Funding agencies, journals, and academic institutions increasingly require research data to be published according to the FAIR data principles – according to which data should be Findable, Accessible, Interoperable and Reusable. To achieve this, every step of the research process needs to be accurately documented, and data need to be securely stored, backed up, and annotated with enough metadata to make it re-usable and re-producible. However, managing the ever-increasing amounts of data generated in scientific research is becoming increasingly challenging. A platform that combines a data management system with a note keeping application and with an inventory management system can support scientists in this demanding task. To this end, SIS has developed the ELN-LIMS module for the openBIS data management platform.

This is available in two versions:

  1. For life-sciences. Predefined default fields used in most biological labs are provided, and can be further customised.
  2. Generic. Most fields need to be customised by the end users, based on their needs.

openBIS is a complete solution for academic research labs working in quantitative scientific disciplines. With the openBIS ELN-LIMS module, scientists can document and annotate their research data from initial acquisition onwards, and can create lab inventories of materials and protocols, thereby facilitating knowledge sharing and transfer within their research group. openBIS does not have any intrinsic functionality for data analysis, however since early 2018, it has been integrated with Jupyter notebooks and the JupyterHub server . Jupyter notebooks are documents that combine code, equations, output and text and can be shared with other people. The notebooks can be launched directly from the openBIS ELN-LIMS user interface to analyse data stored in the system. A notebook is then stored back into openBIS, connected to the data that were analysed, thereby ensuring provenance tracking of the analysis results.

LIMS Key Features

  1. Relationships. Entities of any type can be connected to each other and these connections can be annotated. A genealogical tree view of the relationships is available.

  2. Graphical representation of storage. A graphical representation of the fridges and freezers used in one lab can be configured.

  3. Tsv file import. openBIS provides template tsv files that can be downloaded and filled in with information to register several samples in a single step.

  4. Metadata export to tsv. All openBIS tables, with information about samples and SOPs, can be exported to tsv files.

  5. Easy file upload. Files of any format (pdf, excel, word, etc.), with size <2GB can be easily uploaded from the web browser. (Larger files can be uploaded via a file system.)

  6. Plasmid maps. openBIS is integrated with PlasMapper, which generates plasmid maps on-the-fly from FASTA files.

  7. BLAST search. Nucleotide sequences stored in the database as text fields or in uploaded FASTA files can be searched with BLAST.

Genealogical tree of a yeast.

Graphical representation of storage.

ELN Key Features

  1. Links to samples and SOPs. In the description of experimental procedures it is possible to establish and annotate links to samples and protocols stored in the LIMS.

  2. Links to other experimental steps. In the description of experimental procedures it is possible to establish and annotate links to other experimental steps.

  3. Easy data upload. Files or folders below 2GB can be easily uploaded via the web interface.

  4. Management of large data. Files or folders above 2GB can be uploaded in the background using some custom scripts. openBIS is a powerful data management platform that can handle hundreds of TBs of data.

  5. Integration with measurement instruments. It is possible to connect measurement instruments (e.g. microscopes, sequencers, etc etc) directly to openBIS. The raw data generated by the instrument is then automatically uploaded into openBIS.

Example of annotations in a western blotting experiment.

Genealogical tree of an experimental step.

Additional Features

  1. User roles. Users can have different roles: Instance admin, Space admin, Space User, Space observer, Instance observer. For a detailed explanation of the capability of each role, please check the openBIS documentation.

  2. Change Log. All modifications made to any entity in the system are recorded and stored in the database.

  3. Deletion. By default, Space admins and Instance admins are allowed to delete entities. This permission can be completely removed upon request. The metadata history of deleted entities is kept in the database.

  4. Data preservation. The data uploaded in openBIS is stored in datasets, which are immutable by definition. Data stored in datasets cannot be modified. Modified data must be uploaded in a new dataset.

  5. Data archive. Datasets can be archived to affordable tape storage when no longer needed. The system can unarchive them and put them back on online storage when needed.

Official Web Site

You can find more information about openBIS ELN-LIMS including tutorials and screen casts at the official openBIS ELN-LIMS web site.