Developmental Biology Program, Sloan-Kettering Institute, New York, NY, USA.
BMC Bioinformatics. 2018 Apr 4;19(1):121. doi: 10.1186/s12859-018-2127-0.
AceTree, a software application first released in 2006, facilitates exploration, curation and editing of tracked C. elegans nuclei in 4-dimensional (4D) fluorescence microscopy datasets. Since its initial release, AceTree has been continuously used to interact with, edit and interpret C. elegans lineage data. In its 11 year lifetime, AceTree has been periodically updated to meet the technical and research demands of its community of users. This paper presents the newest iteration of AceTree which contains extensive updates, demonstrates the new applicability of AceTree in other developmental contexts, and presents its evolutionary software development paradigm as a viable model for maintaining scientific software.
Large scale updates have been made to the user interface for an improved user experience. Tools have been grouped according to functionality and obsolete methods have been removed. Internal requirements have been changed that enable greater flexibility of use both in C. elegans contexts and in other model organisms. Additionally, the original 3-dimensional (3D) viewing window has been completely reimplemented. The new window provides a new suite of tools for data exploration.
By responding to technical advancements and research demands, AceTree has remained a useful tool for scientific research for over a decade. The updates made to the codebase have extended AceTree's applicability beyond its initial use in C. elegans and enabled its usage with other model organisms. The evolution of AceTree demonstrates a viable model for maintaining scientific software over long periods of time.
AceTree 是一款软件应用程序，于 2006 年首次发布，用于在 4 维（4D）荧光显微镜数据集探索、策展和编辑跟踪的 C. elegans 核。自最初发布以来，AceTree 一直被用于与 C. elegans 谱系数据进行交互、编辑和解释。在其 11 年的生命周期中，AceTree 定期更新以满足其用户社区的技术和研究需求。本文介绍了 AceTree 的最新版本，其中包含广泛的更新，展示了 AceTree 在其他发育背景下的新适用性，并展示了其作为维护科学软件的可行模型的进化软件开发范例。
对用户界面进行了大规模更新，以提高用户体验。工具根据功能进行了分组，并删除了过时的方法。内部要求发生了变化，这使得在 C. elegans 环境中和其他模式生物中使用更加灵活。此外，原始的 3 维（3D）查看窗口已完全重新实现。新窗口提供了一套用于数据探索的新工具。
通过响应技术进步和研究需求，AceTree 在十多年来一直是科学研究的有用工具。对代码库所做的更新扩展了 AceTree 的适用性，超越了其在 C. elegans 中的最初用途，并使其能够与其他模式生物一起使用。AceTree 的发展展示了维护科学软件的可行模型，适用于长时间使用。
