Journal:Electronic laboratory notebooks in a public–private partnership

Full article title	Electronic laboratory notebooks in a public–private partnership
Journal	PeerJ Computer Science
Author(s)	Vaas​, Lea A.I.; Witt​, Gesa; Windshügel, Björn; Bosin, Andrea; Serra, Giovanni; Bruengger, Adrian; Winterhalter, Mathias; Gribbon, Philip; Levy-Petelinkar, Cindy J.; Kohler, Manfred
Author affiliation(s)	Fraunhofer Institute for Molecular Biology and Applied Ecology, University of Cagliari, Basilea Pharmaceutica International AG, Jacobs University Bremen, GlaxoSmithKline
Primary contact	Email: manfred dot kohler at ime dot fraunhofer dot de
Editors	Baker, Mary
Year published	2016
Volume and issue	2
Page(s)	e83
DOI	10.7717/peerj-cs.83
ISSN	2167-8359
Distribution license	Creative Commons Attribution 4.0 International
Website	https://peerj.com/articles/cs-83/
Download	https://peerj.com/articles/cs-83.pdf (PDF)

Abstract

This report shares the experience during selection, implementation and maintenance phases of an electronic laboratory notebook (ELN) in a public–private partnership project and comments on users' feedback. In particular, we address which time constraints for roll-out of an ELN exist in granted projects and which benefits and/or restrictions come with out-of-the-box solutions. We discuss several options for the implementation of support functions and potential advantages of open-access solutions. Connected to that, we identified willingness and a vivid culture of data sharing as the major item leading to success or failure of collaborative research activities. The feedback from users turned out to be the only angle for driving technical improvements, but also exhibited high efficiency. Based on these experiences, we describe best practices for future projects on implementation and support of an ELN supporting a diverse, multidisciplinary user group based in academia, NGOs, and/or for-profit corporations located in multiple time zones.

Keywords: public–private partnership, open access, Innovative Medicines Initiative, electronic laboratory notebook, New Drugs for Bad Bugs, IMI, PPP, ND4BB, collaboration, sharing information

Introduction

Laboratory notebooks (LNs) are vital documents of laboratory work in all fields of experimental research. The LN is used to document experimental plans, procedures, results and considerations based on these outcomes. The proper documentation establishes the precedence of results, particularly for inventions of intellectual property (IP). The LN provides the main evidence in the event of disputes relating to scientific publications or patent application. A well-established routine for documentation discourages data falsification by ensuring the integrity of the entries in terms of time, authorship, and content. LNs must be complete, clear, unambiguous and secure. A remarkable example is Alexander Fleming’s documentation, leading to the discovery of penicillin.

The recent development of many novel technologies brought up new platforms in life sciences requiring specialized knowledge. As an example, next-generation sequencing and protein structure determination are generating datasets, which are becoming increasingly prevalent especially in molecular life sciences. The combination and interpretation of these data requires experts from different research areas, leading to large research consortia.

In consortia involving multidisciplinary research, the classical paper-based version of a LN is an impediment to efficient data sharing and information exchange. Most of the data from these large-scale collaborative research efforts will never exist in a hard copy format but will be generated in a digitized version. An analysis of this data can be performed by specialized software and dedicated hardware. The classical application of a LN fails in these environments. It is commonly replaced by digital reporting procedures, which can be standardized. Besides the advantages for daily operational activities, an electronic laboratory notebook (ELN) yields long-term benefits regarding data maintenance. These include, but are not limited to, items listed in Table 1. The order of mentioned points is not expressing any ranking. Besides general tasks, some specific tasks have to be facilitated, especially in the field of drug discovery. One such specific task is searching for chemical structures and substructures in a virtual library of chemical structures and compounds (see Table 1, last item in column “Potentially”). Enabling such a function in an ELN hosting reports about wet-lab work dealing with known drugs and/or compounds to be evaluated would allow dedicated information retrieval for the chemical compounds or (sub-) structures of interest.

Table 1. Long-term benefits of an electronic laboratory notebook (ELN) compared to a paper based LN Definitely Potentially • Create (standard) protocols for experiments • Create and share templates for experimental documentation • Share results within working groups • Amend/extend individual protocols • Full complement of data/information from one experiment is stored in one place (in an ideal world) • Storage of data from all experiments in a dedicated location • Search functionality (keywords, full text) • Protect intellectual property (IP) by timely updating of experimental data with date/time stamps • Exchange protocols/standard operating procedures (SOPs) • Remote access of results/data from other working groups • Ensure transparency within projects • Discuss results online • Control of overall activity by timely planning of new experiments based on former results • Search for chemical (sub)structures within all chemical drawings in experiments

Interestingly, although essential for the success of research activities in collaborative settings, the above mentioned advantages are rarely realized by users during daily documentation activities and institutional awareness in academic environment is often lacking.

Since funding agencies and stakeholders are becoming aware of the importance of transparency and reproducibility in both experimental and computational research, the use of digitalized documentation, reproducible analyses and archiving will be a common requirement for funding applications on national and international levels.

