Research Data Workshops: Electronic Notebooks Summary of Feedback

In the spring of this year (March & May) the Research Data Service ran two workshops on Electronic Notebooks (ENs) where researchers from all three colleges were invited to share their experiences of using ENs with other researchers. Presentations and demos were given on RSpace, Benchling, Jupyter Notebooks, WikiBench, and Lab Archives. Almost 70 research and support staff attended and participated in the discussions.

This post is a distillation of those discussions and we will use them to inform our plans around Electronic Notebooks over the coming year. It was obvious from the level of attendance and engagement with the discussions that there was quite a lot of enthusiasm for the idea of adopting ENs across a variety of different schools and disciplines. However, it also quickly became clear that many researchers and support staff had quite justified reservations about how effectively they could replace traditional paper notebooks. In addition to the ENs which were the subject of presentations a number of other solutions were also discussed, including; LabGuru, OneNote, SharePoint, and Wikis.

It appears that across the University there are a very wide range of platforms being used, and not all of them are intended to serve the function of an EN. This is unsurprising as different disciplines have different requirements and an EN designed for the biological sciences, such as Benchling, is unlikely to meet the needs of a researcher in veterinary medicine or humanities. There is also a huge element of personal preference involved, some researchers wish a simple system that will work straight out of the box while others want something more customisable and with greater functionality for an entire lab to use in tandem.

So, within this complex and varied landscape are there any general lessons we can learn? The answer is “Yes” because regardless of platform or discipline there are a number of common functions an EN has to serve, and a number of hurdles they will have to overcome to replace traditional paper lab books.

Firstly, let’s look at common functional requirements:

  1. Entries in ENs must be trustworthy, anyone using one has to be confident that once an entry is made it cannot be accidentally deleted or altered. All updates or changes must be clearly recorded and timestamped to provide a complete and accurate record of the research conducted and the data collected. This is fundamental to research integrity and to their acceptance by funders, or regulators as a suitable replacement for the traditional, co-signed, lab books.
  2. They must make sharing within groups and between collaborators easier – it is, in theory, far easier to share the contents of an EN with interested parties whether they are in the same lab or in another country. But in doing so they must not make the contents inappropriately available to others, security is also very important.
  3. Integration is the next requirement, any EN should be able to integrate smoothly with the other software packages that a researcher uses on a regular basis, as well as with external (or University central) storage, data repositories, and other relevant systems. If it doesn’t do this then researchers may lose the benefits of being able to record, view, and analyse all of their data in one place, and the time savings from being able to directly deposit data into a suitable repository when a project ends or a publication is coming out.
  4. Portability is also required, it must be possible for a researcher to move from one EN platform to another if, for example, they change institutions. This means they need to be able to extract all of their entries and data in a format that can be understood by another system and which will still allow analysis. Most ENs support PDF exports which are fine for some purposes, but of no use if processing or analysis is desired.
  5. Finally, all ENs need to be stable and reliable, this is a particular issue with web based ENs which require an internet connection to access and use the EN. This is also an area where the University will have to play a significant role in providing long-term and reliable support for selected ENs. They also need the same longevity as a paper notebook, the records they contain must not disappear if an individual leaves a group, or a group moves to another EN platform.

Secondly, barriers to adoption and support required:

  1. Hardware:
    1. Many research environments are not suitable for digital devices, phones / tablets are banned from some “wet” labs on health and safety grounds. If they are allowed in the lab they may not be allowed out again, so space for storage and charging will need to be found. What happens if they get contaminated?
    2. Field based research may not have reliable internet access so web based platforms wouldn’t work.
    3. There is unlikely to be space in most labs for a desktop computer(s).
    4. All of this means there will still be a need for paper based notes in labs with later transfer to the EN, which will result in duplication of effort.
  1. Cost:
    1. tablets and similar are not always an allowable research expense for a grant, so who will fund this?
    2. if the University does not have an enterprise licence for the EN a group uses they will also need to find the funds for this
    3. additional training and support my also be required
  2. Support:
    1. technical support for University adopted systems will need to be provide
    2. ISG staff will need to be clear on what is available to researchers and able to provide advice on suitable platforms for different needs
    3. clear incentives for moving to an EN need to be communicated to staff at all levels
    4. funders, publishers, and regulatory bodies will also need to be clear that ENs are acceptable for their purposes

So, what next? The Research Data Support service will now take all of this feedback and use it to inform our future Electronic Notebook strategy for the University. We will work with other areas of Information Services, the Colleges, and Schools to try to provide researchers in all disciplines with the information they need to use ENs in ways that make their research more efficient and effective. If you have any suggestions, comments, or questions about ENs please visit our ENs page (https://www.ed.ac.uk/information-services/research-support/research-data-service/during/eln). You can also contact us on data-support@ed.ac.uk.

