiao, Sheng Yimin, Hu Dongbo, Jay Atishay, Vahedi Golnaz, Faryabi Robert B
Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, PA, USA.
bioRxiv. 2025 Jun 20:2025.06.18.660347. doi: 10.1101/2025.06.18.660347.
Optical chromatin tracing experiments directly capture the three-dimensional folding of thousands of individual alleles, highlighting the need for a tool that enables fast, interactive, and analytical browsing of such data. Here, we introduce Optical Looping Interactive Viewing Engine (OLIVE), a web-based tool designed for high-throughput chromatin tracing data that functions similarly to genome browsers. OLIVE allows users, regardless of computational expertise, to input their own data for automated reconstruction of chromatin fibers at individual alleles or to browse annotated publicly available datasets. Using OLIVE's functionalities, users can interact with three-dimensional presentation of traced alleles and query them based on spatial features, including pairwise distances and perimeters between their segments. Finally, OLIVE calculates and presents several polymer physics metrics of each allele, providing quantitative summaries for hypothesis-driven studies. OLIVE is an open-source project accessible at https://faryabilab.github.io/chromatin-traces-vis/.
光学染色质追踪实验直接捕捉数千个单个等位基因的三维折叠，凸显了对一种能够快速、交互式且可分析浏览此类数据的工具的需求。在此，我们介绍光学环化交互式查看引擎（OLIVE），这是一种基于网络的工具，专为高通量染色质追踪数据设计，其功能类似于基因组浏览器。OLIVE允许用户，无论其计算专业知识如何，输入自己的数据以自动重建单个等位基因处的染色质纤维，或浏览带注释的公开可用数据集。利用OLIVE的功能，用户可以与追踪等位基因的三维展示进行交互，并基于空间特征（包括其片段之间的成对距离和周长）对其进行查询。最后,OLIVE计算并呈现每个等位基因的几个聚合物物理指标，为假设驱动的研究提供定量总结。OLIVE是一个开源项目，可在https://faryabilab.github.io/chromatin-traces-vis/上访问。
