Exploring electronic lab notebooks (ELNs) at a R1 institution in the Southeast USA

Abstract

Purpose

This study aims to build a better understanding of researcher needs regarding support for data that you create, store, and/or manage using an electronic lab notebook (ELN), also referred to as electronic research notebook (ERN). The study also articulates the need for risk assessment for ELN products used by researchers for both open data and sensitive data that require standards.

Design/methodology/approach

The author used a participatory action research mixed-methods approach. A working group was formed from an ELN initial meeting. The working group team investigated several institutional ERN solutions by setting up trials, speaking with representatives from other research universities with ERN solutions and conducting internal and external research. This culminated in a broader-scale survey exploration.

Findings

Findings reveal there is no single institutional ELN license solution to satisfy all scientific disciplines. There is a need to develop foundational tools needed by all, provide additional tools and uses cases with best practices that can be tailored to various labs and research processes and develop a how-to guide on how to assemble the parts to create a useful ELN solution.

Research limitations/implications

The research implications include providing support for researchers selecting an ERN solution through a combination of online guides, short tutorials and training. There is a need to develop foundational tools, uses cases with best practices that can be tailored to various labs and research processes and how-to guide on how to assemble the parts to create a useful hybrid-ELN solution.

Practical implications

Practical implications include aligning available ERN solutions with other institution provided technologies across the research life cycle to provide researchers a suite of tools to conduct and manage their research. Further investigating educational license discounts for courses using eLabJournal, RSpace, Protocols.io, Open Science Framework, LabArchives or other ERNs currently funded by student course fees via grant funded projects are key implications.

Social implications

Social implications include the research computing environments of researchers that use ELN solutions approved through institutional risk assessment for open data are in compliance with university regulatory frameworks for use of the software in research.

Originality/value

The originality of this study includes risk assessments of ELNs solutions to better guide researchers in the selection process. To the best of the author’s knowledge, this survey was the first exploration of ELN on campus resulting in a final report to senior stakeholders. This study also highlights a developing grant proposal to further develop support across labs and campus.

Citation

Smith II, P.L. (2023), "Exploring electronic lab notebooks (ELNs) at a R1 institution in the Southeast USA", Digital Library Perspectives, Vol. 39 No. 1, pp. 23-38. https://doi.org/10.1108/DLP-02-2022-0013

Introduction

In FY 2021, the United States Department of Health and Human Services (HHS) Office of Research Integrity (ORI) Notice for Funding Opportunity: Considerations, Options, and Resources for Data Management in Public Health Service Funded Research Opportunity Number: IR-ORI-21–001 included eight topics of research interest for this funding opportunity. The eight topics included as follows:

1. provenance;

2. recordkeeping;

3. organization of data;

4. storage of data;

5. reporting of research data and results;

6. sharing and access;

7. institutional policies; and

8. data management standard operating procedures (SOPs).

The HHS funding solicitation defined “recordkeeping” as effective “record of how the research/experiment that resulted in the production of data was conducted.” While some universities have devised new services to better manage data and other information derived from research, many researchers flounder in a disorganized way and rising accumulation of useful findings may be lost or unavailable when conducting future research (Kroll and Forsman, 2010, p. 5). “An easy way to increase the legibility, tidiness, and overall quality of documentation, can be the introduction of an electronic laboratory notebook) in a research unit” (Hewera et al., 2021, p. 3).

An electronic lab notebook (ELN) describes a software resource which records how research resulting in the production of data is conducted. The use of a resource that documents research resulting in the production of data is not limited to within laboratory environments. Thus, the term “electronic research notebook” is more applicable to denote use across research units:

An electronic lab notebook is a software system for documenting your research work. In its most basic form it might simply provide a word-process-like interface to replicate the way you currently use a paper notebook, but with additional benefits such as shareability, searchability, password protection and backup (University of Cambridge, 2021a).

“Many electronic lab notebook packages offer a wealth of other features too, enabling data management, collaboration, integration with other software, laboratory information management system (LIMS)” (University of Cambridge, 2021a, 2021b), and research protocols. “Ideally, research protocols should be registered in advance and monitored in virtual notebooks” (The Economist, 2013) to support open science. ELN and electronic research notebook (ERN) are used interchangeably within the scope of this paper.

