Hands-on: Item creation and item list operations

• 45 min
• Easy

Overview

The goal of this hands-on is to create your first consumable (an antibody) and storage equipment (a freezer) to understand how to efficiently manage the location of items. We will then explore the different actions available on all collection list pages, including the list display customization options.

• step 1: Creating our first antibody
• step 2: Naming strategy for complex storage set-up
• step 3: Searching for and filtering items
• step 4: List page customization
• step 5: Sharing multiple items at once
• step 6: Editing multiple items at once
• step 7: Deleting multiple items at once

Walkthrough

Please do not perform this hands-on on a production environment

Step 1. Creating our first antibody

We first want to create an antibody named anti-H3 and indicate that it is stored in the Plate 2 (position C3) in the freezer named Liebherr-30freezer.

• Navigate to the Consumables menu and click the Antibody sub-menu.
  • This displays the antibody list page in the central panel.
  • The actual content may vary depending on the ownership selector position (boxed in red).
• Click on the New antibody button available on the top left of the list page and fill in the name (e.g. "anti-H3") and other mandatory fields (e.g. isotype = "IgG")
• Scroll down to find the Stock locations field and click the Add a stock location

• Set the fields as follows:

  • Location to Liebherr-30freezer
  • Container's Type to 96-well plate
  • Container's Name to Plate 2
  • Container's Position to C3
  • Add an extra Description if you wish
  Adding a location to an item

  

  The stock location allows to define where items are stored. Only the top Location field is required.

  Good to know about stock locations

  • The location field (see picture above) offers a combination of rooms and storage equipments (permissions apply allowing you to define storage equipment that are visible only to relevant collaborators) and is the only mandatory field.

  • Items are stored in containers (e.g. tubes or plates), which model is composed of 3 optional fields:

    • the container type: a list of controlled vocabulary that can be extended by your admin
    • the container name (e.g. tube A, plate XZ56...)
    • the container position is relevant when the container has a positioning system like boxes or plates

  • Finally, a free text field allows you to give all relevant and/or additional details that cannot be described with the other fields.

  • An item can have more than one location i.e. when you keep multiple aliquots to prevent loss of precious material.

  • Storage equipment can have locations too; allowing you to define e.g. the different towers of a cryogenic tank located in a specific room.

  • Rooms (or other pre-defined locations) can only be added by the admin to avoid rooms to be created multiple times.

• Click OK to validate the location. Notice how the location information is turned into a short label, and the new edit and delete buttons allowing you to act on the newly created location.

How is the short location label created?

The label is a concatenation of :

[container_name]:[container_position], [location_name] .

Knowing this will help you come up with nice location names_i.e._making your location labels very informative. Indeed, this short label is used at multiple places and having informative labels offers a much better experience.

• Save your antibody using the Save item button (top right). After saving, the page is automatically available in edit mode to allow further edition e.g. attaching documents.

  My first antibody

  

  LabID items are composed of properties (left) and additional panels (right) which only become accessible after the item is saved for the first time.

• Notice the additional panels (on the right side) that became accessible after the item is saved for the first time:

  • Annotations: Annotations are similar to item properties available in the Item details panel but let you customize your items. For example, add an annotation of type pubmed_id with value 35901960:
    • In the Annotations panel, start typing pubm... in the available dropdown and select pubmed_id
    • Enter 35901960 in the text field that appeared
    • Click the Add
  My first annotation

  

  More about annotations

  While item properties are meant to be universally relevant (i.e. every antibody has an isotype), annotations let you describe aspects that are only relevant to your group (e.g. imagine your group uses a classification system based on the tube color, you may want to have the Tube color as an annotation) or project-specific (this is particularly relevant for samples where the biological annotations are often project-specific, we'll see this in future hands-on).

  Read more about annotations

  • Attachments: every item can have attachments (like we saw for ELN's experiments)
  • Notes: every item can have free text notes and everyone with view permission on an item can take a note:
    • Try to add a not e.g. "works best at dilution 1:12 for immunostaining"
    • Notice how the note's owner and date are well identified (a bit like comments on social media)
    • Notes can only be deleted by their owners

Good to know on item properties

• The code field can be used to assign a unique code to your item (e.g. a barcode or a unique number ). LabID enforces codes to be unique for a group and an item type (here the item type is antibody). In other words, a particular combination code-OwnedByGroup-itemType can only exists once.

• For properties with restricted options, the list of the selectable values can easily be extended by your admin

• Your admin can easily add new properties.

