Author: Valerie

Research Notebooks Community Event August 2026

With thanks to Mary Donaldson, University of Glasgow for capturing these highlights of this drop-in session.

On the 20th August 2026 we held the second drop-in session for our wider Research Notebook Community. This was an informal session without an agenda which provided an opportunity for people to discuss topics of interest or bring up questions in the group situation. 

To start us off, PSDI announced that they have just published their white paper on their experience of rolling out an ELN in the chemistry department at Southampton. https://zenodo.org/records/22014573/latest 

Discussion: 

Where to start with ELNs? Is it a good idea to aim for the same ELN for all schools / departments? They don’t all have the same functionality. Is it better to focus on individual disciplines? 

PSDI decided to specifically focus on Chemistry because their resource came from that department. They worked with the department to find a solution that met the needs of that department (while trying to get something that could provide wider flexibility for the future). The trial roll-out was successful and the tool is now implemented in the chemistry department (see link to white paper above). They are about to start a trial in Cancer Sciences. 

Another facility has been looking at ELNs. They surveyed their scientists (what do they currently use? What are they familiar with from other institutions and facilities? What would they like?). An observation from feedback was that something resembling a free text document where scientists can add any info relevant to the experiment would be most useful. Also helps if it can be connected to the equipment with direct automatic input from machines to the ELN. It must be able to connect to multiple systems to gather all the information about an experiment. 

A third institution that has a well-established ELN process started by asking what users wanted. They discovered that when you ask this, you find out that users all want different things but the most important thing was to document the science accurately, capturing all aspects of the process. To enable this, the institute went down a very general route using a wiki. It can be adapted for the different user requirements and can be linked to different systems. This has now been rolled out to around 40 groups and they haven’t yet found anything it can’t do.  The wiki runs on the Confluence platform. The support team provide a template for the wiki and group leaders control access. Guidance to researchers is provided to researchers in Standard Operating Procedures and can be demonstrated to users. Drop-in sessions are also planned to provide additional support. 

There are lots of case studies and resources available in the community: 

ELN finder – good comparison of the ELNs currently available (mostly academic focussed). Can filter based on approx. 40 criteria and different connectivity and module options. https://eln-finder.ulb.tu-darmstadt.de/  

Case study on ELNs at the University of Glasgow (the situation up until 2020 still pertinent): https://eprints.gla.ac.uk/220623/. 

Glasgow guide on using OneNote as an ELN: https://eprints.gla.ac.uk/220623/ 

PSDI guidance on OneNote https://guidance.psdi.ac.uk/docusaurus-pages/docs/guidance/notebooks/examples/onenote and case study https://zenodo.org/records/18256918  

JISC procurement process. 

The University of Glasgow have been attempting to procure an electronic research notebook tools using this process.  They have been trying to embed better support for electronic research notebooks since 2012. See the case study listed above. Can’t share detailed info on current procurement situation due to confidentiality of procurement process. What was learned: 

  • It wasn’t as light-touch as we imagined 
  • We had to cross-check Jisc’s requirements against our own list. This was not trivial.  
  • We had not been clear about our user numbers. Although we were eventually looking for a site licence, we didn’t expect high numbers. This affected the prices we were quoted.  

Next steps: we will revisit our requirements and try again.  This could be a full tender or another approach working with advice from our procurement experts.  Once we’re finished, we should be able to share more info on our requirements. 

Final thoughts from the drop-in session: 

  • There are lots of resources and case studies available (see above and other entries in this wordpress site) but requirements of individual institutions or departments can be variable. There is no real short-cut to specification and procurement process. 
  • An exit strategy is very important for users and institutions but is missing from some tools.  
  • Lots of institutions are looking for shared templates and guidance. PDSI are keen on sharing templates. They have two at the moment, a general one and a synthesis one. So far they’ve not been asked to develop other ones. 
  • PSDI also interested in interoperability, APIs, technical standards etc. If we were all using standardised templates, the data should be easier to move between systems.  

Coming up: 

Some interest was expressed in updating the OneNote user guides. 

There was a general interest in seeing and sharing templates for ELNs (both subject specific and general) 

The date for our next ELN drop-in meeting will be announced via our mailing list WGRESEARCHNOTEBOOKS@jiscmail.ac.uk Feel free to sign up via the jiscmail lists. 

Please feel free to use the mailing list to ask questions and share news. 

Research Notebooks Community Event June 2026

On the 4th of June the Research Notebook Community held our first drop-in session for the wider community, where people could grab a coffee and come and chat about all things reseach notebooks for an hour. We want these sessions to be an informal meeting where those in the research notebooks community could drop in for as long or as little as they wanted to have a chat about the good, the bad and the confusing particularly when it comes to using an electronic research notebooks in a research institution.

This time around we had a broad range of people join us, from seasoned hands in the research notebooks community to those who are taking the first steps on their electronic research notebooks journeys. There was no set agenda, with those that came bringing topics to discuss or questions to ask the group.

