Application Notes

Criteria

Application notes should describe one or more of the following: a new algorithm or computational method, a new experimental method, an improved version of an experimental protocol or computational approach, a new implementation of an existing algorithm, a new software utility, a new data repository, a new web-server, or related. In all cases, the subject matter of an Application note should be characterized by novelty and utility.

Authors are expected to clearly articulate how their work differs from, and why it represents a significant advance over, what is currently available in the literature. Software applications are expected, at a minimum, to provide new functionality or new interfaces, contribute improvements in performance, be available on a new computational platform, etc. In the case of derivative work, authors must clearly acknowledge the work upon which they are building, both published and unpublished.

Pre-publication history

Open and transparent peer review is at the core of Biology Direct’s ethos and as such all published articles include a ‘Reviewers comments’ section presenting both reviewer comments and author responses.

Our authors are responsible for making the peer review history as comprehensible as possible when submitting the final version of their article. Please therefore include the “Reviewers”, “Open peer review” and “Reviewers’ comments” sections described in our guide for authors, once peer review is complete.

Availability of software to reviewers and other researchers

The application described in the manuscript must be available for testing by reviewers. If published, software applications/tools must be freely available to any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement.

Biology Direct strongly recommends, but does not require, that the source code of the software should be made available under a suitable open-source license that will entitle other researchers to further develop and extend the software if they wish to do so.

We recommend that source code and test data of a defined version are available from an appropriate public repository (e.g GitHub, Sourceforge, Bioinformatics.org etc.), or from the authors' laboratory website.

Alternatively, an archive of the source code of the current version of the software should be included with the submitted manuscript as additional files, to ensure that the software will continue to be available.

Since it is likely that the software will continue to be developed following publication, the manuscript should also include a link to the home page for the software project, and we recommend that websites link to the Application note describing the software when published.

Preparing your manuscript

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, institutional addresses and email addresses for all authors
    • if a collaboration group should be listed as an author, please list the group name as an author. If you would like the names of the individual members of the group to be searchable through their individual PubMed records, please include this information in the “Acknowledgements” section in accordance with the instructions below
  • 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.

See the criteria section for this article type (located at the top of this page) for information on abstract and article word limits.

Keywords

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

Implementation

This should include a description of the overall architecture of the software implementation, along with details of any critical issues and how they were addressed. A brief description of the protocol for data collection, data curation and quality control, and what is being reported in the article should be included. The relevant context and the specific issue which the application is intended to address should be clearly described.

The performance and functionality of the application should be discussed and compared with functionally of similar existing software. A discussion of the intended use of the software, and the benefits that are envisioned together should be included, if possible, with an outline for the planned future development of new features.

The implementation section can be broken into subsections with short informative headings. There is no maximum length for this section but we encourage authors to be concise.

Availability and requirements

Lists 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. licence needed

Main text

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

Declarations

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.

Ethics approval and consent to participate

Manuscripts reporting studies involving human participants, human data or human tissue must:

  • include a statement on ethics approval and consent (even where the need for approval was waived)
  • include the name of the ethics committee that approved the study and the committee’s reference number if appropriate

Studies involving animals must include a statement on ethics approval.

See our editorial policies for more information.

If your manuscript does not report on or involve the use of any animal or human data or tissue, this section is not applicable to your submission. Please state “Not applicable” in this section.

Consent for publication

If your manuscript contains any individual person’s data in any form (including individual details, images or videos), consent to publish must be obtained from that person, or in the case of children, their parent or legal guardian. All presentations of case reports must have consent to publish. You can use your institutional consent form or our consent form if you prefer. You should not send the form to us on submission, but we may request to see a copy at any stage (including after publication).

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

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

Availability of data and materials

For all journals, BioMed Central strongly encourages all datasets on which the conclusions of the manuscript rely to be either deposited in publicly available repositories (where available and appropriate) or presented in the main paper or additional supporting files, in machine-readable format (such as spreadsheets rather than PDFs) whenever possible. Please see the list of recommended repositories in our editorial policies.

For some journals, deposition of the data on which the conclusions of the manuscript rely is an absolute requirement. Please check the Criteria section for this article type (located at the top of this page) for journal specific policies.

For all journals, authors must include an “Availability of data and materials” section in their article detailing where the data supporting their findings can be found. If you do not wish to share your data, please state that data will not be shared, and state the reason.

For information on how to cite your data and format this section see preparing your manuscript.

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.

Funding

All sources of funding for the research reported should be declared. The role of the funding body in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript 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.

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.

Group authorship: 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.

Please note that individual names may not be present in the PubMed record at the time a published article is initially included in PubMed as it takes PubMed additional time to code this information.

Authors' information

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.

Endnotes

Endnotes should be designated within the text using a superscript lowercase letter and all notes (along with their corresponding letter) should be included in the Endnotes section. Please format this section in a paragraph rather than a list.

References

For guidance on the appropriate use of references, see our editorial policies.

For information on how to format your references, see preparing your manuscript.

Illustrations and figures (if any)

For information on how to format your figures, see preparing your manuscript.

Tables and captions

For information on how to format your tables, see preparing your manuscript.

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