Seekest thou the road to, all that's digital and FAIR – the Ballad of the ELN Journey - A PSDI webinar

https://www.psdi.ac.uk/ Seekest thou the road to, all that’s digital and FAIR – the Ballad of the ELN Journey Please use the Q&A feature if you have a question during this webinar and we will answer them at an appropriate time PSDI Webinar 14th August 2025 Dr Samantha Pearman-Kanza University of Southampton Presentation Outline About Me Why are we here? The Twisty Turny ELN Journey Research Challenges & Considerations Case Study Learnings Relevant PSDI Resources I’m here to keep her in line! Now remember…you promised not to sing! About Me Computer Scientist turned Web Scientist masquerading as a Chemist Principal Enterprise Fellow at University of Southampton Principal Investigator for CaSDaR (Careers & Skills for Data-driven Research) Pathfinder Lead on Process Recording for PSDI (Physical Sciences Data Infrastructure) Lab Horizons Columnist: CompSci Cat Advisory Boards/Committees: Future Labs Live, London Labs Live, MADICES, , Machines Learning Chemistry, RSC-CICAG, STRIX Award, KnowLedger: An Open Digital Research Notebook for Research Data Management Research Interests: Data Stewardship, FAIR Data, Semantic Web Technologies, IoT, Research Data Management, Digitisation, Lab of the Future, Paperless Labs, Re-use of Technology Why are we here? Many scientific researchers have a fragmented paper/digital approach to writing up their experiments Research and data generation is being wasted due to these issues as people cannot access or build on others work Consequently, a vast quantity of scientific research cannot be re-used or reproduced “Lab book use at various levels of academia” by ErrantScience.com is licensed under CC-BY-NC So is paper the root of all evil? Not necessarily! Paper records aren’t always bad e.g. Darwin’s early Notebooks Electronic records / methods aren’t always good e.g. spreadsheets with unintelligible column names Just because something is in an electronic form does not immediately make it high quality data! CC BY-ND 4.0 Errant Science - https://errantscience.com / Consequences of paper (or poor electronic sharing…) Cartoon drawn by Dr Cerys Willoughby for Kanza, S., Willoughby, C., Gibbins, N., Whitby, R., Frey, J.G., Erjavec, J., Zupančič, K., Hren, M. and Kovač, K., 2017. Electronic lab notebooks: can they replace paper?. Journal of cheminformatics, 9(1), p.31. https://doi.org/10.1186/s13321-017-0221-3 Therefore… Ultimately, we should be moving towards maintaining electronic records because they are: Easier to share Easier to search Easier to backup Accessible from multiple locations Move over Pencil! Sounds like we need some sort of Electronic System… “It Was A Normal Day Of Office When A Sweet Voice Break - Computer Vs Paper” – free download from SeekPNG Digital tools should enable Capturing data in a more structured form to improve quality Improved capability to search for and find your own work Better sharing between researchers Preservation of valuable research for future use Production of FAIRer data for publication ELNs are a potential solution to this! “Electronic Lab Notebooks are great, but not on vacation” Cartoon by Phil Johnson for MIT. PhD Research (2014-2018) ”What do you mean people are still using paper?! Surely this ELN thing is just THE ANSWER…..I’m sure it’s a simple solution….” Samantha Kanza, 2014 Foolish Mortal! State of Play (2022-2023) ORGANISING & LINKING WORK Similarities •Necessity to link between paper and electronic demonstrates a use of paper •Still a clear pattern of using codes/links to bridge this gap Differences •Increase in software to organise and link work BARRIERS TO DIGITAL RESEARCH •Logistical Barriers (Cost, Time) •People Barriers (Unwilling to adopt, Training) •Data Barriers (Data Import/Export issues, Archiving, Data Integration) •Hardware & Software Barriers (Storage, Hardware & Software Interoperability, Links between software packages) Much the same as 2018 USE OF A DIGITAL NOTEBOOK/ELN In our 2021 Survey 55% said YES to using a Digital Research Notebook (note that is not necessarily an ELN) In our 2022 Survey 50% said NONE to what ELN do you use, with 17% using Generic Notebooks and 33% using 17 Different ELNs USE OF PAPER VS ELECTRONIC Similarities •Researchers still work in different ways using a mix of paper/electronic methods •Paper still more used for planning, with a heavy reliance on computational methods for analysis and writeup Differences •Reduction in only using Paper EVOLUTION OF ELNS •Many different terms for ELN “Digital Research Platform, ERN, RDM Software” •Platforms now exist that encompass •ELNs (Electronic Lab Notebooks) •LIMS (Laboratory Information Management System) •SDMS (Scientific Data Management System) •Inventory / Sample Management •NOT JUST A REPLACEMENT SATURATED MARKET •There are still over 80 active