Tips for Experiments

OpenBIS the ELN-LIMS

As a user working with experiments, you will be most likely working with the Lab Notebook section and using the inventory to reference sample and protocols/SOP’s.

Workflow for laboratory experiments

A typical workflow from an experimentalist may be divided into the following steps:

Acquisition of information
Planning of experiments - formulation of hypothesis
Preparing for experiments and lab work
Analysis of products from experimental work
Analysis and interpretation of data derived from analysis of products and processes
Publishing and Archiving

Before the actual experimental work

There are two Object types present in every openBIS instance. They are called ‘Experimental Step’ and ‘Entry’. The Entry type resembles a Word document and offers basic formatting options such as colouring, creating tables and inserting pictures. If you already have a Word file, you can copy and paste its contents into openBIS Entry and it will retain the standard formatting.

For example, you can create a collection or default experiment to register a group of entries with different hypotheses and links to papers, etc. To test these hypotheses, you can perform an experimental series and register the information in openBIS using the ‘Experimental Step’ object type. You can then link the entry to the associated experiments using parent-children relationships, and later you will be able to trace the reasons for the lab work. Creating a data model can help with this.

Working with protocols and templates to prepare for experimental work

Protocols can be used to register standard operation protocols (SOP) or methods. OpenBIS protocols are connected to the experimental steps via parent-child relations. Templates help to prefill parts of your documentation with values that stay the same in a series of experiments.

Protocols and templates have to be prepared before the experimental work. Protocols need enabling in the settings. Templates are registered in the settings, or can be moved to the templates section, you need to have access to the template section in the settings. Talk to your instance admin about openBIS roles

Experimental work

The workflow for working with an Electronic Lab Notebook (ELN) is similar to the one with a paper notebook:

Note down the chemicals/apparatus/methods and theoretical values for experiments (like weight for powders)
Perform the experiments
Note down actual values for experiments and their observations

In the case of a paper notebook, the values to be used for an experiment would also be written down first, along with the chemicals/apparatus/methods etc. to be used. The same happens with openBIS: The information needed to perform an experiment is recorded in advances with help of protocols and templates Then, when working in the lab, the actual values are added and experimental observations are listed.

It’s possible to work with openBIS on tablets and iPads. Scientific IT distributed already several of them amongst Empa labs and provided a short starting guide. If you are interested to get an iPad, contact your instance admin or contact us via email.

Analyzing data stored in openBIS

Two tools for data analysis are ready to use in openBIS:

Jupyter is accessible from openBIS and can be operated from the ELN UI.
Use the MATLAB toolbox to access your data
You may build your own solution using pyBIS, the API to access openBIS

Furthermore, it’s possible to download all data from openBIS for other type of processing

Data and metadata can be exported.
You can export the tables in openBIS by clicking on the button above of the table called ‘exports’.
You can browse entries by type and export them by using the export button at the top of the table.
Download indicidual data files directly when you click on the file name.
Access your data via SFTP (Secure File Transfer Protocol)

Data evaluation and interpretation

There are different features in openBIS to display the data that is recorded. Most of them are listed here:

Check out parent-child relations from your objects using the hierarchy graph.
Display your data in the table using different filters and search options.
Group together objects from different sources in one table by using advanced search options.
Use the MATLAB toolbox or Jupyter.
For external processing, use Export data to file to export all the metadata and/or data from objects
Use the ‘exports’ in tables for selected records.
Use pyBIS to interact with openBIS via scripts.

Publishing and archiving

OpenBIS offers the function to directly export to zenodo. Zenodo is a FAIR repository accepted by funding agencies to publish research data. Read more about Zenodo here.

Another nice feature of openBIS is the simple archiving feature. Data can be easily stored, but also retrieved just with a click of the mouse. It only takes a few hours until the data is available again.