Talk:MicrobeTrace
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Feedback from New Page Review process
[edit]I left the following feedback for the creator/future reviewers while reviewing this article: Thanks for creating this page for a CDC-developed software platform. The first 3 citations, from 2 authors, help to establish notability, while most of the others show examples of use. Clear and focussed on the topic. It would be helpful to link this page from others.
Requested move 2 September 2026
[edit]- The following is a closed discussion of a requested move. Please do not modify it. Subsequent comments should be made in a new section on the talk page. Editors desiring to contest the closing decision should consider a move review after discussing it on the closer's talk page. No further edits should be made to this discussion.
Procedural close – moved to proposed title. P.I. Ellsworth , ed. – welcome! – 01:34, 3 September 2026 (UTC)
Microbetrace → MicrobeTrace – The official name of the software is MicrobeTrace, with a capital T. This capitalization is used consistently by the CDC MicrobeTrace project, the CDC GitHub repository, and the peer-reviewed publications describing the software. The current article title, "Microbetrace", therefore appears to be an incorrect rendering of the product name.
Disclosure: I am employed by the U.S. Centers for Disease Control and Prevention and work with the MicrobeTrace project. Because of this affiliation, I am not editing the article directly and am requesting that an uninvolved Wikipedia editor review and make the correction. ~2026-47669-04 (talk) 19:00, 2 September 2026 (UTC)
- Speedy moved - Uncontroversial page move, no need for discussion. Shocksingularity (talk) 00:41, 3 September 2026 (UTC)
Requested updates
[edit]== Suggested addition: Development and release history ==
{{edit COI}}
'''Conflict-of-interest disclosure:''' I am employed by the U.S. Centers for Disease Control and Prevention (CDC) and work with the MicrobeTrace project. Because of this affiliation, I am not editing the article directly. I am instead providing the following information and sources for review by an uninvolved Wikipedia editor.
The current article provides useful sections on MicrobeTrace's functionality and applications, but it does not describe how the software has developed over time. In particular, substantial changes introduced with MicrobeTrace 2.0 and subsequent releases are not currently covered.
Would an uninvolved editor consider adding a short section titled '''Development and releases''' after the existing Functionality section? I have proposed neutral wording below. Please feel free to shorten, modify, or omit details as appropriate for Wikipedia.
=== Proposed article text ===
== Development and releases ==
MicrobeTrace was developed by the U.S. Centers for Disease Control and Prevention to integrate molecular, epidemiological, and demographic data for outbreak investigation and infectious-disease research. The software was described in a 2021 publication in ''PLOS Computational Biology'' as a browser-based, client-side application capable of integrating and visualizing multiple types of outbreak data while allowing analyses to be conducted locally.{{cite journal |last1=Campbell |first1=Ellsworth M. |last2=Boyles |first2=Anthony |last3=Shankar |first3=Anupama |last4=Kim |first4=Jay |last5=Knyazev |first5=Sergey |last6=Cintron |first6=Roxana |last7=Switzer |first7=William M. |title=MicrobeTrace: Retooling molecular epidemiology for rapid public health response |journal=PLOS Computational Biology |date=2021 |volume=17 |issue=9 |pages=e1009300 |doi=10.1371/journal.pcbi.1009300 |pmid=34492010 |pmc=8491948}}
'''MicrobeTrace 2.0''' represented a substantial redesign of the software. The codebase was refactored using Angular and TypeScript, and the 2D network visualization engine was changed from D3.js to Cytoscape.js to improve the rendering and interaction of large networks. The user interface was also redesigned and an example dataset was added to allow users to explore the software without first supplying their own data. Version 2.0 expanded several visualization and analytical functions, including the Bubble, EpiCurve, and Alignment views, temporal visualization through a timeline feature, and grouping of nodes into "metanodes." It also added interoperability with external phylogenetic platforms including Nextstrain and UShER, allowing phylogenetic trees generated by those platforms to be imported into MicrobeTrace and combined with epidemiological or demographic metadata.{{cite journal |last1=Shankar |first1=Anupama |last2=Moscoso |first2=Evan |last3=Cowan |first3=David |last4=Kelly |first4=Reagan |last5=Cintron |first5=Roxana |last6=Al-Naimi |first6=Omar Ali |last7=Switzer |first7=William M. |title=MicrobeTrace 2.0: the enhanced visualization multitool for molecular epidemiology and bioinformatics |journal=Molecular Biology and Evolution |date=2026 |volume=43 |issue=1 |pages=msaf334 |doi=10.1093/molbev/msaf334 |pmid=41479018 |pmc=PMC12828226}}
'''Version 2.1''', released in March 2026, added additional visualization controls, including sizing, font, opacity, and grid-line options for Gantt charts and identification of records lacking geographic information in the Map view. The release also included improvements to dashboard resizing, synchronization of cluster definitions after genetic-distance thresholds are changed, map behavior, and node selection across multiple visualization views.{{cite web |title=Releases: CDCgov/MicrobeTrace – MicrobeTrace v2.1.0 |url=https://github.com/CDCgov/MicrobeTrace/releases |website=GitHub |publisher=Centers for Disease Control and Prevention |date=20 March 2026 |access-date=2 September 2026}}
'''Version 2.2''', released on July 22, 2026, expanded data handling and visualization functionality. The release improved ingestion of large phylogenetic trees in Newick format, including trees imported through Nextstrain, and added additional validation and processing for large tree-derived networks. It introduced global node-shape settings that can be applied consistently across the 2D Network, Map, and Phylogenetic Tree views, together with 46 additional node shapes. Visualization keys for attributes such as node color, link color, node shape, and group color can also be docked within the workspace.{{cite web |title=MicrobeTrace v2.2 |url=https://github.com/CDCgov/MicrobeTrace/releases/tag/v2.2 |website=GitHub |publisher=Centers for Disease Control and Prevention |date=22 July 2026 |access-date=2 September 2026}}
Version 2.2 also expanded controls in the 2D Network, Map, Phylogenetic Tree, Alignment, EpiCurve, Gantt, and Bubble views. Among these changes were subtree exploration and branch-label display in the Phylogenetic Tree view, adjustable sequence ranges in the Alignment view, and additional map and EpiCurve display controls. The release also improved file loading and restoration of saved analyses: MicrobeTrace session files can preserve dashboard layouts, and support was restored for loading compressed MicrobeTrace session archives.
=== Sources ===
- Campbell EM, Boyles A, Shankar A, et al. ''MicrobeTrace: Retooling molecular epidemiology for rapid public health response.'' PLOS Computational Biology. 2021;17(9):e1009300. https://doi.org/10.1371/journal.pcbi.1009300
- Shankar A, Moscoso E, Cowan D, et al. ''MicrobeTrace 2.0: the enhanced visualization multitool for molecular epidemiology and bioinformatics.'' Molecular Biology and Evolution. 2026;43(1):msaf334. https://doi.org/10.1093/molbev/msaf334
- CDCgov/MicrobeTrace release history: https://github.com/CDCgov/MicrobeTrace/releases
- MicrobeTrace v2.2 release notes: https://github.com/CDCgov/MicrobeTrace/releases/tag/v2.2
I recognize that the GitHub release notes are a primary source, so I have tried to limit the proposed 2.1 and 2.2 language to directly verifiable descriptions of release dates and software functionality rather than claims about significance, effectiveness, or impact. I would welcome any changes an uninvolved editor considers necessary for Wikipedia's sourcing, due-weight, and neutral-point-of-view requirements.
Thank you for reviewing this request. ~~~~ ~2026-47669-04 (talk) 19:07, 2 September 2026 (UTC)
