lab-notebook.md

Lab Notebook

Register Projects

In a personal folder, users can register one or more Projects they currently work on. Projects in openBIS only have a Description field, no additional fields can be added.

 

1. Navigate to the relevant Space in the Lab Notebook menu and click the + New Project
2. Should you have an empty page, select Show Identification Info and Show Description from the More… dropdown
3. Projects do not have a Name field, but only Code. Codes can only take alphanumeric characters and no spaces.Codes are prettified in the Main Menu.
4. Enter a Description for the project.
5. Click Save on top of the form.

In the More… dropdown you have additional options on what you can do in the Project folder, as shown below.

 

Updated on April 25, 2023

Register Experiments

Inside one Project, a user can register several Experiments, which can in turn be divided into single Experimental Steps.

 

To register one Experiment:

 

1. Navigate to the relevant Project in the Lab Notebook menu
2. Select Default Experiment from the +New dropdown, as shown below. *Please note that your openBIS instance might have different types of Experiments, depending on
3. Fill in the relevant fields in the form.
4. Select Show in project overview = true if the Experiment is important and should be shown in the Project form.
5. Click Save* *on top of the form.

 

Updated on April 25, 2023

Register Experimental Steps

As mentioned above, the various steps executed when performing an Experiment in the lab can be registered in openBIS as  Experimental Steps or Entries.

The default Experimental Step has pre-defined fields, as shown below:

 

An Entry, is a blank page, with no pre-defined fields:

 

To register a default Experimental Step or Entry:

1. Navigate to the relevant Experiment in the Lab Notebook menu and click the + New button, as shown below.
2. Select Experimental Step or Entry
3. Fill in the relevant information or select an available template from the list (see below).
4. If Show in project overview* *is set to true, this Experimental Step or Entry will be displayed on the Project page.
5. Click Save on top of the form. 

 

 

Comments Log

Several comments can be added by different users who have write-access to a given user Space:

1. Click the button in the Comments section*.*
2. Enter the comment.
3. Click Save*.*

Updated on April 25, 2023

Add parents and children to Experimental Steps

In the default Experimental Step and in the Entry, there is a Parents section where it is possible to specify links to materials and methods from the Inventory or to any other Object, e.g. another Experimental Step or Entry.

Parents are all samples/materials used in an experimental procedure, standard protocols from the inventory followed in the experimental procedure, the equipment used. It is also possible to set one Experimental Step/Entry as parent of a second Experimental Step/Entry, to keep the connection between the two.

The name of this section and which parents should be shown in the form, is customisable by the lab manager or group admin as described in Customise Parents and Children Sections in Object Forms

Adding a parent

Adding a parent of a predefined type in the form

In the screenshot above, General protocol is predefined as parent type in the form. We have two options to add a parent of this predefined type:

1. Search

1. 1. Click on the Search button.
   2. Enter the name or code of the entry you want to add as parent.
   3. Select the entry you want to add from the list presented to you.

The parent will be added only when you save the entity.

2. Paste

1. 1. You may copy the identifier of an entry you want to add as parent from a file, or from an advanced search or from another ELN page. You can paste the identifier(s) in the Paste text field.
   2. Click the +Add button

Adding parent of any available type

If you want to add a parent that is not specified in the Experimental Step form, you can use the Search Any or Paste Any options next to Parents.

1. Search Any

1. Click Search Any
2. Select the Object type for which you want to add a parent
3. Search by code or name as explained above
4. Click the + Add button

2. Paste Any

There are cases where you may want to add several parents of the same type or also of different types. In this case, we recommend to use the Advanced Search to find the entries you want to add. You can select the desired entries from the table and the Copy Identifiers button will become visible. You can copy the identifiers and paste them in the Paste Any field in the Experimental Step page, as shown below.

Adding parent via barcodes

If you want to add a parent that is registered in openBIS and has a barcode associated with it by scanning the barcode:

 

1.Click on the barcode icon in the Parents section

2. A Barcode Reader window opens

3. Scan the barcode/QR code of the entry you want to add as parent with a scanner or with the camera of a mobile device

4. Click on the Add Objects button

5. Close

Removing a parent

To remove a parent, choose Remove* from the Operations *drop down in the parent table, as shown below.

 

Adding and Removing Children

Children of Experimental Steps are usually derivative Experimental Steps, or products of the Experimental Step. As for the Parents section, this section can also be customised by a group admin or lab manager in the ELN Settings (Customise Parents and Children Sections in Object Forms).

The procedure for adding and removing children is the same as explained for parents.

Children Generator

The Children Generator creates a matrix of all the parents entered in the* Experimental Step*, as shown below. Combinations of parents needed to generate children can then be selected by the user. The Object type to assign to the children and the number of replicas need to be specified. The children will then be automatically generated by openBIS upon registration of the Experimental Step.

Parent-child relationships between entries in lab notebook

In the Lab Notebook section, if you create a new Object from an existing Object, independently of the type, this will be automatically set as parent of the new Object. For example, if you create a new Experimental Step (measurement 4) from an existing Experimental Step (measurement 3), this will be automatically set as child of measurement 3, as shown below.

If you do not wish to have this relationship established, you need to create the new Object starting from the Experiment level, as shown below.

 

Updated on July 5, 2023

How to use protocols in Experimental Steps

When adding protocols to an Experimental Step, two options are available:

1. Link to a Protocol stored in the Inventory. This can be used if the protocol was followed exactly in all steps as described.
2. Create a local copy of the Protocol from the Inventory in the current Experiment. This should be done if some steps of the main protocol were modified. These modifications can be edited in the local copy of the protocol, while the template is left untouched.