Call for Papers: Software Tools and Resources 2025 Special Issue in Honor of Margaret Dayhoff

The Journal of Proteome Research is welcoming submissions for its Fourth Biennial Special Issue on Software Tools and Resources. The Special Issue will be dedicated to Margaret Dayhoff, a pioneer in bioinformatics, and will be published in March 2025 in honor of her 100^th birthday.

Software tools and data resources are essential to research in all omics domains, including proteomics and metabolomics. The goal of this recurring special issue is to highlight the latest novel and significantly updated software tools, web applications, and databases scientists can use for data analysis and visualization in proteomics and related research.

For readers, this provides an easily identifiable source of tools specifically reviewed for their applicability and ease of adoption. For authors, this provides increased visibility and wider adoption of their tools within the proteomics community through dissemination and documentation.

For inclusion in this special issue, authors must present either a complete description of a relevant novel tool, library, web application, or database (article) or a substantial and meaningful update of a previously published tool or resource (technical note). The full working tool or database must be available free-of-charge to editors and reviewers for evaluation at the time of manuscript submission.

Tools with a graphical or web browser interface are preferred, but the editors will also consider well-documented web service APIs or libraries of functional building blocks for custom data analysis pipelines.

The deadline for submissions is September 30, 2024.

Organizing Editors

Magnus Palmblad, Associate Editor, Journal of Proteome Research
Leiden University Medical Center, The Netherlands

Michael Hoopmann, Guest Editor
Institute for Systems Biology, United States

Viktoria Dorfer, Guest Editor
University of Applied Sciences Upper Austria, Austria

Author Instructions

Manuscripts must be submitted by September 30, 2024 for inclusion in this Special Issue. Submissions must adhere to the appropriate Author Guidelines and the further details laid out in this Perspective article.

Authors, please:

• Indicate in your cover letter that the manuscript is for the Special Issue on Software Tools and Resources and explain why you consider it suitable for this Special Issue.
• Remember that the full working tool or database must be available free-of-charge to editors and reviewers for evaluation at the time of manuscript submission.
• Be concise and focus the manuscript on the unique or novel functionality of the tool. It should be clear to any reader what problem the system addresses and how it is used.
• For tools and libraries, use the table form to describe the input, operations, and output of each tool or function. A screenshot of the interface may be included if it has novel or unusual features.

Learn More

Explore previous editions of our Software and Tools Special Issues from 2019, 2021, 2023, and read the 2023 Editorial by Magnus Palmblad, Michael Hoopmann, and Veit Schwämmle.

How to Submit

• Log in to the ACS Paragon Plus submission site.
• Choose The Journal of Proteome Research.
• Select your manuscript type, and under "Special Issue Selection," choose “Software Tools and Resources 2025.”

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