ELNs on the Market PSDI Process Recording Case Studies Case studies of implementing different Process Recording Systems oGeneric Notebook Implementation oUniversity of Nottingham – OneNote in Chemistry Teaching Labs oUniversity of Southampton – OneNote in Chemistry Teaching Labs oWellington College – OneNote in School Labs across Chemistry, Physics & Biology oOpen Source In House ELN oUniversity of Nottingham -AI4Green in Undergrad & Postgrad Labs (Student Edition & Research Edition) oLarge-Scale Commercial ELN oUniversity of Southampton - Revvity Signals in the Postgraduate Labs across 12 different Research groups CC BY-ND 4.0 Errant Science - https://errantscience.com/ Challenges & Considerations Choice Infrastructure Cost Time Data People / Change Management Image created using imgflip.com Electronic Lab Notebooks There are now over 85 active ELNs on the market! LabFolder Labguru ELN Labii LabKey ELN LabLog LabsForm LabSpace LabStep LabTrack ELN LabTrove LabVantage LabWare ELN Laby Limsophy LIMS LogBook Logilab LOGS-ELN Mbook MyLabBook NOMAD ELN NotebookMaker NuGenesis  ACAS Active LN AgiLab ELN Agilent SLIMS AI4Green Alchemy ELN Arxspan ELN Benchling ELN BioChemLab Solutions ELN BioRails Biovia Notebook Bookitlab CBIS E-Notebook CDD Vault ELN CERF 5.0 ChemCart ELN Chemia Chemotion Colabra ELN CompuDrug ELN Dotmatics ELN E-WorkBook Ec-LabNote eLabFTW eLabJournal eLabNotes EmsoChemLab Espresso ELN eStudy eSystems Formulator Gene Inspector GenoFAB GOLims Herbie iLES Platform InELN iQ Kadi4Mat Lab Integrated Data (LabID) LabArchives LabCloud LabCollector ELN Online ELN Worksheet Open Enventory openBIS OpenText ELN PASTA-ELN PatentSafe ELN quattro/LJ RedFox Rspace SampleDB Sapio Seamless ELN SciCord ELN/LIMS Sciformation ELN Scilligence ELN SciNote Signals ELN Stackwave ELN STARLIMS ELN Studylog Sun Bio ELN Thermo Scientific Core ELN Unacountable Generic Notebooks Note-Taking Apps Apple Notes Evernote GoodNotes app Google Keep Joplin Notability Notion OneNote Simplenote Obsidian Zim Text Editors Emacs Notepad Notepad++ Sublime TextEdit Vi Vim Word Processors Apple Pages Google Docs Libre Office Writer MS Word Cartoon created by ErrantScience.com for AI4SD: licensed under CC-BY-NC Choice Considerations Digitising is great, but WHY are you doing it? What data are you recording? How? Where? What data is not being recorded? What are the actual pain points that you are trying to solve? Does the software align with what you are trying to achieve? Implementing Digital Notebooks isn’t just about the software, is your entire plan/setup moving towards your goal? CC BY-ND 4.0 Errant Science - https://errantscience.com/ Domain Consideration Different domains have different requirements and data types Universities (and many companies) will need to cater for a variety of domains Finding one ELN for your entire institution is unlikely CC BY-ND 4.0 Errant Science - https://errantscience.com/ Career Level Consideration Different career stages can have different needs from Digital Notebooks Undergraduate tools need to facilitate learning – are closed formats an issue here? Postgraduate/Industry tools need to enable the capture and production of FAIR data Important questions How automated do you want/need this ELN to be? Is a fully fledged ELN or a Generic Notebooking tool more appropriate? CC BY-ND 4.0 Errant Science - https://errantscience.com/ Case Study Learnings Generic Notebook Tool Selection of simple notebooking tool to replace paper Chose a known tool already implemented in the current ecosystem AI4Green Creation of a two new ELN Tools (Pedagogical Version for Teaching, Research Version for Researchers) Revvity Signals Selection of a large-scale ELN tool that could meet the needs of different subdomains of Chemistry Chose a tool that is compatible with heavily used departmental software (ChemDraw) There is no “right answer” (although there can be some wrong ones…), its more about HOW you implement it Infrastructure/Institutional Considerations Infrastructure Setup Stakeholders Finances Time Procuring Devices Environmental Setup Cartoon created by ErrantScience.com for AI4SD: licensed under CC-BY-NC Financial Considerations Licensing costs: ELN Licenses, Custom Notetaking Licenses Renovation costs: Installing more power sockets/ethernet sockets / WIFI boosters Power costs: Facilitating charging of devices “University Funding in a Nutshell” by ErrantScience.com is licensed under CC-BY-NC Hardware costs: Replacing legacy equipment, providing devices for digital capture (e.g. in the lab or in the field) Maintenance & Development costs Staffing Costs: Setup & Run ELN Case Study Learnings One Note at Wellington Implemented a policy where students starting in the first year needed to bring a MS Surface, existing students were given a choice, this permeated through to all students having surfaces after several years. Lab