Although the session was an informal drop in, we still want to provide an overview of the conversations, both to provide a record and give those that couldn’t make it (or who are working out if they want to come to the next one) a flavour of what was discussed. So, in no particular order:

  • There is a wide variety of electronic research notebook solutions that are being used across institutions, both in terms of the platforms being used, and in their implementation. Even those using the same platforms utilise them in different ways depending on their needs.
  • People need low-cost solutions due to institution restraints, yet low-cost options (such as OneNote, a popular low-cost option) have drawbacks, such as lacking specialist functionality, the ability to provide true provenance tracking, or any long-term robustness.
  • How the most successful implementations have come from institutions where they have overcome cultural and behavioural barriers, such as:
    o Lack of staff time to set up or support an electronic research notebook installation
    o Resistance from new users that didn’t want to change current practices
    o Lack of understanding from users to the benefits of electronic research notebooks.
  • The importance of engaging with leadership teams to gain support and backing
  • Understanding who your user base is, and providing a tailored electronic research notebook experience for them
    If that all sounds interesting or you’re sitting there thinking “well I can add to those conversations” we will be having our second session on the 20th of August at 10:00 BST, so get ready to grab a coffee and a thought you want to discuss or chat about and come along and join us for an hour (or however long you can) to have a chat about electronic research notebooks. You can find joining details for this meeting here: https://researchnotebooks.org/event/electronic-research-notebook-drop-in-session-2/

Meeting of 15th March 2023

We had a short get together to share some updates and best practice. Some of the attendees had a general interest in research notebooks and how other organisations manage them, some were looking at how to support such tools, and others had worked with them and deployed site wide solutions.

Talk 1

Akane Kawamura from the University of Newcastle https://kawamuraresearchgroup.com/ kindly gave us a Chemical Biology Case Study. You can view the slides here

2023-03-15-labarchivesDownload

The research group has been split across several sites so having a tool helps with sharing.

Paper notebooks can get lost, damaged and take up space but have the advantage of being able to be taken into their lab.

LabArchives was selected at Akane’s previous research organisation after some testing. Akane showed us some screens from the LabArchives tool. There are various organisation options. Akane has chosen to have one notebook for the whole group with team members uploading figures and experiment details. She demonstrated that files can be transferred and downloaded with ease. Members can contact each other from within the system and include hyperlinks to existing files and text.

I personally like how LabArchives looks very useable regardless of research discipline.

Questions Included:

Q Can you invite third party guests to your collaborative notebook if they do not subscribe to LabArchives?

A Yes anyone can be a guest. Unlimited read access and 60 days edit access is granted initially. It is possible to share single pages or folders.

Q Is there a limit on the size of data you can transfer? Do you back up onto local servers?

A Storage is unlimited online. Lab Archives make an annual back up to send to each institution. The speaker also backs up locally.

Q: You said your organisation evaluated research notebooks for multiple different disciplines – did you find the usefulness of a single tool varied for different disciplines? e.g. some are good for small molecule synthetic chemistry with structure searching -others need complex taxonomies for assays and cell lines etc?

A: The speaker had only used LabArchives. It does have good support for next gen sequencing data, images, and chemical diagrams. It does not integrate with Chemdraw at present.

Q Which departments make most use of it?

A Often biological sciences more than physical sciences.

Q When you log in to your account at your organisation are you provided with a pre-defined institutional environment?

A It can be badged with the institutional logo and connected to University single sign on.

Q Do you have the ability to choose to make parts of the electronic notebook openly available?

A The speaker had not made any of their electronic notebook openly available, but was sure you can e.g. the University of Sydney chemistry notebook mentioned in the slides seems to be open for anyone to look at.

Questions specifically about LabArchives can be sent to support@labarchives.com

Talk 2

Hugh Shanahan from Royal Holloway University of London gave us some thoughts on Executable Notebooks – putting software, visualisations and text in one viewable file.

Some slides are available here https://bit.ly/3yJkiol

There are executable ‘cells’ of code, visualisation and text. Examples include Jupyter notebooks which focuses on code, and R Markdown which is often used as a focus to produce outputs. Such tools provide a transparent way to allow others to run code and verify research results.

Challenges include the volume e.g. an estimate of 1.4 Million executable notebooks were deposited on GitHub in 2019 alone (Pimental et al.) It is important to ensure good research data management practice is applied to these in similar ways to other research outputs.

The speaker ran a survey asking how respondents used executable notebooks. Many were used for personal analysis but also many were used for collaboration, teaching, sharing and presenting.

Questions Included:

Q From the point of view of reproducibility, do you think the information surrounding the code (the literate in programming) will have more value than the code itself in the future?

A There’s a short term and a long term – if we think about the long term, then we’ll need to think about a ‘software management plan’ and think about what you want to keep. The ‘lowest hanging fruit’ would be to create a PDF of the notebook, so text, code and visualisations are captured and there the text is what matters but you could also inspect specific code cells to understand the algorithm or for a key visualisation. On the other hand if the goal is to make sure that it is still executable then that would require investment to ensure it still works and hence would have a significant cost. It depends on how the software management plan is written and what the goals are.

Q You mentioned publishing from the notebook – do you mean just making the item available to people within the notebook itself, or do you mean it would be good to for example be able to press a button to ‘publish to Arxiv’ or similar?

I mean the former but the latter is important too. I’ll elaborate. In an ideal world a published notebook will be one where people can access the notebook and run it. So they can check if it’s reproducible, get a better understanding of how it works and build on it or apply to their own data. What the run environment is depends on the domain. In some cases you will be dealing with very large or private data sets that can’t be moved about so a specific run environment will be required with reduced access. Some cases will mean just downloading the notebook locally and running it there. The ‘push a button’ option on the notebook is important to address the findability of these notebooks. That option should require developers to provide metadata before it can be uploaded to an appropriate repository. I don’t think anyone has done this yet.

What next?

We hope to schedule further discussion at least twice a year. We will appeal to the list for future topics so join the list researchnotebooks@jiscmail.ac.uk if you want to know what is next:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=RESEARCHNOTEBOOKS