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Focus and Scope

The Journal of Open Research Software (JORS) features peer reviewed Software Metapapers describing research software with high reuse potential. We are working with a number of specialist and institutional repositories to ensure that the associated software is professionally archived, preserved, and is openly available. Equally importantly, the software and the papers will be citable, and reuse will be tracked.

JORS also publishes full-length research papers that cover different aspects of creating, maintaining and evaluating open source research software. The aim of the section is to promote the dissemination of best practice and experience related to the development and maintenance of reusable, sustainable research software.

See below for submission guidelines and peer-review criteria for each section.


Publication Frequency

This journal publishes continuously, with papers coming online as soon as they have passed peer review.


Open Access Policy

This journal provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge.

Authors of articles published in Journal of Open Research Software remain the copyright holders and grant third parties the right to use, reproduce and share the article according to the Creative Commons license agreement.

Authors are encouraged to publish their data in recommended repositories. For a list of generic and subject specific repositories that meet our peer review criteria, see here.


Archiving Policy

The journal’s publisher, Ubiquity Press, focuses on making content discoverable and accessible through indexing services. Content is also archived around the world to ensure long-term availability.

Ubiquity Press journals are indexed by the following services:#

In addition, all journals are available for harvesting via OAI-PMH.

To ensure permanency of all publications, this journal also utilises CLOCKSS, and LOCKSS archiving systems to create permanent archives for the purposes of preservation and restoration.

If Journal of Open Research Software is not indexed by your preferred service, please let us know by emailing support@ubiquitypress.com or alternatively by making an indexing request directly with the service.


Recommended Repositories

A list of repositories that meet our peer-review requirements and are recommended for the archiving of JORS software is maintained below. Please contact us if you would like to recommend that we add a particular repository to our list. The software described in your metapaper must be placed in a publicly accessible repository. There are two main types of repository which have slightly different purposes:
  • A source code repository holds many versions of the software as it being developed
  • A preservation or institutional repository will preserve a set of files deposited for the long term

We require that the version of software described in your software is available in at least one repository that satisfies the criteria below. Ideally the software will be available through both types of repository. A good source code repository for software should:

  • Allow the deposit of software under the correct licence
  • Provide a unique, persistent identifier which references a particular version of the source code
  • Has a published backup policy and terms of service that do not allow deletion without warning
  • Have a sound business/sustainability model
A good preservation repository for software should:
  • Allow the deposit of software under the correct licence
  • Provide a unique, persistent identifier (e.g. a DOI) which references the deposited software
  • Have a published preservation strategy that guarantees long term preservation
We recommend the repositories below. 
 

Location: http://www.assembla.com

Focus and Suitability: Assembla has a strong following amongst smaller companies and has extensive project-management facilities in addition to software-development services.

Cost: Assembla offers free, full-featured workspaces and portfolios for open source and publicly visible community projects (details).

Licenses: tbc

Identifiers Used: URI

Sustainability: Assembla is well established, with 500,000 users in 100+ countries.

Deposit Instructions: To deposit software associated with a JORS software paper in Assembla, please follow these steps.

  • Create a project in Assembla and upload your code.
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When the software has been made public on the Assembla site, it will be assigned a URI. Please enter this in your JORS software paper under Code Repository Location.
  • Once your JORS paper has passed peer review and been published, please add the DOI of the paper to the information about the code in Assembla.

Location: http://www.codeplex.com

Focus and Suitability: Codeplex is the base for many Windows and Ajax related projects.

Cost: Codeplex is a free open source project hosting site.

Licenses: Codeplex supports the following OSI licenses (details).

  • Apache License 2.0
  • Common Development and Distribution License (CDDL)
  • Eclipse Public License (EPL)
  • GNU General Public License (GPL) v2
  • GNU Lesser General Public License (LGPL)
  • Microsoft Public License (Ms-PL)
  • Microsoft Reciprocal License (Ms-RL)
  • Mozilla Public License 1.1 (MPL)
  • New BSD License
  • The MIT License

Identifiers Used: URI

Sustainability: Codeplex is hosted by MicroSoft.

Deposit Instructions: To deposit software associated with a JORS software paper in Codeplex, please follow these steps.