In continued efforts to better understand and support the needs of researchers, the Libraries conducted an initial meeting to gauge ERNs interest as a potential institutional subscription in August 2019 which followed several previous efforts led by the Libraries and the Faculty Senate Research and Scholarship Council to investigate pursuit of campus-wide ERN solutions.

A working group was formed from the initial meeting. The working group team investigated several institutional ERN solutions by setting up trials, speaking with representatives from other research universities with ERN solutions and conducting internal and external research. This culminated in a broader-scale ELN exploration.

Literature review

Preconfigured commercial software packages (Wirth and Ford, 1986; Winn et al., 1992) such as ELNs which replicate analog (paper) information into digital (electronic) format have led to increasing use in a variety of scientific biological applications in all scientific fields including biology, chemistry, life science, engineering fields and biotechnology (LabsExplorer, 2019). Storing, organizing, and sharing and accessing data within a lab electronically is an ELN dilemma:

How does one store information flexibly enough such that any possible experiment performed in a lab [or research environment] can be recorded, while still organizing that information such that it can be searched and/or mined in a useful way, with enough detail that similar experiments between scientists can be reasonably compared? (Rees et al., 2013, p. 1).

A good approach to the ELN dilemma involves selection of solution based on usefulness to intended scientific disciplines, costs, individual or group, supervisor features, operating systems, devices to operate the lab management application, and data security/compliance to name a few. The evaluation of an ELN solution involves assessments of interface design, workflow suitability, content creation tools, data management/storage, integration with other software and/or online services, collaboration features, PI/supervisor features, and export features[1] for either individual, group, or institutional considerations.

ELNs assist researchers in the management of data during key stages in research throughout the biomedical data lifecycle within the lab and across research environments. The key stages in the biomedical data lifecycle include at the core “Store and Manage” surrounded by non-linear stages of “Plan and Design”, “Collect and Create”, “Analyze and Collaborate”, “Evaluate and Archive”, “Share and Disseminate” and “Access and Reuse[2]” “ELNs comprise software that helps researchers to document experiments, and that often has features such as protocol templates, collaboration tools, support for electronic signatures and the ability to manage the lab inventory” (Kwok, 2018, p. 269). However, the issues of ELN synonymous with “paperless”, accessibility, preservability and legality of electronic documents and signatures can be addressed with a hybrid ELN system.

Key requirements for a successful hybrid electronic lab notebooks system

According to Kihlén and Waligorski (2003, p. 1008), the key requirements for a successful hybrid ELN system include the following:

• End-user acceptance; the ELN must offer ease of use comparable with or better than its paper counterpart.

• Fully featured; an electronic system must be constructed in such a way that paper notebooks can be altogether eliminated.

• Availability; like a paper notebook, the ELN must allow for instant note taking as observations are made. Access to a personal ELN must be provided to each scientist at all the usual workplaces.

• Legal; the system must provide legal evidence for patent protection of the same or higher quality than the currently used paper notebooks.

• Flexibility; data differ significantly between scientific disciplines. An electronic system must be able to accommodate all kinds of scientific data.

• Access; all lab notebook records should be categorized and fully searchable.

• Longevity; the system shall support archiving of all lab records for a period of at least 30 years – beyond the projected lifetime of computers running the ELN system.

Searching electronic lab notebooks via National nstitutes of Health National Library of Medicine PubMed