• We now want to create a second location for our antibody in a freezer named Freezer 6 MY_NAME (please replace MY_NAME with your name) that is itself found in room C2.06. Creating a freezer (under Storage Equipment menu) is pretty similar to creating an antibody so we'll keep instructions at a minimum. For this, you need to:

  • Create your own freezer Freezer 6 MY_NAME:

    1. first option is to navigate to Storage Equipment, click on the Freezer sub-menu and use the New freezer

    2. second option is to use the global available in the top menu left to the global search.

  The top menu

  

  The top menu is always available and offers (left to right) a quick Create new item, a global ID/Name Search, link to user dashboard, task list and shopping cart, the advanced features (ellipsis) and user menus.

  • Give it a unique code (here it could be the name as well). The unique code is meant to uniquely identify the equipment. Organizations usually have such codes assigned centrally and stuck on the equipment.

  • Set its location to the room C2.06 (the room already exists)

    • Notice how the location interface is different: the concept of a container for a storage location is indeed irrelevant

  -Save with & exit

  • Come back to your antibody, edit ( Edit) it to then Add a stock location in Freezer 6 MY_NAME, Box A , Position B12

    • you may see many "Freezer 6 ...", you should be able to easily locate your freezer by typing your name

  -Save with & exit

  Antibody with two locations

  

  The second location does not reflect that the freezer is located in room C2.06

• Final remarks:

  • The second location does not reflect that the Freezer 6 MY_NAME is located in room C2.06, can you think about a way to improve this?

  • The freezer list page (and the location drop-down as we saw above) are now listing many Freezer 6 ..., what do you think about this?

Should everyone create their own freezer?

In the exercise above, we made you create a personalized freezer to avoid having 30 freezers with the same name. In real life, you need to organize at the group, unit or institution level to make sure that storage locations are entered only once and shared among the right people.

We suggest the following:

• each lab/group has one manager who is responsible to create the group storage equipment. Whether those are also visible to colleagues outside the group depends on the situation.

• equipment available to all should be created by an admin or a global data manager and made public (== everyone who can log in LabID can see it)

It is very important to name equipment in a systematic and informative manner. We suggest always having the group name and the room name. This will allow for immediate identification of the equipment.

Examples:

• Moore Group -20 Freezer 1 (room 123)
• Common Bosch Fridge A (cell culture 352)
• General Nitrogen Tank 1 (room 76)

Step 2. Naming strategy for complex storage set-up

In this exercise, we build on what we just learned and try to design a nice naming scheme for a more advanced case of interlinked storage: the cryogenic tank scenario. Such deep cold storages are internally composed of a set of Towers, each of which holds vertically stacked boxes whose shape can vary (square or pyramidal). Examples are visible at this Thermo Fisher page. When working with this kind of storage, it is particularly important to know exactly where is located the tube you are looking for to minimize the time the tank remains open.

A realistic example is to consider a tube (containing our antibody) at position B05 of the "Box 3" in the "Tower XX" of the cryogenic tank "Cryo001" located in room C2.06. Let's try to create the framework for this.

• First we need one Cryogenic (under Storage Equipment) named Cryo001 located in room C2.06. To mimic reality we'll create only one Cryogenic per group, only the trainee1 and trainee51 should create a Cryogenic to simulate a real situation:
  • To follow naming advice, we'll name it Cryo001 (C2.06)
  • Locate it in room C2.06

In case you are self-teaching this training...

In this case, create a Cryogenic and make sure to remove all the permission to your group (i.e. make it personal)

• When the Cryogenic is ready (trainee1 and trainee51, please let everyone know), everyone creates a Tower XX (where XX is your trainee number) and located in Cryo001 (C2.06). Again we will be verbose and name the tower Tower XX (Cryo001, C2.06); e.g. for trainee10, the tower will be Tower 10 (Cryo001, C2.06)

• Now go to your antibody and add another location corresponding to position B05 of Box 3 in your Tower XX (Cryo001, C2.06). When adding this location, take a minute to play with location filter capabilities i.e. try typin e.g. C2 or cryo001 or tower or XX (your trainee number) to appreciate the benefits of good naming.

  Filtering locations made easy

  

  Good location naming is important to be able to find your items among thousands of entries

• Save with & exit

• Done! Appreciate how our naming strategy creates an informative label.

  Informative Naming Across Interlinked Storages

  

Step 3. Searching for and filtering items

In this exercise, we will explore the different options available to look for items. For this, we pre-loaded 50 enzyme consumables with different properties.

