Electronic Lab Notebooks (ELNs) and Laboratory Information Management Systems (LIMS) allow researchers to efficiently document their work, describe materials and methods and collect raw and analysed data. As part of the DLCM project, we have produced practical guidelines on how to introduce ELN and LIMS in an academic research laboratory (link). Whilst these are mainly based on our experiences with life sciences laboratories, these guidelines can be easily extended to other research domains. In addition, we have also curated lists of the ELNs (link) and LIMS (link) available on the market, which can be used to select the appropriate tool for a research laboratory. If you are you thinking about implementing an ELN or a LIMS in your team or research lab, we have expertise in different systems and are more than happy to support you.
openBIS ELN-LIMS is developed by ETH Zurich Scientific IT Services in close collaboration with scientists at ETHZ. It consists of a LIMS for storing information about materials and methods used, an ELN for describing experimental and computational procedures, and a data management module for storing experimental and computed data. The recent integration with Jupyter Notebooks facilitates analysis of the data stored in openBIS. By also storing the Jupyter Notebooks in the system, connected to the analysed data, users can keep track of the complete data cycle. Scientists working with big data (in the order of hundreds of TB) can describe their experiments/computations in the ELN and use the BigDataLink (BDL) module to create links to their data, which potentially could be stored in several different locations.
Key features include:
- Data provenance graph
- Easy data upload via web interface or via background scripts using a dropbox mechanism
- Big data management
- Integration with measuring devices, for automatic upload of raw instrument data
- Data and metadata export functionality
- Data analysis with integrated Jupyter notebooks
- Changelog of all modifications entered in the system
- User management rights
- Interoperable, web based application with a central server installation
- Centralised and secure storage system for research data
- Access via standard REST API for custom applications
- Integration of external instruments or data sources with Camel (Enterprise Integration Patterns)
- High level of customisation to fit to all research laboratory needs
- High level of traceability of samples, experiments and scientific projects
- Structure and link research data with experiments detailed by interactive note-taking
- Management of different versions of protocols - SOPs
- Collaboration with group and user level authorisations to share/restrict access to research projects and data
- Sample management to keep track of modifications and usage of samples
- Turns legacy laboratory specific databases and inventories into one manageable inventory facilitated by excel file import
LabKey is an open-source LIMS-like data management system, developed by the company LabKey. In brief, LabKey Server provides a user-friendly interface to a relational database, with powerful additional functionality, such as easy interface with many languages (including R and Python), data indexing, document store and powerful security protocols including comprehensive audit trails. LabKey was developed as a data management and workflow solution for clinical research, but with the flexible design of the system it can be configured to support any domain of research. LabKey Server is ideal for groups looking to transition to a more robust solution when working in Excel becomes unmanageable.
While the core of the system is open source and free, the company sells extensions, customizations, and support contracts to fund its ongoing development and maintenance. If you need support beyond what the open source local community edition version can offers, or need functionality not covered in the open source version (e.g. for clinical trials and other critical applications), do not hesitate to contact LabKey support directly at .
About the server
This server is a cloud-based instance of LabKey Server which can be used by researchers who want to have a first look at the system: Check the read-only public datasets or the sandbox (ask for an account for full functionality), or ask for a private workspace (as described below). If after testing you are interested to use it productively for your research, please contact sciCORE to get your project started.
Getting a private workspace on this server
To get a private workspace on labkey.dlcm.ch simply send a request to(remove "noclutter." from the e-mail address), specifying the name of your host institution and the name of the workspace. Your e-mail address will be your user name in the system. You will be the manager of the newly created workspace, and can then create new accounts for your collaborators in the workspace.
Only members of Swiss academic institutions can request an account on this server, and only one workspace per research group is allowed. (You can create subspaces in your main workspace if necessary.)
Installing a LabKey server in your institution
LabKey is an open source software published under the Apache 2.0 license, it can thus be freely installed in your home institution or laboratory following the documentation on the LabKey web site. sciCORE can provide initial deployment advice.