On April 26, 2022, a search query for “electronic lab notebook” (ELN) in the United States National Institutes of Health (NIH) National Library of Medicine (NLM) National Center for Biotechnology Information (NCBI) PubMed® (including MEDLINE®) data base yielded 56 results. “PubMed comprises more than 33 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites”[3]. “MEDLINE is the National Library of Medicine’s premier bibliographic database that contains references to journal articles in life sciences, with a concentration on biomedicine [4]”. The PubMed trend analysis displayed “electronic lab notebook” search results of 1 in 1992, 2 in 2003 and 2005, 1 in 2007, 2 in 2009, 1 in 2010 and 2 in 2011. There was an increase to 3 in 2012 and 5 in 2013. There was a decrease to 2 in 2014 and 2 in 2015. There was an increase to 3 in 2016, 4 in 2017, 5 in 2018, 8 in 2019, 7 in 2020, 6 in 2021 and 7 in 2022. The trend analysis (Figure 1) displayed no articles from 1993 to 2002. Articles were mostly 2 in years from 2003 to 2011 followed by a peak in 2013 then decline in 2015 followed by steady increases to present day for a total of 56. However, there was a discrepancy of 6 more results on the PubMed trend analysis visualization than displayed 50 search results. Further review revealed some overlap in Epubs publication date resulted in duplicates in trend. A search query of “electronic laboratory notebook” yielded 107 results. There is growing literature on ELN in PubMed to support further exploratory efforts.

Electronic lab notebook survey at University of Florida (2020)

ERNs are foundational tools for the digital management of research, acting as software versions of physical lab notebooks and collaborative data management tools. Tools designed as ERNs often provide additional features, such as protocol templates, inventory management tools, security controls and audit trails.

In June 2020, the University Library conducted an Electronic Lab Notebook Survey – University of Florida Institutional Review Board (UFIRB # 202001407) to build a better understanding of researcher needs regarding support for using ELNs. The University of Cambridge and Harvard Medical School (HMS) ELN resources were referenced in developing a 14 questions Qualtrics survey. The ELN survey was distributed through the Office of Research, Faculty Newsletter, IT Research Computing, and other campus networks.

Participants, primary college and University of Florida research center affiliations

A total of 157 University of Florida (UF) participants completed the ELN survey. The participants include 115 Faculty, 10 Staff, 10 Graduate/Professional Student, 6 Postdoctoral Fellow, 6 Undergraduate Student and 4 Other (e.g. Extension Faculty, Research Scholar, Lab Manager). The top primary college affiliation of the participants includes Agriculture and Life Sciences 42.95% (64), Medicine 18.79% (28), Engineering 6.71% (10), Veterinary Medicine 6.715 (10), Liberal Arts and Sciences 5.37% (8), Other 4.70% (7) – includes Interdisciplinary Center for Biotechnology Research (ICBR), AUX, IFAS, Public Health and Health Professions 4.03% (6) and Nursing 3.36% (5).

Types of data managed using an electronic lab notebook and types of electronic lab notebook used by UF researchers

A total of 77 (28%) of participants manage experimental data, 53 (19.27%) manage observational data, 39 (14.18%) manage reference data, 30 (10.91%) do not manage data using an ELN, 28 (10.18%) manage Computer code data, 28 (10.18%) manage Derived data and 20 (7.27%) Other – (includes Do not use ELN, image data, lab database, EHR [electronic health record] data).

Top electronic lab notebook features ranked by the participants

The UF researchers that participated in the 2020 ELN survey ranked data management 14.26% (82), export features 13.39% (77), workflow suitability 13.22% (76), principle investigator (PI)/supervisor features 12.87% (74) and interface design 12.35% (71) among the top features relevant to basic set of “core” functions for an institutional-level ELN solution. The Agriculture and Life Sciences, Medicine, Engineering and Veterinary Medicine represented the primary college affiliation of most respondents that completed the survey. The survey was completed by Faculty (115), Staff (10), Graduate/Professional Student (10), Postdoctoral Fellow (6), Undergraduate Student (6) and Other (4). The quantitative and qualitative survey results support a variety of ELN features.

Types of electronic lab notebook used to manage data

The types of products [comprises both productivity tools leveraged as do-it-yourself ELNs and official ELN/ERN] survey participants use to manage data include: Dropbox 21.76% (57), Google Drive 15.65% (41), OneDrive 15.65% (41), Other 12.21% (32), OneNote 9.16% (24), Evernote 4.96% (13), LabArchives 3.44% (9), Benchling 3.05% (8), REDCap 2.67% (7), Confluence 1.91% (5), Studies Notebook 1.53 (4), Open Science Framework 1.15% (3), e-Notebook 1.15% (3), e-Workbook 0.76% (2), Labfolder 0.76% (2), RSpace 0.76% (2), SciNote 0.38% (1), OpenLab 0.38% (1), Labstep 0.38% (1), LabGuru 0.38% (1), Labcollector 0.38% (1), LabCloud 0.38% (1), Docollab 0.38% (1), Brightlab 0.38% (1) and Biovia 0.38% (1).