Details of the pre-loaded enzymes

50 enzymes belonging to different users & groups and with different permissions:

• 16 enzymes belonging to trainee1..16 (1 per trainee) shared with the Tea Lovers group
• 21 enzymes belonging to trainee51..70 (1 per trainee) shared with the Coffee Lovers group
• 13 enzymes belong to the demo user and have been made public (everyone can see them)

• Navigate to the Consumables | Enzyme list page. By default, the ownership filter (boxed in red in below picture) is set on All so the list page displays all the enzymes you can see i.e. 29 and 34 for Tea and Coffee Lovers, respectively (these numbers only hold if no defaults have been changed).

• Click on the Group and Personal to set the ownership granularity you'd like to see. Remember that we only created enzymes for some of you explaining why you may have an empty table when selecting the Personal filter.

  The Different Filters on List Pages

  

  Global Search (orange), Free Text Table Search (purple), Ownership Filter (red) and Column Filter (green)

• Now try to look for pol using the free text table search (boxed in purple), make sure to set the ownership filter on All . The free text table search allows to search all properties of the enzymes e.g. here, the pol token is sometimes found in the enzyme's name but most often it matches the enzyme's category (Polymerase). Note that the search is not case-sensitive.

• In contrast to the free text table search, you can use the Column Filters (boxed in green) to filter on a unique enzyme's property; or to filter on many properties at once. For example, try to find all Polymerase from NEB (NEB is a vendor). Note that:

  • the (also boxed in green in above picture) allows to hide/unhide the Column Filters.
  • the search is not case-sensitive.
  • depending on the property value type, the column filter offers free text search or e.g. a drop-down selection.
  Column filters icons

  

  When column filters are set, the number of filters is displayed next to the . Columns with active filters have a small , which can be clicked to drop the filter (boxed in green)

• Finally, a Global Search is available in the top menu under the button (boxed in orange). Click on to bring the search input field, type in pol and press enter. Note that:

  • the global search only searches the name property of all items in LabID.
  The Global Name Search Result Page

  

  Global search result for pol returns all items which name contains pol. The category filter (purple) allows to narrow down the search to a unique category.

  • the global search also accepts ID (i.e. the ID field of any LabID item); in which case it will directly open the view page of the item. Try it.
  Grabbing the ID of an item

  

  Item's ID can be easily copied using the clipboard item available in the field

Step 4. List page customization

We continue our exploration of the list page to look into the customisation options.

• Go back the enzyme list page. Make sure that the ownership filter is on All and that all column filters are removed.

• The picture below outlines the different list customization controls:

  The List Customization Options

  

  Handles (boxed in blue) are available in column headers to sort and modify column position, list size control is boxed in orange and global customization buttons are boxed in green

  Customization Options Description

  • List Size Control (boxed in orange): from 10 (default) to display up to 500 items
  • Column Header Handles (boxed in blue):
    • The table can be sorted in ascending or descending order using any column by clicking on the )
    • The columns can be
      • re-ordered by dragging using
      • sent in the first position by clicking the
      • removed from display using the
  • • : Open the table column settings panel allowing you to select which properties and annotations should shown/hidden and define their display order

    List Customization buttons (boxed in green):

    • : Save the current list settings as the new default. This saves the column on display and their order as well as list size and any filter set i.e. the ownership selector position, column filters or free text search.

    • : automatically adds the relevant annotation columns given items on display

• Set the max number of displayed items to 50 (boxed in orange)

• Use the handles available in column headers (see picture above) to change the table display such that:

  • the columns Description and Storage Conditions are not visible anymore (hint: )
  • the first column is the Stock location (hint: )
  • The owner column is between the category and the code (hint: )
  Customized Enzyme List Display

  

• Use the above the table (boxed in green) to save this new table set-up. The enzyme table will now always display this way even if you log out. Note that if you don't save the new settings, these are still kept as long as you stay in the same tab ; but they will be lost if you open a new window or refresh your web browser.

• Open the table column settings panel () This panel allows you to select which columns should be visible and their order in a much more productive way than using the column header handles. On the right, the item properties and the annotation types are available.

  Column Settings Panel

  

  Drag'Drop Attributes and Annotations onto the Visible columns list. Once there, use the handle to order them and use the save button (bottom) to persist your settings. Filters allow you to quickly locate the attributes/annotations you are looking for.

