AceTree: A major update and case study in the long term maintenance of open-source scientific software Journal Article
| Authors: | Katzman, B.; Tang, D.; Santella, A.; Bao, Z. |
| Article Title: | AceTree: A major update and case study in the long term maintenance of open-source scientific software |
| Abstract: | Background: 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. Results: 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. Conclusion: 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. © 2018 The Author(s). |
| Keywords: | biology; fluorescence; fluorescence microscopy; embryogenesis; c. elegans; software design; user interfaces; 3d; elegans; interface; 4d; Affine transformation; open source software; iterative methods; interfaces (materials); affine transformations; automated lineaging; application programs; open systems; evolutionary software development; long-term maintenances; scientific researches; software applications |
| Journal Title: | BMC Bioinformatics |
| Volume: | 19 |
| ISSN: | 1471-2105 |
| Publisher: | Biomed Central Ltd |
| Date Published: | 2018-04-04 |
| Start Page: | 121 |
| Language: | English |
| DOI: | 10.1186/s12859-018-2127-0 |
| PROVIDER: | scopus |
| PMCID: | PMC5885296 |
| PUBMED: | 29618316 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 May 2018 -- Source: Scopus |
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