Software Article

Software articles should describe a tool likely to be of broad utility that represents a significant advance over previously published software (usually demonstrated by direct comparison with available related software).

Software articles are intended for software developers and advanced analysts who have developed innovative or useful ways of implementing existing methods. Manuscripts should generally be around 5,000 words and describe implementations of models and methods to analyze large-scale assessment data using software tools. It is important that manuscripts include the necessary background, theory, and relevant concepts to understand the implementation or tool and the importance of the submission. Workflows should be well-documented, ideally with a completely worked example (see the Applications section below). All submissions should include examples that are fully reproducible, including data and source code. Alternatively, for relevant tools, detailed supporting documentation of performance (e.g. comprehensive test files and results) should be provided or made available on a free, open-source repository.

Review criteria should include applicability to large-scale assessment, scientific merit, a fully described background, evidence of feasibility and performance, and full reproducibility.

Introduction

The Introduction section should explain the relevant context and the specific issue that the software described is intended to address, what the software does to solve it, what competing software already exists, and how this tool is different.

Background

This section should present underlying theories or necessary background to understand the problem in sufficient detail to appreciate what the tool offers.

About the tool

This should include a short explanation of the basic features of the tool (e.g., a list of functions in an R package, a short description of the steps to use the package, etc), and a description of the overall architecture of the software implementation, along with details of any critical issues and how they were addressed.

Applications

This section contains a basic overview and demonstration of some of the tool’s key features. This would include input (data, .in files, other relevant inputs), a “prototypical” worked example that illustrates how to use the tool, and the results. 

The user interface should be described and a discussion of the intended uses of the software, and the benefits that are envisioned, should be included, together with data on how its performance and functionality compare with, and improve, on functionally similar existing software. A case study of the use of the software may be presented. The planned future development of new features, if any, should be mentioned.

Conclusions

This should state clearly the main conclusions and provide an explanation of the importance and relevance of the software reported.

Title page

The title page should:

• present a title that includes, if appropriate, the research design or for non-research studies: a description of what the article reports
• list the full names and institutional addresses for all authors
  • if a collaboration group should be listed as an author, please list the Group name as an author and include the names of the individual members of the Group in the “Acknowledgements” section in accordance with the instructions below
  • Large Language Models (LLMs), such as ChatGPT, do not currently satisfy our authorship criteria. Notably an attribution of authorship carries with it accountability for the work, which cannot be effectively applied to LLMs. Use of an LLM should be properly documented in the Methods section (and if a Methods section is not available, in a suitable alternative part) of the manuscript
• indicate the corresponding author

Abstract

The abstract should briefly summarize the aim, findings or purpose of the article. Please minimize the use of abbreviations and do not cite references in the abstract.

Keywords

Three to ten keywords representing the main content of the article.

Introduction

The Introduction section should explain the background to the article, its aims, a summary of a search of the existing literature and the issue under discussion.

Main text

This should contain the body of the article, and may also be broken into subsections with short, informative headings.

Conclusions

This should state clearly the main conclusions and include an explanation of their relevance or importance to the field.

List of abbreviations

If abbreviations are used in the text they should be defined in the text at first use, and a list of abbreviations should be provided.

All manuscripts must contain the following sections under the heading 'Declarations':

• Availability of data and materials
• Competing interests
• Funding
• Authors' contributions
• Acknowledgements
• Authors' information (optional)

Please see below for details on the information to be included in these sections.

If any of the sections are not relevant to your manuscript, please include the heading and write 'Not applicable' for that section.

Availability of data and materials

All manuscripts must include an ‘Availability of data and materials’ statement. Data availability statements should include information on where data supporting the results reported in the article can be found including, where applicable, hyperlinks to publicly archived datasets analysed or generated during the study. By data we mean the minimal dataset that would be necessary to interpret, replicate and build upon the findings reported in the article. We recognise it is not always possible to share research data publicly, for instance when individual privacy could be compromised, and in such instances data availability should still be stated in the manuscript along with any conditions for access.

Data availability statements can take one of the following forms (or a combination of more than one if required for multiple datasets):

• The datasets generated and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS]
• The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.
• All data generated or analysed during this study are included in this published article [and its supplementary information files].
• The datasets generated and/or analysed during the current study are not publicly available due [REASON WHY DATA ARE NOT PUBLIC] but are available from the corresponding author on reasonable request.
• Data sharing is not applicable to this article as no datasets were generated or analysed during the current study.
• The data that support the findings of this study are available from [third party name] but restrictions apply to the availability of these data, which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of [third party name].
• Not applicable. If your manuscript does not contain any data, please state 'Not applicable' in this section.

More examples of template data availability statements, which include examples of openly available and restricted access datasets, are available here.

SpringerOpen  also requires that authors cite any publicly available data on which the conclusions of the paper rely in the manuscript. Data citations should include a persistent identifier (such as a DOI) and should ideally be included in the reference list. Citations of datasets, when they appear in the reference list, should include the minimum information recommended by DataCite and follow journal style. Dataset identifiers including DOIs should be expressed as full URLs. For example:

Hao Z, AghaKouchak A, Nakhjiri N, Farahmand A. Global integrated drought monitoring and prediction system (GIDMaPS) data sets. figshare. 2014. http://dx.doi.org/10.6084/m9.figshare.853801

With the corresponding text in the Availability of data and materials statement:

The datasets generated during and/or analysed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS].^{[Reference number]}

If you wish to co-submit a data note describing your data to be published in BMC Research Notes, you can do so by visiting our submission portal. Data notes support open data and help authors to comply with funder policies on data sharing. Co-published data notes will be linked to the research article the data support (example).

Competing interests

All financial and non-financial competing interests must be declared in this section.

See our editorial policies for a full explanation of competing interests. If you are unsure whether you or any of your co-authors have a competing interest please contact the editorial office.

Please use the authors’ initials to refer to each authors' competing interests in this section.

If you do not have any competing interests, please state "The authors declare that they have no competing interests" in this section.

Funding

All sources of funding for the research reported should be declared. If the funder has a specific role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript, this should be declared.

Authors' contributions

The individual contributions of authors to the manuscript should be specified in this section. Guidance and criteria for authorship can be found in our editorial policies.

Please use initials to refer to each author's contribution in this section, for example: "FC analyzed and interpreted the patient data regarding the hematological disease and the transplant. RH performed the histological examination of the kidney, and was a major contributor in writing the manuscript. All authors read and approved the final manuscript."

Acknowledgements

Please acknowledge anyone who contributed towards the article who does not meet the criteria for authorship including anyone who provided professional writing services or materials.

Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements section.

See our editorial policies for a full explanation of acknowledgements and authorship criteria.

If you do not have anyone to acknowledge, please write "Not applicable" in this section.

Group authorship (for manuscripts involving a collaboration group): if you would like the names of the individual members of a collaboration Group to be searchable through their individual PubMed records, please ensure that the title of the collaboration Group is included on the title page and in the submission system and also include collaborating author names as the last paragraph of the “Acknowledgements” section. Please add authors in the format First Name, Middle initial(s) (optional), Last Name. You can add institution or country information for each author if you wish, but this should be consistent across all authors.

Authors' information

This section is optional.

You may choose to use this section to include any relevant information about the author(s) that may aid the reader's interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.

Footnotes

Footnotes should be designated within the text using a superscript number. It is not allowed to use footnotes for references/citations.