  • Create a project in Codeplex and upload your code.
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When the software has been made public on the Codeplex site, it will be assigned a URI. Please enter this in your JORS software paper under Code Repository Location.
  • Once your JORS paper has passed peer review and been published, please add the DOI of the paper to the information about the code in Codeplex.

Location: http://figshare.com

Focus and Suitability: Figshare takes software from all subject areas, and is suitable for small to medium sized projects that do not require specialised curation.

Cost: Free. "Figshare gives users unlimited public space and 1GB of private storage space for free."

Licenses: "All figures, media and multiple file uploads are published under a CC-BY license.All datasets are published under CC0."

Identifiers Used: Handle

Sustainability: "Figshare is an independent body that receives support from Digital Science. 'Digital Science's relationship with figshare represents the first of its kind in the company's history: a community- based, open science project that will retain its autonomy whilst receiving support from the division.'"

Deposit Instructions: To deposit software associated with a JORS software paper in figshare, please follow these steps.

  • Create an account with figshare.
  • Upload your software as either a fileset (most appropriate if you have multiple files) or a dataset.
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When the software has been made public on the figshare site, it will be assigned a handle identifier. Please enter this in your JORS software paper under Repository Location.
  • Once your JORS paper has passed peer review and been published, please add the reference to the description field in figshare, and add the JORS DOI to the links also.

Location: http://github.com

Focus and Suitability: GitHub provides a more developer-focussed environment (as opposed to a project-focussed one). It is developing a strong following in the biosciences.

Cost: Free accounts can have as many public repos as you'd like, with unlimited collaboration (details).

Licenses: tbc

Identifiers Used: URI

Sustainability: GitHub is currently the largest code host in the world.

Deposit Instructions: To deposit software associated with a JORS software paper in GitHub, please follow these steps.

  • Create a GitHub repository and upload your code.
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When the software has been made public on the GitHub site, it will be assigned a URI. Please enter this in your JORS software paper under Code Repository Location.
  • Once your JORS paper has passed peer review and been published, please add the DOI of the paper to the information about the code in GitHub.
 
Location: https://gitlab.com

Focus and Suitability: As well as providing the platform for many university code repositories, GitLab provides their own hosting service with built in issue trackers and continuous integration and unlimited public and private repositories.

Cost: Free accounts can have as many public and private repos as you'd like, with unlimited collaboration, but CI services are limited on private repos (details: https://about.gitlab.com/gitlab-com/).

Licenses: All open source licenses allowed

Identifiers Used: URL

Sustainability: GitLab is used by many institutions and companies.

Deposit Instructions: To deposit software associated with a JORS software paper in GitLab, please follow these steps:

  • Create a GitLab repository and upload your code.
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When the software has been made public on the GitLab site, it will be assigned a URL (e.g.https://gitlab.com/myid/myname). Please enter this in your JORS software paper under Code Repository Location.
  • Once your JORS paper has passed peer review and been published, please add the DOI of the paper to the information about the code in GitLab.

Location: http://code.google.com

Focus and Suitability: Google provides Project Hosting. Google Code does not allow access from some countries, most notably Iran and Syria.

Cost: Project Hosting on Google Code provides a free collaborative development environment for open source projects.

Licenses: Google Code allows the following licences (details).

  • Apache License, 2.0 (Apache-2.0)
  • BSD 3-Clause "New" or "Revised" license (BSD-3-Clause)
  • BSD 3-Clause "Simplified" or "FreeBSD" license (BSD-2-Clause)
  • GNU General Public License (GPL)
  • GNU Library or "Lesser" General Public License (LGPL)
  • MIT license (MIT)
  • Mozilla Public License 2.0 (MPL-2.0)
  • Common Development and Distribution License (CDDL-1.0)
  • Eclipse Public License (EPL-1.0)

Identifiers Used: URI

Sustainability: The repository benefits from a large community since it is used to host most Google projects and the Google Summer of Code projects.

Deposit Instructions: To deposit software associated with a JORS software paper in Google Code, please follow these steps.

  • Create a project in Google Codeand upload your code.
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When the software has been made public on the Google Code site, it will be assigned a URI. Please enter this in your JORS software paper under Code Repository Location.
  • Once your JORS paper has passed peer review and been published, please add the DOI of the paper to the information about the code in Google Code.

