Citation

citing softwareBy Will Usher, Senior Researcher: Infrastructure Systems Modeller, University of Oxford

Plagiarism is a serious issue, and we are all familiar with the horror stories of students unceremoniously ejected from courses for copying essays. Any undergraduate degree worth its salt teaches students how to cite work correctly, acceptable bounds on quotation and how to attribute ideas and concepts to their sources. But in the growing world of open-source research software, best practices have yet to be universally understood, as I recently found out.

During my PhD at University College London, I became involved in the heady enthusiasm of the Research Software Programming group, attending and then helping out at Software Carpentry workshops. As a consequence, I was keen to apply my new knowledge of Python, version control and software development to my research. As luck would have it, I discovered an existing Python library on Github, which implemented several Global Sensitivity Analysis routines I could make use of. As I used the library, I started adding bits and pieces, and so by the end of the PhD I had made a considerable contribution to the package.

It's probably safe to say that SALib (sensitivity analysis library) is the go-to Python library for the unfortunately still-far-too-niche use of global sensitivity analysis in modelling, and our…

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Conference proceedings, journals and other articles on the work of the Institute or projects we have collaborated with.

Papers with the Institute as an author or co-author

2017

Lane, Simon I.R.; Crouch, Stephen; Jones, Keith T. (2017): "Imaging Chromosome Separation in Mouse Oocytes by Responsive 3D Confocal Timelapse Microscopy", Methods in Molecular Biology, Vol. 1471, pp.245-254, March 2017. DOI: 10.1007/978-1-4939-6340-9_13.

2015

Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel (2015): "Cutting edge: Anatomy of BioJS, an open source community for the life sciences", eLife;4;e07009, July 2015. DOI: 10.7554/eLife.07009.001.

Pawlik, Aleksandra; Petrie, Marian; Segal, Judith; Sharp, Helen (2015): "Crowdsourcing Scientific Software Documentation: A Case Study of the NumPy", Computing in Science & Engineering, Vol. 17, No. 1, pp.28,36, January/February 2015. DOI: 10.1109/MCSE.2014.93.

Budd, A, Corpas, M., Brazas, M.D., Fuller, J.C., Goecks, J., Mulder, N.J., Michaut, M., Ouellette, B.F.F., Pawlik, A., Blomberg, N. "A Quick Guide for Building a Successful Bioinformatics Community", PLOS Computational…

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By Mike Jackson.

Researchers face significant challenges when trying to understand, reproduce or reuse research in which software has played an integral part. In this green paper, I give examples of the problems that can arise when reproducing someone else's research, and propose some practical approaches to resolving, or at least reducing, them. I also look at the important distinction between describing the software that was used, and citing it.

1 Can I get a copy of the software that was used?

For many years I worked on a research project called OGSA-DAI (a novel framework for distributed data management), and I recently came across a paper in which OGSA-DAI forms a key component. Like any researcher who would want to reproduce the research, I wanted to know which version of the software had been used in the paper. This required some difficult detective work.

The authors had cited an OGSA-DAI paper that should have meant they were using a version of the software between OGSA-DAI 1 and 6. Later in their paper, the authors mentioned a component that was specific to OGSA-DAI versions 2.5 to 6. However, the authors then talked of another component and a toolkit, which was only available with a completely different version of the software. Without my highly detailed knowledge of the OGSA-DAI project, it would have been impossible to determine what software was used.

Even if a researcher had determined which version of OGSA-DAI to use, they would have found that the version they needed is no longer readily available, and that the available releases are…

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By Megan Potter & Tim Smith, CERN.

For Open Science, it is important to cite the software you use in your research, as has been mentioned in previous articles on this blog. Particularly, you should cite any software that made a significant or unique impact on your work. Modern research relies heavily on computerised data analysis, and we should elevate its standing to a core research activity with data and software as prime research artefacts.  Steps must be taken to preserve and cite software in a sustainable, identifiable and simple way. This is how digital repositories like Zenodo can help.

Best practice for citing a digital resource like code is to refer to a digital object identifier (DOI) for it whenever possible. This is because DOIs are persistent identifiers that can be obtained only by an agency that commits to the obligation to maintain a reliable level of consistency in and preservation of the resource. As a digital repository, Zenodo registers DOIs for all submissions through DataCite and preserves these submissions using the safe and trusted foundation of CERN’s data centre, alongside the biggest scientific dataset in the world, the LHC’s 100PB Big Data store. This means that the code preserved in Zenodo will…

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Citation needed placardBy Mike Jackson, Software Architect

The Institute are firm believers in software citation. Citing software, directly or via its associated publications, provides deserved credit for those who develop this vital research infrastructure. In this blog post I look at some ways in which research software developers are helping to promote the citation of software, by making it easier for researchers to do this. That's another thing we are firm believers in, automating the grunt work of using and developing software to free up time for research...​

As part of recent open call collaborations with both BoneJ and QuBIc I was taken aback by how involved citing software could get. For example, BoneJ request that their journal paper is cited, but, depending upon the plug-ins and additional features used, there are other papers that also need to be cited. Likewise, the FSL software library request citation of one of their three overview papers. Again, depending upon the specific tools used, there are additional papers to be cited. For example, using QuBIC's FABBER tool, bundled in FSL, requires citation of one paper, though citing three is recommended.

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A copy of this paper, as published in Computing and Science and Engineering in its Nov-Dec 2013 edition, is available via its Digital Object Identifier (DOI) 10.1109/MCSE.2013.133. Alternatively, if you don't have access to this article, a post-print PDF version is also available.

If you want to cite us, please reference this paper using the citation as described here.

By Stephen Crouch, Neil Chue Hong, Simon Hettrick, Mike Jackson, Aleksandra Pawlik, Shoaib Sufi, Les Carr, David De Roure, Carole Goble, and Mark Parsons.

To effect change, the Software Sustainability Institute works with researchers, developers, funders, and infrastructure providers to…

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If you have worked with us, we’d appreciate it if you would acknowledge the support and assistance you’ve received. This helps our funders to see the work we have done with all our partners and collaborators.

The general citation for the work of the Institute is:

Crouch, Stephen; Chue Hong, Neil; Hettrick, Simon; Jackson, Mike; Pawlik, Aleksandra; Sufi, Shoaib; Carr, Les; De Roure, David; Goble, Carole; Parsons, Mark, "The Software Sustainability Institute: Changing Research Software Attitudes and Practices," Computing in Science & Engineering , vol.15, no.6, pp.74,80, Nov-Dec 2013. DOI: 10.1109/MCSE.2013.133.

Citations for different media

Paper

(co-authored with the Institute)

"STAFF NAME was supported by the UK Engineering and Physical Sciences Research Council (EPSRC) Grant EP/H043160/1 and EPSRC, BBSRC and ESRC Grant EP/N006410/1 for the UK Software Sustainability Institute."

If the work resulted from a joint project, please add the following to the last sentence:

"and NAME OF FUNDER through grant REFERENCE."

Paper

(acknowledging our help)

"We would like to acknowledge the assistance of the Software Sustainability Institute. The work carried out by the Software…

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