• Add the ID column in the second position of the Visible columns (use the )

• Save ( notice the at the bottom of the Visible columns) and close the Column Settings Panel ( at the top-right corner)

Step 5. Sharing multiple items at once

In the ELN Hands-on Permissions & Lifecycle, we learned how experiments can be shared. Sharing is a general concept in LabID and works similarly for all items. For example, if you open a particular enzyme and scroll down to the Permissions attribute, you could share this enzyme with colleagues like we did with an experiment.

But what if you want to share (or make private) a list of enzymes, all in one go? That's what we'll learn in this exercise.

We want to share two items with the demo user who is not part of the Tea/Coffee Lovers (it is part of the demo group).

Checking what the demo user can see

you can check this by opening an incognito window and logging in as the demo user.

• Go back to the enzyme list page. Make sure that the ownership filter is on All and that all column filters are removed.

  How to remove all column filters at once

  

• By default, the demo user has 13 enzymes that are all public _i.e._you should see them in your enzyme list (hint: check the owner column).

  Default permissions

  In LabID, items get default permissions at creation. The default set of permissions is:

  • all permissions (read, edit, delete) for the item's owner
  • read & edit permissions for all the group members unless the item is an experiment in which case, the group can not edit.

• Sets the ownership filter is on Group so only enzymes that belong to your group are visible.

• Select 2 enzymes and click the button (boxed in red)

  Sharing Multiple Items at Once

  

• This brings up the batch sharing component, click on the click the Fine Tune Access Rights .

• You can either grant new permissions or revoke some; here we want to Grant access (the default)

• You then need to select which permissions you want to grant. Here we want to enable the demo user to see our enzymes but not modify them. Click on the View .

• Select the demo user in the Users list (hint: you can start typing to filter the list on the fly). Note that multiple users could be selected and that you could also select groups at the same time.

  Granting view permission to the demo user

  

• Validate by clicking on Apply access rights

• A green confirm message appears. Close the batch sharing component by clicking on Quit

• Voila!

  Checking what the demo user can see

  you can check this by opening an incognito window and logging in as the demo user.

Step 6. Editing multiple items at once

Similarly to batch sharing, LabID offers ways to edit many items at once. Here we learn about the first option that allows you to edit one property -_i.e._set, unset or add (when multiple options can be set)- on multiple items in one go.

We will set the Responsible Person to trainee1 (Tea Lovers) or trainee51 (Coffee Lovers) on multiple enzymes.

• Go back to the enzyme list page. Since you want to edit enzymes, you need to act on enzymes for which you have edit permissions. This is the case for all the enzymes that belong to your group (assuming no one removed permissions). Make sure that the ownership filter is on Group so only enzymes that belong to your group are visible.

• Select 2 enzymes and click the button (next to the share button) to bring the batch editor widget. Notice the permission level check visible at the top (boxed in green).

  The property batch editor

  

  Permission level check is visible at the top (boxed in green), the details link provides in case some you don't have edit permission on some selected items. The Operation section (boxed in orange) will be updated upon selection of the Attribute to edit; indeed the Add & Remove options are only applicable to attributes accepting multiple values.

• Start typing respon... in the dropdown to easily find the Responsible Person. Upon selection, the Operation section is activated and the only option is Replace since a unique person can be set as a Responsible Person.

• Select the right person as a "Value"i.e.trainee1 (Tea Lovers) or trainee51 (Coffee Lovers) and click Save

  Setting the responsible person to trainee1 (Tea Lovers) or trainee51 (Coffee Lovers)

  

• A green confirm message appears. Close the batch editor widget by clicking on Quit

Step 7. Deleting multiple items at once

• Go back to the enzyme list page, select all enzymes (increase the list size on display) and remember how many items you selected; then click the button (next to the share button)

• Confirm the deletion in the confirm dialog. You should witness one of these two possibilities:

  • You see a success green message indicating successful deletion. It does not mean all selected enzymes were actually deleted (many enzymes are indeed still listed); rather it means that those enzymes on which you had delete permissions have been deleted.

  • You see a red error message telling you no enzymes were deleted by lack of delete permissions

• If you got a green confirmation message, select all enzymes again and delete them all. Now you'll get the red error message as all you could delete was deleted from the previous operation.

  Lack of delete permission

  

  Items on which you lack delete permissions are simply ignored during the batch delete operation

Congrats! You now have completed this hands-on! In the next hands-on, we will learn how to create or edit many items using excel-based templates.