The notes that were taken during both events can be read here Combined_discussion_notes_V1.2

Some presentations from the two workshops are available below, others will be added when they become available:

Speaker(s) Topic Link
Mary Donaldson (Service Coordinator, Research Data Management Service, University of Glasgow) Jisc Research Notebooks Study Mary_Donaldson_ELN_Jisc
Ralitsa Madsen (Postdoctoral Research Fellow, Centre for Cardiovascular Science) RSpace 2019-03-14_ELN_RSpace_RRM
Uriel Urquiza Garcia (Postdoctoral Research Associate, Institute of Molecular Plant Science) Benchling
Yixi Chen (PhD Student, Kunath Group, Institute for Stem Cell Research) Lab Archives 20190509_LabArchives_Yixi_no_videos
Andrew Millar (Chair of Systems Biology) WikiBench
Ugur Ozdemir (Lecturer – Quantitative Political Science or Quantitative IR) Jupyter Notebooks WS_Talk
James slack & Núria Ruiz (Digital Learning Applications and Media) Jupyter Notebooks for Research Jupyter_Noteable_Research_Presentation

Kerry Miller, Research Data Support Officer, Research Data Service

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Research Data Workshop Series 2019

Over the spring of 2019 the Research Data Service (RDS) is holding a series of workshops with the aim of gathering feedback and requirements from our researchers on a number of important Research Data topics.

Each workshop will consist of a small number of short presentations from researchers and research support staff who have experience of the topic. These will then be followed by guided discussions so that the RDS can gather your input on the tools we currently provide, the gaps in our services, and how you go about addressing the challenges and issues raised in the talks.
The workshops for 2019 are:

Electronic Notebooks 1
14th March at King’s Buildings (Fully Booked)

DataVault
1200-1400, 10th April at 6301 JCMB, King’s Buildings, Map
Booking Link – https://www.events.ed.ac.uk/index.cfm?event=book&scheduleID=34308
The DataVault was developed to offer UoE staff a long-term retention solution for research data collected by research projects that are at the completion stage. Each ‘Vault’ can contain multiple files associated with a research project that will be securely stored for an identified period, such as ten years. It is designed to fill in gaps left by existing research data services such as DataStore (active data storage platform) and DataShare (open access online data repository). The service enables you to comply with funder and University requirements to preserve research data for the long-term, and to confidently store your data for retrieval at a future date. This workshop is intended to gather the views of researchers and support staff in schools to explore the utility of the new service and discuss potential practicalities around its roll-out and long-term sustainability.

Sensitive Data Challenges and Solutions
1200-1430, 16th April in Seminar Room 2, Chancellors Building, Bioquarter, Map
Booking Link – https://www.events.ed.ac.uk/index.cfm?event=book&scheduleID=34321
Researchers face a number of technical, ethical and legal challenges in creating, analysing and managing research data, including pressure to increase transparency and conduct research openly. But for those who have collected or are re-using sensitive or confidential data, these challenges can be particularly taxing. Tools and services can help to alleviate some of the problems of using sensitive data in research. But cloud-based tools are not necessarily trustworthy, and services are not necessarily geared for highly sensitive data. Those that are may not be very user-friendly or efficient for researchers, and often restrict the types of analysis that can be done. Researchers attending this workshop will have the opportunity to hear from experienced researchers on related topics.

Electronic Notebooks 2
1200-1430, 9th May at Training & Skills Room, ECCI, Central Area, Map
Booking Link – https://www.events.ed.ac.uk/index.cfm?event=book&scheduleID=34287
Electronic Notebooks, both computational and lab-based, are gaining ground as productivity tools for researchers and their collaborators. Electronic notebooks can help facilitate reproducibility, longevity and controlled sharing of information. There are many different notebook options available, either commercially or free. Each application has different features and will have different advantages depending on researchers or lab’s requirements. Jupyter Notebook, RSpace, and Benchling are some of the platforms that are used at the University and all will be represented by researchers who use them on a daily basis.

