Journal:A pocket guide to electronic laboratory notebooks in the academic life sciences

NOTE: The original publisher has labeled this as an "opinion article." However, due to the open peer review process (see end of article), you can view reasoning for inclusion.

Abstract

Every professional doing active research in the life sciences is required to keep a laboratory notebook. However, while science has changed dramatically over the last centuries, laboratory notebooks have remained essentially unchanged since pre-modern science. We argue that the implementation of electronic laboratory notebooks (ELN) in academic research is overdue, and we provide researchers and their institutions with the background and practical knowledge to select and initiate the implementation of an ELN in their laboratories. In addition, we present data from surveying biomedical researchers and technicians regarding which hypothetical features and functionalities they hope to see implemented in an ELN, and which ones they regard as less important. We also present data on acceptance and satisfaction of those who have recently switched from paper laboratory notebook to an ELN. We thus provide answers to the following questions: What does an electronic laboratory notebook afford a biomedical researcher, what does it require, and how should one go about implementing it?

Keywords: Code of Federal Regulations Title 21, Documentation, Data storage, Good Scientific Practice, Good Laboratory Practice, Laboratory information management systems, Software

Introduction

In this article we argue that the implementation of electronic laboratory notebooks (ELN) in academic research is overdue, and we provide researchers and their institutions with the background and practical knowledge to select and initiate the establishment of an ELN in their laboratories. Based on our own extensive experience in moving from laboratory notebooks (LN) to ELN, we try to answer the following questions: What does it afford you, what does it require, and how should you go about implementing it?

Every professional doing active research in the life sciences is required to keep a LN. This is imperative for group leaders, post-docs, students, as well as technicians. LNs are the core element of record keeping, data management, and initial analysis and interpretation of results in research. Details of its specifications, storage, etc. are laid down in institutional, national, as well as international codes of conduct for research integrity and good laboratory practice. These codes usually stipulate sequentially numbered and bound pages, use of permanent ink, storage for a minimum of 10 years; they often require that entries be signed and dated by a witness. The use of LN has a long history, which parallels the development of modern science since the Renaissance. However, while science has changed dramatically over the last centuries, LNs have remained essentially unchanged since pre-modern science (Figure 1). This is highly remarkable for a number of reasons. For one, most of the data gathered is no longer analog, but digital. Gone are the days when researchers read numbers from instrument for transfer to the LN. Today there is a complex mixture of (often repetitive) protocols, digital images, links to large data files, etc. In addition, the recent realization that there is a ‘reproducibility’ crisis in the life sciences, and an increasing number of high profile cases of research misconduct and subsequent retraction of publications has put record keeping in the spotlight. It is therefore not surprising that the pharmaceutical industry, with its superior resources and regulatory pressures (e.g. Code of Federal Regulations Title 21) has moved to ELNs. Many researchers and institutions in academia now realize that the implementation of ELNs is overdue. However, only a tiny fraction of university laboratories are using them. Major hurdles for implementation appear to include ignorance about practical issues, perceived scarcity of available options, and a lack of resources. As part of the implementation of an ISO 9001-certified quality management system, our department (Department of Experimental Neurology) has recently moved from LNs to an ELN. At this department with approximately 100 students, researchers, and technicians we carry out multi-professional academic research in preclinical biomedicine with such standard approaches and techniques as in vivo and and in vitro modeling of disease, cell biology, molecular biology, biochemistry, as well as imaging (from multi-photon microscopy to magnetic resonance imaging). We therefore believe that our experience is applicable to a wide range of research operations in the life sciences.

Figure 1. Laboratory notebooks have remained essentially unchanged throughout the last centuries. A: Page from the laboratory notebook of the father of experimental electrophysiology, Emil Dubois-Raymond (7 November 1818 – 26 December 1896). [Staatsbibliothek Berlin, 1865–1868, XIII, 22. VII. 65–9. VI. 68, reproduced with permission]. B: Pages from a contemporary laboratory notebook from the laboratory of the authors.

