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) |
 |
This article should not be considered complete until this message box has been removed. This is a work in progress. |
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.[1] LNs must be complete, clear, unambiguous and secure. A remarkable example is Alexander Fleming’s documentation, leading to the discovery of penicillin.[2]
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.[3] The combination and interpretation of these data requires experts from different research areas[4], 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.[5][6][7] 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.[8] 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.
References
- ↑ Myers, J.D. (10 July 2014). "Collaborative Electronic Notebooks as Electronic Records: Design Issues for the Secure Electronic Laboratory Notebook (ELN)". ResearchGate. ResearchGate GmbH. https://www.researchgate.net/publication/228705896_Collaborative_electronic_notebooks_as_electronic_records_Design_issues_for_the_secure_electronic_laboratory_notebook_eln. Retrieved 08 January 2015.
- ↑ Bennett, J.W.; Chung, K.T. (2001). "Alexander Fleming and the discovery of penicillin". Advances in Applied Microbiology 49: 163–84. doi:10.1016/S0065-2164(01)49013-7. PMID 11757350.
- ↑ Du, P.; Kofman, J.A. (2007). "Electronic Laboratory Notebooks in Pharmaceutical R&D: On the Road to Maturity". JALA 12 (3): 157–65. doi:10.1016/j.jala.2007.01.001.
- ↑ Ioannidis, J.P.; Greenland, S.; Hlatky, M.A. et al. (2014). "Increasing value and reducing waste in research design, conduct, and analysis". Lancet 383 (9912): 166–75. doi:10.1016/S0140-6736(13)62227-8. PMC PMC4697939. PMID 24411645. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697939.
- ↑ Special Programme for Research and Training in Tropical Diseases (2006). "Handbook: Quality practices in basic biomedical research". World Health Organization. pp. 122. http://www.who.int/tdr/publications/training-guideline-publications/handbook-quality-practices-biomedical-research/en/.
- ↑ Schnell, S. (2015). "Ten Simple Rules for a Computational Biologist's Laboratory Notebook". PLoS Computational Biology 11 (9): e1004385. doi:10.1371/journal.pcbi.1004385. PMC PMC4565690. PMID 26356732. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565690.
- ↑ Nussbeck, S.Y.; Weil, P.; Menzel, J. et al. (2014). "The laboratory notebook in the 21st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity". EMBO Reports 15 (6): 631–4. doi:10.15252/embr.201338358. PMC PMC4197872. PMID 24833749. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197872.
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.