Location: http://launchpad.net

Focus and Suitability: "Launchpad is a unique collaboration and hosting platform for software projects. It brings communities together - regardless of their choice of tools — by making it easy to share code, bug reports, translations and ideas across projects."

Cost: Launchpad is free of charge for free software projects (details).

Licenses: tbc

Identifiers Used: URI

Sustainability: Launchpad is hosted by Canonical and lists some significant projects as users, such as Ubuntu and MySQL.

Deposit Instructions: To deposit software associated with a JORS software paper in Launchpad, please follow these steps.

  • Create a project in Launchpad and upload your code.
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When the software has been made public on the Launchpad site, it will be assigned a URI. Please enter this in your JORS software paper under Code Repository Location.
  • Once your JORS paper has passed peer review and been published, please add the DOI of the paper to the information about the code in Launchpad.

Location: http://savannah.gnu.org

Focus and Suitability: Savannah hosts the majority of GNU software and some non-GNU software. Savannah's focus is on hosting for free software projects. To ensure that only free software is hosted, Savannah implements very strict hosting policies, including a ban against the use of non-free formats (such as Macromedia Flash).

Cost: Savannah is free to use.

Licenses: GNU General Public License (GPL) and GNU Library or "Lesser" General Public License (LGPL)

Identifiers Used: URI

Sustainability: Savannah is operated by the Free Software Foundation, with over 3,400 projects.

Deposit Instructions: To deposit software associated with a JORS software paper in Savannah, please follow these steps.

  • Create a project in Savannah and upload your code.
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When the software has been made public on the Savannah site, it will be assigned a URI. Please enter this in your JORS software paper under Code Repository Location.
  • Once your JORS paper has passed peer review and been published, please add the DOI of the paper to the information about the code in Savannah.

Location: http://eprints.ucl.ac.uk/

Focus and Suitability: UCL Discovery showcases UCL's research outputs, giving access to journal articles, book chapters, conference proceedings, digital web resources, theses, datasets, software and much more, from all UCL disciplines. The repository also enables UCL researchers to comply with research funder policies on open access.

Cost: Free to UCL researchers.

Licenses: All open licences permitted

Identifiers Used: DOI

Sustainability: SUCL Discovery is maintained by UCL, a major international research institution ranked seventh in the world's top ten universities by the QS World University Rankings (2011).

Deposit Instructions: Depositing data associated with a JORS data paper in UCL Discovery is currently done manually.

  • Log in to the UCL RPS system.
  • Follow the general guide to depositing, with the following modifications:
  • Expand the publications window so that it includes software, and click 'Add new'.
  • If your software consists of more than one file, please compress these into one zip file and upload this.
  • Place your licence information in the Notessection. Example text: "This software is licensed under a GNU General Public License (GPL)."
  • Check that your deposit also conforms to the JORS peer review requirements.
  • When your software has been made public on the UCL discovery site, notify the JORS editor and you will receive a DOI. Please enter this in the DOI field.
  • Once your JORS paper has passed peer review and been published, please enter the reference for it into the Notes section in UCL Discovery (e.g. 'This software is described in the following software paper: …').

Location: https://zenodo.org

Focus and Suitability: Zenodo takes software from all subject areas, and is suitable for all projects. It also supports automated import from GitHub, DOI versioning and reservation of DOIs.

Cost: Free. Maximum deposit per project is 50GB.

Licenses: Supports range of licenses, including (but not exclusively) CC-BY and CC0.

Identifiers Used: DOI

Sustainability: Zenodo is hosted by CERN, and supported the EU through the OpenAire project.

Deposit Instructions: To deposit software associated with a JORS software paper which has been developed in GitHub in Zenodo, please follow these steps.

  • Log in to Zenodo with your GitHub account.
  • Check that your software conforms to the JORS peer review requirements.
  • Use their automated uploader (https://zenodo.org/account/settings/github/) to start preserving your code
  • Your software will be assigned a DOI by Zenodo. Please enter this in your JORS software paper under Repository Location.

FAQ: Software Metapapers

What kinds of software can I publish?

All kinds of software are welcome. We are particularly interested in software that may have reuse potential or which is required to validate your research. Many research outputs meet these requirements. For example:

  • simulation models
  • data analysis tools
  • function libraries
  • software infrastructure
  • software you've written that is used in a published paper
  • etc.

