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Open Research Skills Framework: a Practical Guide

Open Research Lifecycle

This Practical Guide provides helpful support and links to recommended external resources for a range of open research practices.

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Open research practices can be embedded at different stages of a project: Develop, Acquire, Process and Publish.

This lifecycle model was created in partnership with practitioners from across the University and provides a broad overview of the practices that can be applied throughout your research project. It can be adapted to suit different disciplines, and according to the requirements and objectives of your research.

UKRN (UK Reproducibility Network) have collated further guidance and resources for open research across disciplines

Open Research in practice at York

Most of these practices include links to example projects or case studies from our York Open Research community.

If you also have any reflections on applying open research to your work (including benefits, challenges and lessons learned) then please consider submitting an Open Research in Practice Case Study, which will be featured on our York Open Research wiki space and used for training and advocacy purposes.

Open licensing for research outputs

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Researchers can apply a public copyright licence such as Creative Commons in order to facilitate wider use and reuse of their work. Such licences can be applied to a wide range of outputs throughout the research lifecycle (documents, datasets, images, multimedia material, publications...) although this may be limited in accordance with institutional, funder or publisher policies.

For further guidance see our dedicated practical guide on Creative Commons licensing for Researchers

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Develop

Preregistration is the practice of creating a public record of your rationale, hypotheses and methodology before you conduct your research.

This helps to improve research transparency, accountability and credibility and eliminates poor practices such as HARKing and p-hacking. The pre-results of your research can be shared in an open repository (e.g. OSF, AEA Registry, EGAP, AsPredicted) where you can invite feedback from the community to help improve your study design. 

Preregistration in practice

A number of projects which engage in preregistration methods have been highlighted in the York Open Research Awards. These include Play and Child Development: A Twin Study of Genetic and Environmental Influences on Young Children’s Play, by Dr Gill Althia Francis and Dr Umar Toseeb (Education).

Further reading

Registered reports emphasise the importance of research questions and the quality of methods by conducting peer review prior to data collection.

This helps to eliminate a variety of questionable research practices, including selective reporting of results and publication bias. Researchers submit their study design for review and upon acceptance receive a commitment from the journal to publish their final results.

Registered reports in practice

Dissociating memory accessibility and precision in forgetting: writing a Registered Report, a case study by Dr Aidan Horner (Psychology)

Further reading

Study protocols are similar to preregistration and registered reports, and the terms are sometimes used interchangeably.

In health related research study protocols are typically mandated for randomised clinical trials, for example MRC require protocols to be made publicly available prior to the start of any funded studies. Study protocols help to inform the wider scientific community about recent or ongoing research, thereby reducing the likelihood of duplicate studies being undertaken.

Note that there is a distinction between study protocols and review protocols, which focus on ascertaining the scope of a systematic literature review (see Systematic Reviews Practical Guide for further information on these).

Further reading

  • BMC Public Health: Study Protocol criteria
  • SPIRIT statement recommendations to ensure research integrity in study protocols for clinical trials
  • Protocols.io - a platform to create and share dynamic and interactive research protocols

You can share your whole project workflow through an open research notebook (sometimes referred to as lab notebooks, or electronic notebooks).

The primary research record, including notes, data, and 'null results' from failed or otherwise insignificant experiments, can be shared openly and transparently as your project proceeds. Notebooks also enable researchers to share their code with accompanying annotations and visualisations.

There are various free and open source applications available for you to create an open notebook, (e.g. eLabFTW and JupyterLab). You can also document your research using GitHub, a Google Site, or a blog. 

Open notebooks in practice 

Research in digital archaeology, heritage and marginalia, an academic blog by Dr Colleen Morgan (Archaeology).

The Real-Time Systems Lab Wiki is hosted in the York Wiki Service (Confluence) and contains documentation for components and systems in the Real-Time Systems Research Group

Further reading

A Data Management Plan (DMP) is a document which describes how you will create, organise, document, store and share data used or generated throughout research, including considerations for open data.

Many research funders require a DMP as part of the funding application process. A DMP should acknowledge good practice and reassure the funder that you proposal is in line with their data policy. Note that research data means all the materials or assets you generate in your research - the evidence which may underpin the answers to your research questions. 

Further guidance is provided on the Library's Planning your data management web pages.

Further reading

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Acquire

Participatory research encourages the generation and sharing of knowledge between researchers and participants (often members of the public). 

There are many different approaches and methodologies to participatory research such as Community-based Research, Participatory Action Research and DIY Science. Participatory approaches to open research rely on establishing trust and rapport between researchers and participants. 

Researchers need to consider potential ethical and legal issues before embarking on a participatory research project, especially when it involves the collection of personal data. 

Participatory research in practice

Romans at Home: a collaborative outreach project with people living with dementia, a case study by Eleanor Drew (Archaeology)

Covid Realities: participant-led research in response to the pandemic, a case study by Dr Ruth Patrick, Dr Maddy Power and Dr Geoff Page (Social Policy and Social Work)

Further Reading

Citizen science is a form of participatory research, referring to the active engagement of the public in scientific research.

Citizen science is often performed through crowdsourcing activities in which people can contribute to the collection, analysis and monitoring of research. Citizen science is an important vehicle for the wider democratisation of research and scientific knowledge.

Researchers need to consider potential ethical and legal issues before embarking on a citizen science project, especially when it involves the collection of personal data. 

Citizen science in practice

Stockholm Environment Institute (SEI) York has a long history of engaging people in citizen science research at a range of scales, geographic locations, and involving a variety of research topics and methods. See SEI York Research Areas: Citizen Science.

Further reading

Open data can be used to interrogate or extend the findings of previous research and address new research questions.