Findings

The University of Florida researched the following similar findings in 2020 about ERN and ELN as previously conducted by the University of Cambridge and Harvard Medical School . The findings include but not limited to the following:

• There is no single ELN solution to satisfy all researchers across all disciplines.

• An ERN solution must be foundationally modular, discipline agnostic, universally relevant and its features extensible.

• Tools designed as ERNs (i.e. LabArchives, SciNote, Benchling) are currently costly for institutional subscriptions, but have affordable or free options for individuals and research groups who need specialized tools.

• UF already provides institutional-grade, discipline-agnostic tools that meet many researchers’ needs, including Dropbox, Google Drive and Microsoft products including OneDrive, Teams and OneNote though not feature-rich actual ELNs.

Recommendations

The working group recommended the following based on working group and survey results:

• Provide support for researchers selecting an ERN solution through a combination of online guides, short tutorials, and training. The guide would describe the use of tools already available to researchers and students to assemble the solution that meets their lab and research process needs.

• Develop foundational tools, most likely needed by all.

• Provide additional tools and uses cases with best practices that can be tailored to various labs and research processes.

• Develop a how-to guide on how to assemble the parts to create a useful ELN solution.

Developing support for electronic lab notebook at an institution requires collaborations

The ability to effectively manage data, logically organize and annotate data, process large data sets and extract information (Ludtke et al., 2003, p. 556) and documentation of experiments data quality (Gerlach et al., 2020, p. 257) are necessary for good data management in research practices. ELNs are tools that can augment data acquisition, analysis, presentation and archiving (Gerlach et al., 2020, p. 257) processes to support good data management in research practices. The Harvard University Longwood Medical Area ELN Resources[5] include support for eLabJournal, RSpace and LabArchives for its researchers. LabArchives, eLabJournal, and RSpace are intended for all scientific fields and topped the ELN list in 2019 and 2021 (LabsExplorer, 2021). The University of Cambridge Data Management Guide Electronic Research Notebook Products (University of Cambridge, 2021b) resource includes a table of ERN products last updated March 3, 2021. The resource includes the categories of suitability, platform, storage and free/cost as criteria to assess ERNs.

The developing support for ELN at the University of Florida (UF Libraries, 2021) includes conversations between campus stakeholders such as Libraries, IT Research Computing, Research and scientists from Division of Infectious Diseases and Global Medicine in the UF College of Medicine, Department of Molecular Genetics and Microbiology and Department of Biomedical Engineering. External stakeholders include RSpace, eLabJournal and LabArchives.

Electronic lab notebook features comparison considerations

With a plethora of ELN products available to researchers across institutions, there are some important factors suggested by Harvard University Medical School Information Technology Research Computing ELN Services (Harvard University Medical School Information Technology, 2022) to consider in the selection of ELN for researchers. Some important factors to consider in the selection of ELN include but not limited to:

• experiment journaling;

• journal organization;

• protocols and SOPs;

• inventory support;

• integration with other platforms;

• mobile devices;

• onboarding, training, and support; and

• single sign-on.

Other important factors include interface design, workflow suitability, data management and storage, collaboration features, principle investigator (PI) and supervisor features, and Export features. Lastly, in relation to storage and security, other key factors include cloud vs local, back-ups, data security standards and data retention. Ultimately, the purchase decision should result from collaborations between stakeholders, principally academic units, labs, researchers, IT research computing, research office and libraries.

