Software In Bioinformatics

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).Availability of software to reviewers and other researchersThe software application/tool described in the manuscript must be available for testing by reviewers in a way that preserves their anonymity. 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. Because weblinks frequently become broken, BMC Bioinformatics strongly recommends that all software applications/tools are included with the submitted manuscript as additional files to ensure that the software will continue to be available.BMC Bioinformatics 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. Typically, an archive of the source code of the current version of the software should be included with the submitted manuscript as a supplementary file. 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.

For open source projects, we recommend that authors host their project with a recognized open-source repository such as orShould a description of a website be submitted as a software article or a database article?Descriptions of websites and web-based tools should be submitted as software articles if the intention is that the software that drives the website will be made available to other researchers to extend and use on other websites. On the other hand, if a website's functionality is closely tied to a specific database then the article should instead be submitted as a database article. The information below details the section headings that you should include in your manuscript and what information should be within each section.Please note that your manuscript must include a 'Declarations' section including all of the subheadings (please see below for more information).

Title pageThe 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, 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 authorAbstractThe Abstract should not exceed 350 words. Please minimize the use of abbreviations and do not cite references in the abstract. The abstract must include the following separate sections:. Background: the context and purpose of the study. Results: the main findings.

Biological Software

Conclusions: a brief summary and potential implicationsKeywordsThree to ten keywords representing the main content of the article. BackgroundThe Background section should explain the relevant context and the specific issue that the software described is intended to address. ImplementationThis should include a description of the overall architecture of the software implementation, along with details of any critical issues and how they were addressed. ResultsThis should include the findings of the study including, if appropriate, results of statistical analysis which must be included either in the text or as tables and figures. This section may be combined with the Discussion section for Software articles.

Discussion (if appropriate)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. ConclusionsThis should state clearly the main conclusions and provide an explanation of the importance and relevance of the case, data, opinion, database or software reported. Availability and requirementsLists the following:Project name: e.g.

My bioinformatics projectProject home page: e.g. System(s): e.g. Platform independentProgramming language: e.g. JavaOther requirements: e.g. Java 1.3.1 or higher, Tomcat 4.0 or higherLicense: e.g.

GNU GPL, FreeBSD etc.Any restrictions to use by non-academics: e.g. Licence needed List of abbreviationsIf 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':. Ethics approval and consent to participate. Consent for publication.

Software Used In Bioinformatics

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.