Data, Software, Reproducibility and Open Research
Due to unforeseen circumstances this event has been postponed. We will update with the new event details as soon as they are confirmed.
In this workshop we will examine real-life use cases wherein datasets combine with software and/or notebooks to provide a richer, more reusable and long-lived record of Edinburgh’s research. We will also discuss user needs and wants, capturing requirements for future development of the University’s central research support infrastructure in line with (e.g.) the LERU Roadmap for Open Science, which the Library Research Support team has sought to map its existing and planned provision against, and domain-oriented Open Research strategies within the Colleges.

Kerry Miller
Research Data Support Officer
Library & University Collections

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DwD2018 – Videos now on Media Hopper

Dealing with Data 2018 was once again a great success in November last year with over 100 university staff and Post-Graduate students joining us to hear presentations on topics as diverse as sharing data in clinical trials and embedding sound files in linguistics research papers.

As promised the videos of each presentation have now been made publicly available on Media Hopper (https://media.ed.ac.uk/channel/Dealing%2BWith%2BData%2BConference/82256222), while the PDFs can be found on https://www.era.lib.ed.ac.uk/handle/1842/25859. You can also read Martin Donnelly’s reflections on the day http://datablog.is.ed.ac.uk/2018/11/28/dealing-with-data-2018-summary-reflections/.

We hope that these will prove both useful and interesting to all of our colleagues who were unable to attend.

We look forward to seeing you at Dealing with Data 2019.

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DataVault is now live

After extended development, the Research Data Service’s DataVault system is now operational, adding value to research data for principal investigators and their funders alike by offering a long-term retention solution for important datasets.

DataVault is a companion service to DataShare, the institutional digital repository for researchers to openly license and share datasets and related outputs via the Web. DataVault comprises an online interface connected to the university’s data centre infrastructure and cloud storage.

Each research project can store data in a single vault made up of any number of deposits. DataVault is currently able to accept individual deposits (groups of files) of up to 2 TB each; this will increase over time as project development continues.

DataVault sprint meeting before launch

Immutable

DataVault is designed for long-term retention of research data, to meet funder requirements and ensure future access to high value datasets. It meets digital preservation requirements by storing three copies in different locations (two on tape, one in the cloud) with integrity checking built-in, so that the data owner can retrieve their data with confidence until the end of the retention period (typically ten years).

Secure

The DataVault interface helps to guide users in how to deposit personal and sensitive data, using anonymisation or pseudonymisation techniques whenever possible, as prescribed by the University’s Data Protection Officer (DPO). Because all data are encrypted before deposit, they are protected from unauthorised disclosure. Only the data owner or their nominated delegate is allowed to retrieve data during the retention period. Any decisions about allowing access to others are made by the data owner and are conducted outside the DataVault system, once they have been retrieved onto a private area on DataStore and decrypted.

Discoverable

Although DataVault offers a form of closed archive, the design encourages good research data management practice by requiring a metadata record for each vault in Pure. These records are discoverable on the Web, and linked to the respective data creators, projects and publications.

In exchange for creating this high level public metadata record, the Principal Investigator benefits from the assignment of a unique digital object identifier (DOI) which can be used to cite the data in publications.

The open nature of the metadata means that any reader may make a request to access the dataset. The data owner decides who may have access and under what conditions. Advice can be provided by the Research Data Support team and the DPO.

University data assets

DataVault’s workflow takes into account the possibility/likelihood that the original data owner will have left the university when the period of retention comes to an end. Each vault will be reviewed by representatives of the university in schools, colleges or the Library, acting as the data owner, to make decisions on disposal or further retention and curation. If kept, the vault contents become university data assets.

Plan ahead for data archiving

The Research Data Support team encourages researchers to plan ahead for data archiving, right from the earliest conception stages of the project, so that appropriate costs are included in bids, and enabling the appropriate steps to be carried out to prepare data for either open or closed long-term archiving.

The team can be contacted through the IS Helpline and offers assistance with writing data management plans and making archival decisions. See our service website and contact information at https://www.ed.ac.uk/is/research-data-service or go straight to the DataVault page to learn more about it, get instructions for use, or look up charges. An introductory demo video is available  at  https://media.ed.ac.uk/media/Getting+started+with+the+DataVault/1_h4r4glf7 .

Robin Rice
Data Librarian and Head, Research Data Support
Library & University Collections

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