A typical example for a large private-public partnership is the Innovative Medicines Initiative (IMI) New Drugs for Bad Bugs (ND4BB) program (see Fig. 1 for details). The program’s objective is to combat antibiotic resistance in Europe by tackling the scientific, regulatory, and business challenges that are hampering the development of new antibiotics.

Figure 1. Structural outline of the New Drugs for Bad Bugs (ND4BB) framework

The TRANSLOCATION consortium focus on (i) improving the understanding of the overall permeability of Gram-negative bacteria, and (ii) enhancing the efficiency of antibiotic research and development through knowledge sharing, data sharing and integrated analysis. To meet such complex needs, the TRANSLOCATION consortium was established as a multinational and multisite public–private partnership (PPP) with 15 academic partners, five pharmaceutical companies and seven small- and medium-sized enterprises (SMEs).

In this article we describe the process of selecting and implementing an ELN in the context of the multisite PPP project TRANSLOCATION, comprising about 90 bench scientists in total. Furthermore we present the results from a survey evaluating the users’ experiences and the benefit for the project two years post-implementation. Based on our experiences, the specific needs in a PPP setting are summarized and lessons learned will be reviewed. As a result, we propose recommendations to assist future users avoiding pitfalls when selecting and implementing ELN software.

Methods

Selection and implementation of an ELN solution

The IMI project call requested a high level of transparency enabling the sharing of data to serve as an example for future projects. The selected consortium TRANSLOCATION had a special demand for an ELN due to its structure — various labs and partners spread widely across Europe needed to report into one common repository — and due to the final goal, data was required to be stored and integrated into one central information hub, the ND4BB Information Centre. Fortunately, no legacy data had to be migrated into the ELN.

The standard process for the introduction of new software follows a highly structured multi-phase procedure, as outlined in Fig. 2.

Figure 2. Schematic outline of stepwise procedure for the implementation of a new system

For the first step, we had to manage a large and highly heterogeneous user group (Fig. 3) that would be using the ELN, scheduled for roll-out within six months after project launch. All personnel of the academic partners were requested to enter data into the same ELN, potentially leading to unmet individual user requirements, especially for novices and inexperienced users.

Figure 3. Technical and organizational challenge: schematic overview of paths for sharing research activity results within a public–private partnership on antimicrobial research

As a compromise for step 1 (Fig. 2), we assembled a collection of user requirement specifications (URS) based on the experiences of one laboratory that had already implemented an ELN. We further selected a small group of super users based on their expertise in documentation processes, representing different wet laboratories and in silico environments. The resulting URS was reviewed by IT and business experts from academic as well as private organisations of the consortium. The final version of the URS is available as Supplemental File 1.

In parallel, based on literature (Rubacha, Rattan & Hossel, 2011) and internet searches, presentations of widely used ELNs were evaluated to gain insight into state-of-the-art ELNs. This revealed a wide variety of functional and graphical user interface (GUI) implementations differing in complexity and costs. The continuum between simple out-of-the-box solutions and highly sophisticated and configurable ELNs with interfaces to state-of-the-art analytical tools were covered by the presentations. Notably, the requirements specified by super users also ranged from “easy to use” to “highly individually configurable.” Based on this information, it was clear that the ELN selected for this consortium would never ideally fit all user expectations. Furthermore, the exact number of users and configuration of user groups were unknown at the onset of the project. The most frequently or highest prioritized items of the collected user requirements are listed in Table 2. We divided the gathered requirements into ‘core’ meaning essential and ‘non-core’ meaning ‘nice to have, but not indispensable.’ Further, we list here only the items, which were mentioned by more than two super users from different groups. The full list of URS is available in Supplemental File 1.

Table 2. Overview of user requirements organized as ‘core user requirements’ for essential items, and ‘non-core user requirements’ representing desirable features Core user requirements Non-core user requirements • System set-up and implementation should be fast and simple • Access from different platforms should be possible: Windows, Linux, Mac OS • Low training requirements (for high level of acceptance • Hosted system with state-of-the-art security settings • Simple user management (only limited support by project members possible) • Suitable for both chemical (including e.g., drawings of molecules) and biological (including e.g., capture fluorescent images) experiments • Low costs, especially for long-term usage in the academic area • Conform with Good Laboratory Practise • User management with dedicated access permissions (expectation: all users working on the same project, but in different work packages) • Workflow management • Order management • Chemical structure handling • Dedicated tree structure for storing experiments • Legally-binding procedures (signatures) • Modular expandability • Appropriate integrated analytical features • Social networking and collaborative (chat) features • Storage for large sets of “raw” data for re-analysis

Notes

This presentation is faithful to the original, with only a few minor changes to presentation, including regionalizing spelling. In some cases important information was missing from the references, and that information was added. The original lists references in alphabetical order; this version lists them in order of appearance due to the nature of the wiki.