Developing electronic lab notebook support at the University of Florida

On April 14, 2022, a postdoctoral associate from the Shen Lab at the UF Scripps Biomedical Research facility contacted the Libraries with questions about implementing a Laboratory Information Management System (LIMS) along with an attachment of details for system requirements. The Shen Lab joined the new UF Scripps Biomedical Research (https://scripps.ufl.edu/departments/). The postdoctoral associate shared that their lab is planning to implement a LIMS to support Natural Products Discovery Center (https://scripps.ufl.edu/departments/centers-and-specialties/natural-products-discovery-center/) project the lab’s general data management needs. The postdoctoral associate articulated the following three questions:

Q1.

Whether or not UF have existing (generic) solutions for LIMS that can be implemented by labs?

Q2.

Do you know what kind of proprietary systems people in UF typically use, if any?

Q3.

Do you have any personal recommendation on a system that we can use, based on our requirements?

In reference to Question 1, the libraries consulted with campus information technology research computing and clinical and translational science information technology departments in reference to Question 1. Their responses included but not limited to referral to several faculty/scientists involved in previous LIMS efforts along with referral to the UF Southeast Center for integrated Metabolomics (http://secim.ufl.edu/) unit most qualified to address Question 1.

In reference to Question 2, the libraries provided data from the 2020 ELN survey previously discussed in Types of ELNs used to manage data section under the Electronic Lab Notebook Survey at UF (2020) section in addition to University of Cambridge and HMS references also mentioned in this paper which the postdoctoral associate found very useful.

In reference to Question 3, the Libraries suggested eLabJournal and RSpace based on previous exploration of these two products by HMS with additional support for eLabJournal by the Boulant Lab who previously used the product at Heidelberg University.

A scientist from the Department of Infectious Diseases, Virology at Heidelberg University recruited by the University of Florida Department of Molecular Genetics and Microbiology contacted the University of Florida George A. Smathers Libraries on June 14, 2021 to inquire about ELN and inventories at UF. The scientist inquired if there were any restrictions for using an ELN at the University of Florida. The scientist was using eLabNext’s eLabJournal and wanted to continue using eLabJournal for his new lab at UF. Some researchers use ELNs also referred as ERN (www.data.cam.ac.uk/data-management-guide/electronic-research-notebooks) to document project management, data archival, and other research processes. There are many ELN solutions with varied features that support data management, collaboration, integration with other software, LIMS, and more. Researchers sometimes ask the libraries for ELN recommendations. The libraries do not endorse specific ELN but can provide recommendations based on University of Florida Integrated Risk Management Fast Path Solutions institutional risk assessments of ELNs for open data. The UF IRM FPS, https://irm.ufl.edu/, is a comprehensive list of pre-assessed software and computing environments. The institutional risk assessments of two ELNs [eLabJournal, www.elabnext.com/products/elabjournal/ and RSpace, www.researchspace.com/] for open data required collaborations between the libraries information technology, researchers and ELN vendors to complete risk assessments for ELN products to enable support for researchers.

On October 5, 2021, the UF Libraries Data Management and Curation Working Group organized a RSpace Academic ELN Trial inquiry meeting with select researchers, staff, and stakeholders that resulted into a RSpace demo for the University of Florida on October 25, 2021. The initial scoping meeting followed by a demo prompted UF IRM FPS assessment of RSpace for open data which influenced the vendor to explore certification standards such as International Standard Organization (ISO) 27001 certification with National Institute of Standards and Technology (NIST) 800-HIPAA reference framework to increase capacity for sensitive data. The UF IRM FPS risk assessment was completed for RSpace ELN on 12/2/2021 (Figure 2).

The UF IRM FPS risk analyst provided the following risk assessment closure detail for RSpace which was titled Risk Assessment Complete for: Smathers Libraries: Researchspace (RSpace) eLab Notebook 2021–10-29. Below is an email response from the UF IRM risk analyst.

12/02/2021 Review and approved for FPS for open data only. They are working towards ISO27001 compliance in the next 18 months. Once this has been completed, then we can add sensitive data to the FPS but still recommend restricted data to be reviewed. Reviewed for cloud deployment. Recommend implementation of SSO [Single Sign-On]. When vendor has completed ISO27001 certification with NIST800-HIPAA reference framework we can review again for sensitive data for FPS. Once this has been completed, then we can add sensitive data to FPS but we still recommend restricted data to bereviewed on a case by case basis. – UF IRM Risk Analyst

What are sensitive data?

