Journal of Cheminformatics will only publish research or software that is entirely reproducible by third parties. This means that any datasets, software and algorithms that are required to reach the conclusions stated in the paper must be provided as supplemental materials, or be otherwise accessible without the need for registration, login or agreement with license terms other than Creative Commons licenses for data and text and OSI-approved Open Source Licenses for software. For any software, the source code must be provided.
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 researchers
The 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 and anonymously available under an OSI-approved Open Source license to any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement or a registration to access the package. Because weblinks frequently become broken, Journal of Cheminformatics 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. If not possible, weblinks should be archived in the Internet Archive.
Journal of Cheminformatics requires 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 gitlab.com, github.com, bioinformatics.org or sourceforge.net.
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.
Because software should be easy to reuse, the quality of the software will be assessed in the review process too. Minimally, a source code distribution must include documentation that states the software license(s), the list of authors (and/or copyright owners). Ideally, it also includes instructions on how to compile (if applicable) and run your code. Second, we strongly encourage to archive the specific version of the software on Zenodo or something equivalent, see for example this GitHub guideline. Authors are encourage to read and use suggestions from these papers, while reviewers are encourage to assess these aspects, where they will improve the software:
- Ten Simple Rules for Developing Usable Software in Computational Biology
- Ten Simple Rules for Taking Advantage of Git and GitHub
- Ten Simple Rules for the Open Development of Scientific Software
- Ten Simple Rules for Reproducible Computational Research
- Ten simple rules to make your computing more environmentally sustainable
A graphical abstract can be supplied which, together with the article title, should provide the reader with a visual description of the type of chemistry covered in the article. The graphical abstract should be 920 x 300 pixels and a maximum of 150KB jpeg, png or svg file. Authors are encouraged to make judicious use of colour in graphical abstracts. All graphical abstracts should have a white background and where possible should fill the available width.
Citation Typing Ontology pilot
The Journal of Cheminformatics started a pilot using the Citation Typing Ontology (http://purl.org/spar/cito) to annotate citations in articles with the reason why that paper is cited. For software papers, authors should annotation citations to articles about the software used in this article with cito:usesMethodIn. For more information, please see here.