Software Article

Software Article

Criteria

Software articles should describe a tool with broad utility that represents a significant advancement over existing software. This should be demonstrated by directly comparing it to available related software.

Availability of software to reviewers and other researchers
The software described in the manuscript must be available for anonymous testing by reviewers.

  • Upon publication, the software must be freely available for non-commercial use without restrictions like material transfer agreements.
  • Include the software as an additional file with the submitted manuscript. This is strongly recommended to ensure continued availability due to potential link rot.

While not required, IJOMAHIP recommends making the source code available under an open-source license, allowing other researchers to develop and extend the software.

  • Include an archive of the source code of the current version as a supplementary file.
  • Provide a link to the software project’s homepage in the manuscript.
  • For open-source projects, hosting the project on a recognized open-source repository like bioinformatics.org or sourceforge.net is recommended.

Website description as a software or database article

Submit website and web-based tool descriptions as software articles if the goal is to allow other researchers to extend and use the underlying software on other websites. If a website’s functionality is tightly linked to a specific database, submit the article as a database article.

Data sharing
IJOMAHIP strongly promotes open research, including transparency in reporting. More about our Data and Materials Availability Policy  can be found on the journal’s About page.

Preparing your manuscript

Your manuscript must include specific section headings, with each section containing the required information. Crucially, you must include a “Declarations” section with all of its specified subheadings (see below for details).

Title page

The title page should:

  • present a title that includes, if appropriate, the study design e.g.:
    • “A versus B in the treatment of C: a randomized controlled trial”, “X is a risk factor for Y: a case control study”, “What is the impact of factor X on subject Y: A systematic review”
    • or for non-clinical or 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, list the Group name as an author. To make individual members of the Group searchable through their individual IJOMAHIP records, include this information in the “Acknowledgements” section.
    • Large Language Models (LLMs), such as ChatGPT, do not meet authorship criteria. Accountability for the work is a key component of authorship, which LLMs cannot effectively fulfill. Any use of an LLM must be documented in the Methods section (or a suitable alternative part) of the manuscript.
  • indicate the corresponding author

Abstract

The Abstract should not exceed 300 words. Minimize abbreviations and do not include references. Include these separate sections:

  • Background: the study context and purpose
  • Methods: study design and statistical tests
  • Results: the main findings
  • Conclusions: the summary and potential implications

Keywords

  • Three to seven keywords representing the main content of the article.

Introduction

  • The Introduction section should explain the relevant context and the specific issue that the software described is intended to address.

Implementation

  • Describe the overall architecture of the software.
  • Detail any critical issues encountered during implementation and how they were resolved.

Results

  • Present the study’s findings, including results of statistical analyses (either in the text, tables, or figures).
  • For software articles, this section can be combined with the Discussion section.

Discussion (if appropriate)

  • Describe the user interface.
  • Discuss the software’s intended uses and anticipated benefits.
  • Compare the software’s performance and functionality to functionally similar existing software, highlighting improvements.
  • A case study demonstrating the use of the software may be included.
  • Mention any planned future development of new features.

Conclusions This should clearly state the main conclusions and explain the study’s importance and relevance of the case, data, opinion, database or software reported.

Availability and requirements

  • List the following:

         Project name: e.g. My bioinformatics project
         Project home page: e.g. http://sourceforge.net/projects/mged
         Operating system(s): e.g. Platform independent
         Programming language: e.g. Java
         Other requirements: e.g. Java 1.3.1 or higher, Tomcat 4.0 or higher
         License: e.g. GNU GPL, FreeBSD etc.
         Any restrictions to use by non-academics: e.g. license needed

List of abbreviations

  • Define any abbreviations used in the text upon their first use and include a comprehensive list of all abbreviations used.

Declarations

All manuscripts are required to include a section titled ‘Declarations’ which must contain the following:

  • Ethics approval and consent to participate
  • Consent for publication
  • Availability of data and materials
  • Competing interests
  • Funding
  • Authors’ contributions
  • Acknowledgements
  • Authors’ information (optional)

Refer to the information below for details on what to include in each section. If a section is not relevant to your manuscript, include the heading and state “Not applicable.”

Ethics approval and consent to participate

For manuscripts reporting studies involving human participants, human data, or human tissue:

  • Include a statement on ethics approval and consent, even if approval was waived.
  • Provide the name of the ethics committee that approved the study and the committee’s reference number, if applicable.

For studies involving animals:

  • Include a statement on ethics approval.
  • For experimental studies involving client-owned animals, include a statement on informed consent from the client or owner.

See our editorial policies for further details.

If your manuscript does not involve animal or human data or tissue, state “Not applicable” in this section.

Consent for publication

If your manuscript includes any individual person’s data (details, images, videos, etc.), you must obtain consent for publication from that person, or their parent/guardian if they are a child. Consent is required for all case reports.