Within the scope of this article, some sensitive data (UF, 2012) include data types such as animal research protocols, system security plans, and unpublished research results with justification descriptions as competitive and commercial potential and security concerns. Other sensitive data types (non-exhaustive) include exams with justification description of exam integrity and employee data (except social security number) with justification description employee privacy. UF Research Computing HiPerGator-RV (UF Research Computing HiPerGator-RV, 2018) and UF Clinical and Translational Science Institute REDCap (UF CTSI, 2022) are technology applications available for use with restricted and sensitive data for UF researchers. HiPerGator-RV is a secure computing environment. REDCap is a secure Web-based application.

What is International Standard Organization/ International Electrotechnical Commission 27001:2013?

The International Standard Organization (ISO)/International Electrotechnical Commission (IEC) 27001:2013 (commonly referred as ISO27001) “specifies the requirements for establishing, implementing, maintaining and continually improving an information security management system within the context of the organization”. ISO (2022) “ISO/IEC 27001 was prepared by Joint Technical Committee ISO/IEC JTC 1, Information technology, Subcommittee SC 27, IT Security techniques” (ISO, 2013).

What is National Institute of Standards and Technology800–66 (Health Insurance Portability and Accountability Act)?

The National Institute of Standards and Technology (NIST) SP 800–66 Rev. 1 An Introductory Resource Guide for Implementing the Health Insurance Portability and Accountability Act (HIPAA) Security Rule (commonly referred as NIST800-HIPAA) “focuses on the safeguarding of electronic protected health information (EPHI) (NIST, 2008)” for federal agencies with information types subjected to the HIPAA Security Rule . The NIST SP800-66 Rev.1 (2008) is available for download via https://nvlpubs.nist.gov/nistpubs/Legacy/SP/nistspecialpublication800-66r1.pdf. The NIST SP 800-66 Rev. 2 PRE-DRAFT Call for Comments: Implementing the NIST, (2021) is currently not available for download:

The Health Insurance Portability and Accountability Act of 1996 (HIPAA) is a federal law that required the creation of national standards to protect sensitive patient health information from being disclosed without patient’s consent or knowledge (US HHS, 2018).

UF libraries electronic lab notebook conversation with a vendor as stakeholder/collaborator

On December 21, 2021, a LabArchives representative requested a UF Integrated Risk Management Fast Path Solution for January 2022. The request articulated:

• awareness software product risk assessment; and

• eagerness to comply with risk assessment for LabArchives

The request prompted a response to the vendor detailing current ELN efforts to support researchers at UF. The following response was sent to a vendor on January 7, 2022 to clarify software product risk assessment for ELN for open data.

In efforts to support ELN at UF, the position of the UF Libraries working in collaboration with UF IT Research Computing and UF Research is to provide support for three ELNs (also referred as ERNs (ERN)) similar to the Harvard University Longwood Medical Area (LMA) ELN support for eLabNext (eLabJournal), RSpace and LabArchives. [See: Harvard University Supported ELNs Across the LMA https://datamanagement.hms.harvard.edu/analyze/electronic-lab-notebooks/elns-lma.]

The UF Libraries IT department recommends college/department that is using a particular ELN to initiate institutional risk assessment of the software product for open data. Sensitive and restricted data requires extensive security protocols beyond institutional assessment for open data. Thus, institutional assessment fast path solutions (basic security standards) is recommended for open data not sensitive or restricted data. The following ELNs have been institutionally risk assessed for open data:

• eLabJournal – initiated by a scientist in the UF Department of Molecular Genetics and Microbiology – approved by institutional risk assessment in August 2021.

• RSpace – initiated by the Data Management Librarian in the UF George A. Smathers Libraries – approved by institutional risk assessment on December 2, 2021.

• LabArchives – submitted request for a scientist in the UF Department of Biomedical Engineering to initiate institutional risk assessment for LabArchives for open data – January 7, 2022 (Update: discovered LabArchives was approved by institutional risk assessment for teaching in early 2021).

