About
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.
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:
CrossRef, JISC KB+, SHERPA RoMEO, Directory of Open Access Journals (DOAJ), EBSCOHost, and Google Scholar. 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.
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.
If you wish to propose a potential advert then please contact the editorial team. All adverts are displayed in the right column of the journal and will need to fit a 120 pixel wide space. All advert images will have to be provided to the publisher.
FAQ: Software Metapapers
- What kinds of software can I publish?
- What is a software paper?
- How do I submit a software paper?
- How does the JORS peer review work?
- Which open license should I apply to my software?
- Which repositories do you recommend for software?
- What are the criteria for a repository to be accepted?
- What does ‘open’ mean?
- What are the benefits of openly publishing software?
- Do I have to make my software open?
- How do I cite software?
- How do I define authorship?
- Can I submit a software paper on behalf of software which I have not authored?
- Do I have to pay to publish in this journal?
- Can I deposit a preprint version of a metapaper on a server?
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 that is designed to make other researchers software of data that is 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:
- 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)
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:
- Shining Light Into Black Boxes
- The Case for Open Computer Programs
- Secret Computer Code Threatens 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 £100 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.
Recommended Repositories
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
- 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
- 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
| Code repositories | Preservation repositories | Institutional repositories |
| Assembla Codeplex Github Google Code Launchpad Savannah | Figshare | UCL Discovery |
 | 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:
|
 | 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):
| |
| 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:
|
 | 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:
|
 | 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:
|
 | 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):
| |
| 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:
|
 | 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:
|
 | 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 |
| |
| 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:
|
 | 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 | UCL 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:
|