Data is increasingly available for reuse in open data repositories such as the Registry of Research Data Repositories (re3data) and FAIRsharing. Research data that follow the FAIR principles are more easily findable than data published on personal websites or data included within journal articles.

Further reading

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Process

Good organisation and documentation is essential to the management of open data.

Once you start to create, gather and manipulate data, it can quickly become disorganised. It is important to decide on how you will name and structure data files and folders to prevent errors from happening later on. It's also important to ensure that others can find, use and properly cite your data. Documentation and metadata provide the necessary information for others to interpret, understand and reuse data. 

The University's Research Data Management Policy applies to all University members engaged in research, including staff and research students, and those who are conducting research on behalf of the University. General guidance on good research data management is provided on the Library's RDM web pages.

Further reading

Open source software can be useful when it comes to processing your research. If you are producing your own research software then sharing versions of your code alongside documentation as your project progresses allows other researchers to access, reuse, modify and redistribute your work.

If you have created code or software to visualise or interrogate your research data then you can also preserve this in a data repository, alongside full documentation to help others verify your findings or reproduce your methodology. Guidance on this is provided on the Library's Research data management web pages.

Open sourcing is key to sustainable software practice, defined by the Software Sustainability Institute (SSI) as ensuring that ”the software you use today will be available - and continue to be improved and supported - in the future”.

Open source software in practice

York Structural Biology Laboratory (YSBL) has contributed to open source software for X-ray crystallography over the course of 40 years. Giving away software has led to massive impact, with the 'Coot' software developed under the GNU public license being cited in typically 10 new scientific papers every day, as well as achieving significant commercial income.

A number of projects which have produced open source software, code and documentation are featured in the York Open Research Awards. These include David Shaw and Prof Nicola Carslaw's INCHEM-Py model for solving indoor air chemistry with time (Environment and Geography).

Further reading

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Publish

Open access is about making research publications freely available with reduced restrictions on use and re-use.

Open access benefits researchers by helping them maximise the dissemination of their own research to wider audiences, and exercise greater sharing and reuse rights over their own research. The University Research Publications and Open Access policy sets out requirements for research articles authored by York-affiliated members of staff submitted from 1st March 2023. More information on the new policy is provided on this dedicated practical guide.

The Library's Open Access webpages also provide further guidance on the benefits of open access, meeting REF and funder requirements and paying APCs (article processing charges) from the York Open Access Fund and our publisher agreements. 

Open access publication in practice 

The York Research Database provides access to thousands of peer-reviewed articles and other outputs by our researchers. There are also a number of student-led open access journals in different departments across York (see Open Research Community).

The University of York, along with Universities of Sheffield and Leeds, also supports the White Rose University Press (WRUP), an open access digital publisher of peer-reviewed academic journals and books, publishing across a wide range of academic disciplines. WRUP is committed to open access dissemination of research and teaching materials, ensuring academic quality, and supporting innovation in digital publishing.

Open peer review describes how aspects of the peer review process can be made openly available, either before or after publication. 

Traditional peer review is being transformed, with author and reviewer identities made visible and participation opened up to the wider community (not just invited experts). This provides opportunity for a more open and transparent dialogue between researcher and reviewer. 

An increasing number of publishers (such as BMJPLoS and Nature) and platforms (such as Wellcome Open Research and F1000Research) support open peer review by displaying prepublication histories and review reports alongside papers. Some academic communities use web-based annotation tools such as Hypothes.is to facilitate open peer review, as well as to initiate discussions and add tags to online resources.

Further reading

Preprints are early versions of scholarly publications, shared openly with the research community.

Preprints enable faster dissemination of results, increase the attention given to a study, and allow researchers to establish the primacy of their findings. They are usually shared before a paper is submitted to a journal; many publishers accept this as standard practice and encourage authors to engage with the process, but it's important for researchers to understand publisher preprint policies when considering submitting a paper.

Preprints are hosted by discipline-specific servers, the most well-established of which is arXiv (primarily for physics, mathematics and computer science). New preprint servers are now appearing in a wide range of disciplines - see Research Preprints: Server Lister (created by Martyn Rittman).

Preprints in practice

Many of the researchers recognised in the York Open Research Awards have shared preprints of their work. For example, Emre Deniz and colleagues in the Child and Adolescent Neurodevelopmental Diversity Research Group (Education) have shared a preprint of their systematic review and meta-analysis protocol, Parent-mediated play‐based interventions to improve social communication and language skills of preschool autistic children, on PsyArxiv.

Further reading

You can enable others to reuse and reproduce your work by sharing your research data openly in a suitable repository or archive. 

Repositories also help ensure that data is correctly preserved and retains usability and value in the long term. You can search for relevant repositories for your data at re3data.org or deposit with the University's Research Data York service (via Pure) in order to make your data openly accessible in the York Research Database.

Researchers should consider how and when their research data can be shared (if it can be shared), what might limit or prohibit data sharing, and what can be done to enable others to make correct use of it. A researcher’s ability to make data openly available for reuse by others may be limited by legal, ethical or commercial considerations - consider the Horizon 2020 principle: ‘as open as possible, as closed as necessary'.

Further guidance is provided on the Library's Sharing, preserving and depositing your data web pages.

Open data sharing in practice

A number of projects which engage in open data sharing are featured in the York Open Research Awards. These include Scott Cairney and his lab team's research on understanding the role of sleep in mental health and cognition (Psychology).

Further reading

Postgraduate researchers are required to deposit a copy of their thesis in White Rose E-Theses Online (WREO) where it will be made openly available to the general public in full, unless approval is obtained for embargo or redaction. 

Guidance on the submission of theses for research degree programmes is provided on the York Graduate Research School web pages, and further advice on licensing options in WREO is provided in our Copyright Practical Guide for Researchers.

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Illustrations by Manfred Steger, licensed for reuse under a Pixabay licence