refurbed to have power sockets and space for devices. OneNote/AI4Green in Teaching labs at Nottingham MS Surfaces purchased for the lab as part of refurb, Lab refurbed to have power sockets and space for devices. AI4Green in Postgraduate Lab 1 Screen per fumehood raised above lab bench, tucked away mini PCs, mice and keyboard on benches, wired internet connection Revvity Signals Group Leaders/Students asked about hardware preference, hardware obtained if desired DEDICATED LAB HARDWARE IS KEY! NO CROSS CONTAMIMATION! Data Considerations Backup, Storage & Security Data Capture Experiment Templates FAIR Data Data Sharing Data Publishing CC BY-ND 4.0 Errant Science - https://errantscience.com / Backup, Storage & Security Many researchers mistrust Digital Tools, particularly if they don’t know where the data is stored There are concerns about data exit strategies – need to make sure data is stored and backed up in a way that this is feasible Consider what export functionalities are available? Security measures and vulnerabilities need to be considered CC BY-ND 4.0 Errant Science - https://errantscience.com / Case Study Learnings Generic Notebook/OneNote Backed up regularly as part of MS Ecosystem AI4Green Custom made solution with embedded backups – less concern about vendor trust as this was an in-house solution Revvity Signals Custom backup created pre trial using API, script runs daily to collect all closed experiments, providing a formal data exit strategy and additional backup in case of any issues Trust & Data Exit Strategy is KEY! Always implement a Data Exit Strategy before putting your data into any new system! Data Capture / Templates Different domains will require different levels of data capture What data formats need to be supported for import/export? Consider the different types of data that will be recorded and make templates to ensure that all the relevant data is captured Fewer templates are ideal, but need to cover the range of data CC BY-ND 4.0 Errant Science - https://errantscience.com / Sharing / Publishing / FAIR Data A key reason to implement any Digital Notebook is to produce FAIRer Data for Publication – so your implementation plan needs to take this into account Another key reason is sharing data among colleagues/groups, its important to identify if people are finding it easier to locate relevant Digital Notebook entries to save time / inform Cartoon created by ErrantScience.com for AI4SD: licensed under CC-BY-NC Case Study Learnings Generic Notebook Simple Templates created to match lab and classroom work within the OneNote system. Notebooks shared between classes and teachers. AI4Green Structured sections for notes and writeup provided for students. Notebooks shared between classes and teachers (undergraduate labs) and between researchers and supervisors (postgraduate labs) Revvity Signals Custom templates were created based on the areas of chemistry that the trial would be supporting Group Leaders dictated sharing across groups depending on privacy/embargo requirements. All notebooks shared with Group Leaders. Work with the users and group leaders to create templates to capture structured relevant data! Change Management / Adoption People are arguably one of the biggest barriers Top-down influence can make or break this Need to get the whole group on board Concerns about changing processes Hard to persuade people to embark on a journey with a lot of front-loaded work, unless they really understand the benefits CC BY-ND 4.0 Errant Science - https://errantscience.com/ Case Study Learnings Define the problem you are trying to solve Identify stakeholders, roles and required involvement Engage with relevant groups and hierarchies to fully understand the landscape Build a vision of success – make people understand the benefits and what you are trying to achieve Regular Support IS KEY! Nobody will engage long term without it! The Final Reveal It was Agatha all along! Hey who turned me into a witch?! https://www.reddit.com/r/MemeRestoration/comments/lynitm/agnes_winking_in_marvels_wandavision/ https://www.marvel.com/tv-shows/agatha-all-along/1 Acknowledgements PhD Supervisory Team: Nick Gibbins & Jeremy Frey PSDI/Southampton ELN/OneNote Team: Matthew Partridge, Nicola Knight, Cerys Willoughby, Colin Bird, Jeremy Frey, Simon Coles, Sally Bloodworth, Philip Leadbitter, Andrew Hector, Janice Sumner, Mark Goulding, Mansoor D’Lavari, Bobbie McVey, Mark Light, Sam Perry, Thomas Logothetis Data Revival Team Samuel Munday, Jeremy Frey, Louis McLean, Finlay Morrison, Ashley Unitt ERN Community Valerie McCutcheon, Cerys Willoughby AI4Green Team Jonathan Hirst, Peace Nwafor, Cerys Willoughby, Katherine Jolley Wellington School Caroline Evans, Jo Grundy Witchy Imagery https://collider.com/agatha-all-along-witch-references-end-credits/ AND SHARKCAT! If you want to see more of me sign up to our showcase!