What is a software paper?

A software paper is a publication designed to make other researchers aware of software or data of potential use to them. As such it describes what problem the software addresses, how it was implemented and architected, where it is stored, and its reuse potential. It is important to note that a software paper does not replace a research article, but rather complements it. When mentioning the software behind a study, a research paper should reference the software paper for further details. The software paper similarly should contain references to any research papers associated with the software. This also enables the software paper to be published before the research papers, if this is appropriate.

How do I submit a software paper?

Please see our ‘how to submit a software paper’ page. JORS has an online system that leads you through the process, or you can complete a document template.

How does the JORS peer review work?

Please see our overview of the peer review process. The aim of the peer review process is to ensure the accessibility of the software and correctness of the metadata associated with the software so that it is reusable by others. It does not aim to check that the software is efficient, only that it is possible for someone else to understand how to build and deploy the software, as well as being able to understand whether the software is operating as expected.

Which open license should I apply to my software?

We recommend that software in JORS has an Open Source Initiative (OSI) approved license to encourage reuse.

Commonly used OSI approved licenses include:

In addition, it is possible to use the Creative Commons Zero (CC0) (aka Public Domain) license. The advantage of this license is that many institutional repositories already support this license during the deposit process. The disadvantage of this license is that you have completely waived all rights you might have to the software.

All of the above licenses carry an obligation for anyone using the software to properly attribute it. The less restrictive your license, the greater the potential for reuse.

We do not recommend licenses that impose commercial or other restrictions on the use of software. Generally, such licenses can prevent use of software by charities and the media, and make the remixing of software from various international sources legally problematic. There are of course some situations in which software must have a more restrictive license (e.g. funder requirements), and the editorial team will consider these on a case-by-case basis.

Which repositories do you recommend for depositing software?

Please see our list of recommended repositories for examples. Other repositories may be acceptable, provided they meet the criteria below. Please contact us if you would like to discuss adding a new repository to the recommended list.

What are the criteria for a repository to be accepted as suitable?

Software must be made available via a suitable repository. To meet our acceptance criteria, repositories must:

  • be suitable for the type of software involved
  • be sustainable (i.e. it must have funding and plans in place to ensure the long-term preservation of the data)
  • allow open licences
  • provide persistent identifiers (e.g. DOI, handle, ARC etc.)

We are currently working with a number of repositories to better streamline the process of depositing software into a repository.

What does ‘open’ mean?

The term ‘open’ in this context is well described by the Open Knowledge Foundation: “A piece of content or data is open if anyone is free to use, reuse, and redistribute it — subject only, at most, to the requirement to attribute and share-alike.”

What are the benefits of publishing software?

Allowing others to reuse your software is both of benefit to you, and to the research community in general.

By publishing your software, others can scrutinise your code and reproduce your results. They can build on this software to look at new kinds of studies. They can use this for other purposes such as teaching, journalism and citizen science. And they can cite your software when they do.

At the same time open software is important for good science:

Making research outputs available for others to work with and build upon is part of the social contract of academia. Software papers mean that software you have released can be cited and that those citations can be tracked. This is not only an indirect measure of impact and therefore important for career progression, but it can also help you understand who is using the software, and lead to new collaborations.

How do I cite software?

If you use software from a repository that has been released under an open license then you are obliged to cite it (even under a CC0 license). By citing the software paper you also reward the author for sharing their data, as these citations can be tracked as for any scholarly paper (unfortunately there is no system for tracking the software citations themselves yet, which is another reason that a software paper is so useful). You should therefore include a reference to the software paper describing the software, followed by a reference to the software in the repository itself. In order for this to work it is essential that the citations are in the references section of the article and include the DOIs (or any other identifier the repository might use), e.g.:

References
Jackson, M. et al. 2012. OGSA-DAI REST 4.2.1. Journal of Open Research Software 1(1), DOI: http://dx.doi.org/10.5334/xxxxxx

How you do cite the software itself?

This very much depends upon the style guidelines recommended for your paper. If there is a recommended citation then use it. If there is no recommended citation from the software publishers, then Mike Jackson from the Software Sustainability Institute has suggested the following examples based on examples from other publishers and inspired by DataCite’s guide on “why cite data?”.

