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.
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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produced by today’s readout machines adds a level of complexity as the devices the data are stored on might soon be outdated.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.
Here, we describe the open-source database openBIS (open Biology Information System) electronic laboratory notebook and a laboratory information management system (ELN-LIMS), a software specifically developed with academic life science labs in mind. The structure of the database ensures that the results are represented in a logical and meaningful fashion, and it guarantees that the users can find, understand and reuse the data. openBIS ELN-LIMS consists of two interconnected parts: the LIMS, where the information about materials and methods is stored and kept up to date and the ELN, where data obtained from experiments are uploaded and annotated. The system is based on the openBIS platform, which, since 2007, is actively developed and maintained by a dedicated team of software engineers at the ETH and is productively used in several academic institutions and a few private companies.