Thus, one role of the Libraries is as facilitator/resource broker in efforts to procure institutional risk assessment for select electronic notebook solutions and other data management products/tools used by researchers, students and staff, proactively and retroactively, where appropriately applicable.

The Libraries submitted a federal grant proposal under ensuring research integrity – research, development and demonstration program solicitation from U.S. Health and Human Services (HHS) that includes collaboration with scientists from the Boulant Lab to incentivize research integrity and good laboratory practice (GLP) via ELN (i.e. RSpace and eLabJournal) supported by selectively relevant Collaborative Institutional Training Initiative (CITI Program) courses, (i.e. Research Study Design, GLP, Data Management and Security for Student Researchers: An Overview, Responsible Conduct of Research and False Claims Act: A Primer and Guide for Research Organizations), Figshare instance, Open Science Framework and Protocols.io tools on March 14, 2022 which is currently pending sponsor review. UF scientists from two different departments support the grant proposal project idea and have already contributed information for their respective ELNs for the project proposal budget and budget narrative on January 5, 2022.

Electronic lab notebooks investigations from Harvard Medical School to an Health and Human Services grant proposal

The Finding the Right Electronic Lab Notebook with the Corey Lab (Harvard University Long Research Data Management, 2020) news announcement developed by Joanna Loveluck at Harvard University on October 8, 2020 is an interestingly relevant article for the University of Florida and other institutions exploring ELNs. The article describes final selection of two ELNs, RSpace and eLabJournal, for further exploration following an initial ELN assessment process that started in September 2019. The HMS Research Computing began a Blavatnik Funded Discovery project to investigate potential ELN software for the HMS community. Below is an excerpt from the Loveluck article on supporting further investigation of two particular ELNs:

“From the original list of 6 products, we landed on 2 that we wanted to investigate further, RSpace, and eLABJournal. During a 90-day Proof of Concept (PoC) users from the Corey lab, in addition to other groups from BCMP (Blacklow lab and Adelman lab), andthe Wyss Institute (Immuno-Materials Platform), were given access to trial versions of these products. Users could create protocols (or templates), and document experiments including attached data files, analysis, annotated images and more. We asked users to test each of the products using old experiments. Everything needed to be securely saved, with every change tracked for compliance purposes, and to prove provenance. It was also important to all users that they could organize their data, collaborate with otherresearchers, and search through experiments” (Loveluck, 2020).

Presently, eLabJournal and RSpace are part of a U.S. Department of Health and Human Services (U.S. HHS, 2022) grant proposal to support a.) research related to ensuring research integrity through transparency and b.) develop practical approaches, tools, and ELN resources. A goal is to pilot institutional support for data repository, protocols, and ELN services through grant budgets. Since, “a dedicated one-size-fits-all product has, to date, not been developed” (Gerlach et al., 2020, p. 262), costs for multiple institutional support services will have to be written into grant budgets to “connect everything in a lab, from research protocols and pipettes to data storage and manuscripts” (May, 2017). LabArchives is currently used by an instructional assistant professor and undergraduate coordinator in the University of Florida J. Clayton Pruitt Family Department of Biomedical Engineering. ELabJournal is currently used by the Boulant Lab at the University of Florida. According to the lab at UF, eLabJournal follows all regulation for ‘Good Laboratory Practice (GLP)’ (OECD, 2022a) compliance. RSpace is currently used by two researchers according to the 2020 Electronic Lab Notebook at UF survey. RSpace current investigation is influenced by the integrations with data management planning, protocols, and repositories tools (Figure 3), pilots by other universities, and the HMS Research Computing ELN investigation.

Universities in the USA that have completed RSpace pilots are Harvard University, Harvard Medical School, and the University of Nebraska. Universities in Europe that have completed RSpace pilots are UiT Arctic University of Norway, University of Edinburgh, Delft University of Technology, École polytechnique fédérale de Lausanne and University of Liege. ELN tools such as RSpace enables open science (Figure 4) through enabling transparency in the conduct of research via integrations that support the reporting of research to enable findable, accessible, interoperable, reusable (FAIR) data across communities of practice. “Open science encompasses unhindered access to scientific articles, access to data from public research, and collaborative research enabled by ICT [Information and Communications Technology] tools and incentives” (OECD, 2022b).