Software purchased off-the-shelf:

  • ProductName. Version. ReleaseDate. Publisher. Location.
  • SuperScience. 1.2. December 2012. ResearchSoftware. Edinburgh, UK.

Software downloaded from the web:

  • ProductName. Version. ReleaseDate. Publisher. Location. DOIorURL. DownloadDate.
  • OGSA-DAI REST. 4.2.1. December 2012. OGSA-DAI Project. http://sourceforge.net/projects/ogsa-dai. 27/04/2012.

Software checked-out from a public repository:

  • ProductName. Publisher. URL. CheckoutDate. RepositorySpecificCheckoutInformation.
  • OGSA-DAI REST. OGSA-DAI Project. http://sourceforge.net/projects/ogsa-dai. 27/04/2012. Check-out: ogsa-dai/branck/ogsadai4.1/, revision 1657.

Software provided by a researcher:

  • ProductName. Author. Location. ContactDetails. ReceivedDate.
  • BestFFTroutine ever file. Fred Bloggs, EPCC, The University of Edinburgh, UK. Fred.bloggs@epcc.ed.ac.uk. 27/04/2012.

How do I define authorship?

Although the question of authorship for software in general is complex, when submitting a software paper to JORS the authorship of the software should be considered the list of authors currently recognised on that version of the software. It may be useful to place the product manager / community liaison / project lead (i.e. the person who at that time is most likely to answer queries about the software) as the first named author. In some cases, authorship is considered to be part of a collective project, in which case it is this project or foundation which is the author.

Can I submit a software paper on behalf of software which I have not authored?

Whilst this is unusual, it may be the case that the software is no longer maintained or the original authors are no longer contactable or willing to submit a paper. In this case, a third-party may still choose to submit a software paper so that they can cite it in their own research, but the credit will go to the original authors. The submitter will still get a warm fuzzy feeling of having done a service to the research community.

Do I have to pay to publish in this journal?

If your paper is accepted for publication, you will be asked to pay an Article Publication Fee of £350 to cover publications costs. This fee can normally be sourced from your funder or institution, and we recommend approaching them about this at the time of submission.

You will be able to pay any amount from nothing to full charge, as we recognise that not all authors have access to funding, and we do not want fees to prevent the publication of worthy work. The editor and peer reviewers of the journal will not know what amount (if any) you have paid, and this will in no way influence whether your article is published or not.

Can I deposit a pre-print version of a metapaper on a server?

Yes. We encourage people to submit preprint servers such as arXiv at time of submission to JORS. JORS does not require the removal of preprints, but authors should ensure that the entry on the preprint server is updated to include a link or reference to the final published JORS paper so that it is clear that the paper has been superceded.


Publication Ethics

Ubiquity Press, the journal’s publisher, is a member of the Committee on Publication Ethics (COPE), the Open Access Scholarly Publishers Association (OASPA), and the Association of Learned and Professional Society Publishers (ALPSP). The Press recognises its responsibility as a guardian of the scholarly record and takes an active role in establishing standards and policies in publication ethics.

The Editors of Journal of Open Research Software have committed to maintaining high editorial standards through rigorous peer review and strict ethical policies. The Editors follow the COPE code of conduct and refer to COPE for guidance as appropriate. The journal and the publisher ensure that advertising and commercial interests do not impact or influence editorial decisions.

The journal uses anti-plagiarism software to ensure academic integrity.



Annotation and post-publication comment

The journal platform permits readers to leave comments on the publication page, via the Disqus service. Readers will need a Disqus account to leave comments. Comments may be moderated by the journal, however, if they are non-offensive and relevant to the publication subject, comments will remain online without edit.

The journal platform also includes in-browser annotation and text highlighting options on full text formats via hypothes.is. Readers will require a hypothes.is account to create annotations, and will have the option to make these publicly available, available to a group, or private.


Advertisement policy

The journal only displays advertisements that are of relevance to its scope and will be of interest to the readership (e.g. upcoming conferences). All advertising space is provided free of charge and the editor and publisher have the right to decline or withdraw adverts at any point. Adverts will include a text heading to make it clear that they are adverts not related to the journal.

If you wish to propose a potential advert then please contact the editorial team. All advert images will have to be provided to the publisher.


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