Why you will switch to an ELN

We believe that the question is not whether ELNs will become standard or even required in the academic life sciences, but when. The advantages of an ELN are as obvious as the disadvantages of the conventional LN. Most of the original data obtained in laboratories worldwide is already digital and can easily be integrated or linked to the ELN. ELNs foster collaboration, as protocols, data and concepts can be shared within or between groups. Entries can be time stamped, changes are recorded, and versions controlled. Protocols used frequently can simply be integrated as templates. Project progress and ELN use can be easily monitored by group or project leaders. ELNs are searchable, archiving is simple, and copies are easily made for the institution and the individual researcher, many of whom will leave the institution at some point. These features include just a few of the functionalities which are already available in ELNs and are completely absent in a LN. Future ELNs will provide further benefits, including direct data links to standard laboratory hardware through an application programming interface (API) and automatic alerts when instruments are malfunctioning or not calibrated, or direct links to open data repositories (such as Figshare or Dryad). LNs, on the other hand, tend to get lost, must stay within the institution, which in turn has to keep track of them and is charged with keeping reliable records of LNs, storing them and enabling access for at least 10 years.

Selecting an ELN

If you are contemplating a switch to ELNs, you first need to decide what you expect from it, and match this with your resources (see also below). Table 1 summarizes the principal features of three different categories of ELNs. The simplest form (‘do-it-yourself’ – DIY - type) is a word processor or note-taking system. It is cheap, easy to use, and has many of the features a conventional LN; its major drawback is its lack of any kind of audit trail or certification. Such DIY-ELNs thus do not even conform to the standards of classical LNs, and therefore are not a serious option for their replacement. Dedicated ELNs have many additional features. Importantly most commercially available ELNs are compliant with the Code of Federal Regulations Title 21 (CFR Title 21) of the U.S. Food and Drug Administration (FDA). CFR Title 21 part 11 sets rigorous specifications for electronic record keeping, including electronic signatures and version control. CFR Title 21 is a must if protection of intellectual property or use of the records for regulatory processes (such as FDA) is a factor. Dedicated ELNs also allow complex rights management within institutes and workgroups, and can integrate original data. High-end systems include all the features of an ELN, but also function as laboratory information management systems (LIMS), facilitating inventory management or direct link to laboratory equipment (such as microscopes, sequencers, etc.). Not surprisingly, while DIY-ELNs are very easy to use, the increasing functionality of dedicated ELNs and ELNs integrated into LIMS comes at the price of growing complexity in its use. This might be a particular concern when non-academic personnel need to work with the ELN. Another issue is language – the user menus and help functions of practically all commercially available ELNs are in English; only a few allow the user to switch to other languages. Again, this may, in combination with a complex functionality, pose problems, and hamper the acceptance of the ELN in non-academic and less tech-savy work environments. Several articles have reviewed and compared various ELNs.

Table 1. Comparison of specifications of three different types of ELNs. Note that ease of use and the availability as well as power of features of ELNs are inversely related. Abbreviations: API, Application programming interface; 21 CFR 11, code of federal regulations title 21 part 11; LIMS, Laboratory Information Management System. *Indicates that this feature is available in some systems of this category only. Basic systems, such as repurposed word processors (e.g. Word) or note taking systems (e.g. Evernote) Dedicated, commercial ELNs (e.g. iLabber, Labfolder, eCat) High-end systems (ELNs including a LIMS, e.g. IDBS E-WorkBook, iLAB Laboratory Execution System) Ability to enter text as in conventional handwritten LN All features from the basic systems plus (see below) All features from the dedicated, commercial systems plus (see below) Notes can be made available on multiple devices (stored in the cloud) Freehand drawing Inventory management: Complete tracking of samples/reagents through all experiments Attach files to notes Complex rights management (with roles and individual rights) Workflows for certain samples, tasks, experiments Visualization of attachments in the note 21 CFR 11 compliance: All previous versions of a note are stored/changes are logged (full audit trail); prevents deletion of notes by their author; electronic signatures for completed notes; witnessing and freezing (makes note immutable after the author and a witness have signed it) Direct link to laboratory equipment (e.g. microscopes, spectrometers, sequencers): Automatic delivery of raw data by device; delivery of metadata (e.g. date of last calibration) from device Annotation of attachments (e.g. images)* Extensions/API for customization available Analysis of raw data within the system Search within the written text Assigning of tasks between colleagues* Data mining (aggregate and cluster structured data) Search in attachments* Inventory management: Only amount and location of samples/reagents Notes can be shared with colleagues/collaborators*

Competing interests

No competing interests were disclosed.

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In some cases important information was missing from the references, and that information was added. The originally used acronym "eLN" was replaced with the more common "ELN." Finally, an introductory note was added to explain that this article appeared as an opinion article in the original journal.