  • You can use your institutional consent form or our form. Do not submit the form with your manuscript, but be prepared to provide it upon request (even after publication).

See our editorial policies for detailed information on consent for publication.

If your manuscript does not contain data from any individual person, state “Not applicable” in this section.

Availability of data and materials

All research papers must contain a section called “Availability of data and materials.” This section should detail where the data supporting the paper’s findings can be accessed. If the data is publicly available, provide links to the online archives. “Data” refers to the minimum amount necessary to understand, reproduce, and expand upon the research. We understand that data sharing is not always possible due to privacy or other concerns. In these cases, the data availability statement should explain why the data is not publicly available and describe any conditions for accessing it.

Authors are also encouraged to archive their search strategies on searchRxiv (https://searchrxiv.org/). This platform allows researchers to store, share, and cite their search strategies by providing a DOI.

Your “Availability of data and materials” section should use one of the following statements (or a combination if multiple datasets have different access conditions):

  • Public Repository: “The datasets generated and/or analyzed during this study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS]”
  • Available Upon Request: “The datasets used and/or analyzed during this study are available from the corresponding author upon reasonable request.”
  • Included in Publication: “All data generated or analyzed during this study are included in this published article and its supplementary information files].”
  • Not Publicly Available (with explanation): “The datasets generated and/or analyzed during the current study are not publicly available due to [REASON WHY DATA ARE NOT PUBLIC] but are available from the corresponding author on reasonable request.”
  • No Data Generated/Analyzed: “Data sharing is not applicable to this article as no datasets were generated or analyzed during the current study.”
  • Third-Party Restrictions: “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 (No Data): “Not applicable. If your manuscript does not contain any data, please state ‘Not applicable’ in this section.”

IJOMAHIP strongly encourages you to cite any publicly available data that your paper’s conclusions depend on. These citations should be included in the manuscript and, ideally, in the reference list. Data citations must include a persistent identifier, such as a DOI, expressed as a full URL. When including datasets in your reference list, provide the minimum information recommended by DataCite, formatted according to the journal’s style.

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 analyzed during the current study are available in the [NAME] repository, [PERSISTENT WEB LINK TO DATASETS].[Reference number] 

Competing interests

  • You must declare all financial and non-financial competing interests. Refer to the editorial policies for a detailed explanation. Contact the editorial office if you are unsure whether a conflict exists.
  • Use author initials when describing each author’s competing interests.
  • If no competing interests exist, state: “The authors declare that they have no competing interests.”

Funding

  • Declare all funding sources for the research.
  • If the funder influenced the study’s conceptualization, design, data collection, analysis, publication decision, or manuscript preparation, specify their role.

Authors’ contributions

  • Clearly state each author’s specific contributions to the manuscript. Refer to the editorial policies for authorship guidelines.
  • Use initials to indicate each author’s contribution. Example: “FC analyzed the data… RH performed the histological examination… All authors read and approved the final manuscript.”

Acknowledgements

  • Acknowledge anyone who contributed to the article but doesn’t meet authorship criteria. This includes those who provided writing assistance or materials.
  • Obtain permission from individuals before including them in the Acknowledgements section.

Refer to our editorial policies for detailed information on acknowledgements and authorship criteria.

  • If no one needs to be acknowledged, state “Not applicable” in the Acknowledgements section.

Group Authorship:

  • For collaborative manuscripts, to ensure individual members of a collaboration group are searchable, include the collaboration group’s title on the title page and in the submission system.

List collaborating author names in the last paragraph of the “Acknowledgements” section, using the format: First Name, Middle initial(s) (optional), Last Name. Include institution or country information for each author, ensuring consistency across all authors if provided.

Authors’ information (Optional)

  • This section allows you to provide context about the author(s) to help readers better understand the article and the authors’ perspectives.
  • This may include qualifications, current positions at institutions or societies, or other relevant background information.
  • Use author initials when referring to authors.
  • Do not include any information about competing interests in this section.

Footnotes

  • Use footnotes for additional information, including citations of references already in the reference list.
  • Footnotes should not only contain a reference citation, nor should they include complete bibliographic details of a reference. Do not include figures or tables in footnotes.
  • Number text footnotes consecutively. Use superscript lowercase letters (or asterisks for significance values) for table footnotes.
  • Do not use reference symbols for footnotes to the title or authors.
  • Always use footnotes instead of endnotes

References

For Medical research, use the International Committee of Medical Journal Editor (ICMJE) recommendations while for Health Sciences-related research, use the American Psychological Association (APA) reference style.

See our Editorial Policies for author guidance on good citation practice

Figures, tables and additional files

See Author Guidelines for information on how to format figures, tables and additional files.

Submit Software Article