Journal:openBIS ELN-LIMS: An open-source database for academic laboratories

Full article title	openBIS ELN-LIMS: An open-source database for academic laboratories
Journal	Bioinformatics
Author(s)	Barillari, Caterina; Ottoz, Diana S.M.; Fuentes-Serna, Juan M.; Ramakrishnan, Chandrasekhar; Rinn, Bernd; Rudolf, Fabian
Author affiliation(s)	ETH Zürich, Lifescience Zürich
Primary contact	Email: brinn at ethz dot ch -or- fabian dot rudolf at bsse dot ethz dot ch
Year published	2015
Volume and issue	32 (4)
Page(s)	638-640
DOI	10.1093/bioinformatics/btv606
ISSN	1460-2059
Distribution license	Creative Commons Attribution 4.0 International
Website	http://bioinformatics.oxfordjournals.org/content/32/4/638.long
Download	http://bioinformatics.oxfordjournals.org/content/32/4/638.full.pdf (PDF)

Abstract

Summary: The open-source platform openBIS (open Biology Information System) offers an electronic laboratory notebook and a laboratory information management system (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched.

Availability and implementation: The openBIS software, a user guide and a demo instance are available at https://openbis-eln-lims.ethz.ch. The demo instance contains some data from our laboratory as an example to demonstrate the possibilities of the ELN-LIMS (Ottoz et al., 2014). For rapid local testing, a VirtualBox image of the ELN-LIMS is also available.

Introduction

Scientific recording is an essential part of research, as progress in science depends among other factors on existing knowledge and reproducibility. Recording is the process by which the scientific question, the choice of an experimental procedure, materials and methods, data analysis and interpretation of the results are gathered. Traditionally, all these details were kept in paper notebooks.

In today’s academic life science laboratories, most raw data, analyzed data and scripts are stored electronically, while the experimental details are often recorded in paper notebooks. This makes linking and retrieving experimental details and results problematic. Moreover, the large amount of data produced by today’s readout machines adds a level of complexity as the devices the data are stored on might soon be outdated.

Databases represent a solution to store all the necessary information together because (i) they ensure long-lasting data storage by being independent of the operating environment; (ii) they are installed on a dedicated server, enabling long-term data storage and regular backups; (iii) they allow storage of large amounts of data; (iv) they are easily accessible via a local area network or the internet; (v) custom applications can be easily added.

Several commercial database solutions for ELNs are available, but they are not commonly adopted by academia. An internal evaluation among the research groups of the departments of Biosystems Science and Engineering and Biology of ETH Zurich found that the options affordable to academic labs had either unsuitable user interfaces (UI) or lack of features. The combination of an easy-to-use UI, flexible adaptation to a labs needs, support of an audit trail, physical support of the data server, support for managing large amounts of data and for integrating new measurement devices was only available at very high costs. On the other hand, the available open-source platforms lack many of the above features and, as they often originate from a single person within a research group, they also lack maintenance and support during the required data management life cycle.

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.