Tips for experiments¶
OpenBIS the ELN-LIMS¶
As an 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¶
Two Object types are present in every openBIS instance, they are called Experimental Step and Entry. The Entry type has looks like a Word document and has similar features. Copy paste from word files in to an Entry does work, as long as it doesn't contain pictures. Embed images using drag and drop, or the insert image feature from the text editor.
As an Example, you could create a Collection or Default Experiment to register a group of entries with different hypothesis and links to papers etc. To test this hypothesis, you create experimental series for hypothesis testing. You can link the corresponding Entry with parent-children relationships to the associated experiments and later you will be able to trace back the reasons of the lab work.
Working with protocols and templates to prepare for experimental work¶
Protocols are used as a general term to describe a workflow that always stays the same within some experimental series, e.g. Assay, Standard Operation Protocol (SOP), Method. OpenBIS Protocols are connected to the Experimental Steps via Parent-Child relations. Templates help to prefill Experimental Steps with values that stay always the same throughout a series of experiments.
Protocols and templates have to be prepared before the Experimental work. Protocols need enabling in the settings, templates are registered directly in the settings, therefore this has to be done by an Admin, or the instance admin should give to the user the Admin role for the space settings, view openBIS roles for help. Once the protocols and/or templates are prepared, experimental information needed for the practical work can be filled out.
Experimental work¶
Working with a Electronic Lab Notebook (ELN) is very similar to working with a paper notebook. 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 is prepared for an ELN, simply on the PC, with the 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. The 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 available in openBIS. Jupyter is directly implemented in openBIS and can be operated from the ELN UI. To access the data with MATLAB it has to be locally installed on your device but it's available from the DSM Software shop which is available on every Empa computer.
Further it's possible to download all data from openBIS for external processing. Data and metadata can be exported. You can export the tables in openBIS by clicking on the button above of the table called Export. You can browse entries by type and export them by using the export button at the top of the table. Individual data files attached to objects or collections are downloaded directly when clicked on it.
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]https://openbis.readthedocs.io/en/latest/user-documentation/general-users/tools-for-analysis-of-data-stored-in-openbis.html#jupyter-notebooks)
- For external processing use Export data to file to export all the metadata and/or data from objects or use the export function that can be found on the top of every table, choosing only the relevant information
- Use pyBIS to interact with openBIS
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 in openBIS is the simple archiving feature where data easily can be stored, but also retrieved by one mouse click, only takes few hours until data is available again.