openBIS ELN-LIMS for the Life Sciences

Nowadays, most data produced in a scientific laboratory is in electronic format, but experimental procedures are still often documented in paper laboratory notebooks. Linking the data to the procedures in this way is not straightforward and this often makes retrieval of relevant information in the mid and long term very problematic. Electronic laboratory notebooks (ELNs) are software aimed at replacing the classic paper notebooks and they are becoming increasingly popular. However, only the combination of an ELN with a data management platform and a laboratory information management system (LIMS), which is used to manage samples and SOPs, allow users to keep track of the complete history of the work perfomed in the lab, from bench to publication. Keeping track of this history is a requirement for reproducibility of published results, which is fundamental for scientific progress.

In close collaboration with laboratories in D-BIOL and D-BSSE at ETH Zurich, SIS has developed an ELN-LIMS system based on our data management platform openBIS. It consists of three interconnected parts:

  1. the LIMS, where the information about materials and methods used in the laboratory is stored,
  2. the ELN, where experimental procedures can be described,
  3. the Data Management Module, where experimental and computed data are stored. Experimental data of any format and size can be uploaded and annotated here together with analyzed data and analysis scripts.

All entities (like samples, experiments or data sets) in the system can be linked to each other, which enables full data history tracking. This structure ensures that the users can always easily find, understand and reuse the data, even years after it was produced.

openBIS ELN-LIMS comes with a set of predefined fields, which should encompass the needs of the majority of biology labs, however these fields can be easily modified and extended to suit specific needs.

In the Lab notebook part, each user can create a personal space to organize projects and experiments. Experiments can be divided into individual experimental steps where data (of any size and format) can be uploaded. Within each experimental step it is possible to establish links to samples and SOPs and to other experimental steps, to track data provenance.

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.