Lab note¶
Creating a new experiment¶
A lab notebook entry (or Experiment) can be created from the Experiment list page by clicking the New Experiment button. Upon clicking, a pop-up prompting for an experiment name will appear. Write the new experiment name and click create.
Once you reach the experiment detail page, a parent project must be set - and only then can it be saved. The status is set to IN PROGRESS and the Estimated Completion Date is set to 7 days later. The visual editor can be used to write and format text, tables and images.
New blank experiment page
Deriving an experiment from a protocol¶
When the experiment simply consists of following an existing protocol, we advise deriving the lab note from the protocol. In this situation, the protocol text is copied into the experiment description and can be adapted there. The attachments and pictures are also transferred to the new lab note. From there, the text can be enriched if needed, particular consumables can be linked, new pictures added, etc. As this is a copy, modifying the original protocol does not affect the lab note content.
To derive a lab note from a protocol, go to the protocol detail page and click the Derive lab note button
Writing notes¶
Like other items, lab notes have a Notes panel. This panel should not be used to record important information about an experiment. Indeed, anyone with read access to the experiment can add a note. In addition, notes can be added after an experiment has been frozen. In order for important information to be recorded and digitally signed, it should be written in the main description text.
Editing relationships with samples¶
Properly defining the ELN-Sample relationship will bring you many benefits, i.e. the sample parent-child relationships are used to create logical connections between your experiments as shown in the picture. Imagine three ELN experiments A, B, and C that logically follow each other, e.g. A could represent the sample acquisition, B the mRNA extraction, and C the Illumina library preparation. By properly defining the sample-ELN relationships, LabID will always be able to follow the sample parent-child relationships to reconstruct the lineage of your complete lab book.
When describing input and output samples, always make sure to also describe the sample parent-child relationship. Note that we will need the sample parent-child relationships to be defined when we export your data to public repositories, so you will have to do this at some point. Better to do it straight away!
LabID does not enforce defining experiment's input/output samples as this might not fit all situations. For example, in the above picture, experiment A only defines output samples that are directly linked to their specimen (from your collections).
Sharing¶
By default, your experiments can only be modified by you (your group can read them unless you have modified the permissions). You can allow a collaborator to edit your experiment, but we recommend doing so only if required as your lab book primarily reflects your work. Note that LabID does NOT track who edits what on the experiment. You might want to agree with your collaborator on how edits should be made (e.g. by using different colours or explicitly writing the editor's name). The experiment can only belong to a unique person, and this means that uploaded attachments will also belong to the experiment's owner.
Exporting¶
PDF format¶
A PDF of an Experiment or Protocol can be obtained by pressing the Export PDF button on the detail page.
Archive (Zip)¶
Upon freezing, an archive of the experiment is created. The archive contains a PDF document, a browsable HTML document, as well as all the attachments. The archive is then digitally timestamped and can be downloaded.