Similar to some of the results from the HMS investigations of two ELNs, the following additional recommendations resulted from ELN investigations at the University of Florida:

• Conduct focus group interviews with researchers to understand best practices for using a range of UF-provided and other ERN tools.

• Align available ERN solutions with other UF-provided technologies across the research life cycle to provide researchers a suite of tools to conduct and manage their research.

• Consider investigating educational license discounts for courses using eLabJournal, RSpace, Protocols.io, Open Science Framework (OSF), LabArchives or other electronic research notebooks currently funded by student course fees.

Some barriers to implementing institutional licenses include funding, lack of collaborations with research labs, and nascent stakeholders’ collaborations to enable multidisciplinary support. Thus, the last recommendation is part of a submitted federal grant proposal pending sponsor review which addresses some of these barriers in providing broader research support services.

Conclusions

The University of Florida reached the following similar findings in 2020 concerning ELNs as previously concluded by the University of Cambridge and Harvard Medical School. The findings include but not limited to the following:

• There is no single ELN solution to satisfy all researchers across all disciplines.

• An ERN solution must be foundationally modular, discipline agnostic, universally relevant, and its features extensible.

• Tools designed as ERNs (i.e., LabArchives, SciNote, Benchling) are currently costly for institutional subscriptions, but have affordable or free options for individuals and research groups who need specialized tools.

• UF already provides institutional-grade, discipline-agnostic tools that meet many researchers’ needs, including Dropbox, Google Drive, and Microsoft products including OneDrive, Teams, and OneNote. However, there is a need for institutional, university-wide support of two to three ELN solutions similar to the ELN infrastructure support at Harvard Medical School.

An ELN can be used to store images for testing a machine learning approach for sharing data via a repository in a standardized form for access in data mining (Jablonka et al., 2021, p. 3590). “Within university settings, ELNs are marketed as an improvement to paper notebooks, including improved information retrieval and data sharing” (Foster et al., 2022, p. 222). Researchers within, across, and outside lab environments “need to record and provide [research] information in a structured, harmonized, and digitized way” (Elberskirch et al., 2022, p.1). ELNs can enable researchers to provide research in audited, harmonized, managed, and structured environments. Transitioning from physical notebooks to ELNs can prepare students for professional settings such as efficient sharing, tracking, and storage of information (Kong et al., 2022, p. 120) in addition to teaching GLPs. ELNs can be used to document laboratory activities, wet-lab experiments knowledge, and research data documentation such as metadata (Schröder et al., 2022, p. 2).In order for researchers to make data findable, accessible, interoperable and reusable, researchers need “a platform that seamlessly integrates the process of data collection, data processing and data publication with minimal overheads for the researcher” (Jablonka et al., 2022, p. 365). ELNs enable research support services and academic libraries as partners in data science ecosystems.

Figures

Figure 1.

NIH National Library of Medicine PubMed – ‘electronic lab notebook’ result (4/26/2022)

Figure 2.

UF Integrated Risk Management Fast Path Solutions RSpace risk ranking (open data only)

Figure 3.

RSpace and its ecosystem: Supporting Reproducibility and FAIR data

Figure 4.

European Open Science cloud Open Science infographic developed by Karel Luyben at Delft University of Technology (TU Delft)

Notes

1. University of Cambridge. Data Management Guide. Electronic Research Notebooks. How to pick a notebook? www.data.cam.ac.uk/data-management-guide/electronic-research-notebooks

2. Harvard University Longwood Research Data Management. Biomedical Data Lifecycle. What is the Data Lifecycle? https://datamanagement.hms.harvard.edu/about/what-research-data-management/biomedical-data-lifecycle

3. NIH NLM PubMed. https://pubmed.ncbi.nlm.nih.gov/

4. NIH NLM MEDLINE. www.nlm.nih.gov/medline/index.html

5. Harvard Longwood Research Data Management. ELNs at LMA. https://datamanagement.hms.harvard.edu/analyze/electronic-lab-notebooks/elns-lma