Hands-on: Create an experiment & explore LabID' ELN functionalities

• 25 min
• Easy

Overview

The goal of this first hands-on is to write your first lab note and explore the main options available.

• Creating an experiment (a.k.a. a lab note) in your ELN
• Include images and tables
• Link to other LabID items
• Clean up useless images
• Attach documents, and edit them online
• Discover mobile device functions

Walkthrough

Material

Download

Download the material archive to your computer and unzip it

Archive content

- Tea-Coffee_consumables.xlsx
- Tea-Coffee_equipment.xlsx
- pexels-chevanon-photography-324028.jpg
- pexels-jessica-lewis-creative-593328.jpg
- pexels-lisa-7393900.jpg
- pexels-pratik-gupta-2748535.jpg
- water_boiler.jpg

Step 1. Create a new experiment

• Navigate to the Lab Notebook menu and click the Experiment sub-menu.
  • This displays the Experiments in the central panel as visible on the picture below.
  • The content you see may vary based on the ownership selector position (boxed in red).

The Experiment list page

The ownership selector (boxed in red) allows to list experiments that belongs to you (Personal), your group (Group) or anyone (All) who shared data with you.

• Click on the New experiment button available on the top left (boxed in green)

  • In the pop-up, enter a name for the experiment: Making myself a cup of Tea (tea group) or Making myself a cup of Coffee (coffee group) as your experiment name. Click Create.

  • You are redirected to the newly created experiment detail page. This page features a text editor, where you can write and format notes.

• Before editing our notes, we need to set the project our experiment belongs to.

  • Here select the Tea Project or the Coffee Project according to your group.
  • With a few sentences and/or bullet points, describe how to make yourself a cup of tea/coffee.
  • For example:
    • Tea: put water in the boiler and switch it on. Meanwhile, grab a cup of tea and put a bag of tea in the cup. Finally pour boiling water into the cup and remove the tea bag after 2 minutes. Add a spoonful of sugar. Ready.
    • Coffe: put water in the boiler and switch it on. Meanwhile, grab a french press and put 4 spoons of ground coffee. Finally pour the boiling water into the french press, mix well with a spoon and wait 2 minutes. Ready.

Be creative and explore the available formatting options.

• Save your work using & exit button

Experiment Making myself a cup of Tea after step 1

Creating your own projects

Here we already have created the projects and shared them with the groups, giving permissions to all group members so that they can all use it to associate their experiments to.

You normally would need to first create a project using the Lab Notebook | Project menu entry, before creating your first experiment. In real life, it also make sense to share projects between collaborators to group all related experiments under the same project.

It is always possible to edit your experiments and move them to a different project later.

Experiment or lab note ?

We interchangeably use the terms experiment and lab note.

Step 2. Insert pictures

• Enter edit mode (click Edit at the top)

• Click in the text where you would like to insert the boiler picture

• Click on the picture icon available in the text editor menu (squared in red in below picture)

Embedding an image using the Image Plug-in

The image plugin allows to embed images inside your note. Upon click on the image icon (boxed in red), a pop-up allows to drag'n'drop a picture.

• In the data pack, you'll find a picture of a boiler and one of a tea/coffee cup. Drag & Drop this boiler image. Once uploaded, the image is listed under the Choose from attachments section. Click on it. Two additional options are available:

  • the width (in pixels), this is helpful when your image is too large. The default (580) fits most situations, and you can of course change this later if needed.

  • a checkbox "Remove copy from attachments": if you leave it unchecked, the embedded picture will also be available as an attachment. Leave it unchecked so we can see what happens.

  The Image Plug-in options

  

• Click on Embed image and check the result. In addition to the picture embedded in your text, you now also have:

  • one file in the Attachments section
  • one file in the Embedded images section

The Embedded images section (you may have to scroll down) indicates the number 1 next to the title. This section is closed by default; click to open it. You can now see listed the image that we embedded in the text. Notice the absence of to trash the picture (as opposed to the copy in attachment).

• Repeat this procedure to embed the tea/coffee cup picture where you see fit
  • Notice how the image plugin now also offers to embed the attached boiler picture
• Save your work with & exit button

Attachment & Embedded Images sections

Embedded images are listed in the Embedded images section. By default a copy is also available as an attachment.

Should I keep a copy of my embedded images in the attachment section ?

• Although this is not the default, you usually do not need to keep the original version of the image in the attachment section (this is a duplicate).

• One exception to this rule is when you wish to embed the same picture at multiple places of your note.

• Please think about removing embedded images from your attachments when you are done with your notes.
• Note that if you cancel your image embedding after you drag and drop an image, the image will be saved in your attachments. Think about cleaning this up!

Why isn't it possible to copy/paste images in the editor ?

This option was voluntarily disabled to ensure images are properly registered when uploaded. With the plug-in, an image is always:

• (1) uploaded as an attachment,
• (2) duplicated as an embedded images
• (3) linked into your notes (notes are indeed saved in the HTML format, embedding a picture is therefore a simple link to the image file)
• (4) the original attachment is optionally deleted

This procedure guarantees that each embedded image is a separate file (which is electronically signed). We indeed faced situations where the copy-pasted image ended up inside the text

_i.e._not as a separate file; as a result the image is saved in the database (as part of the text) and not as a separate file. In some situations, the size of the note became unmanageable and it was decided to disable this behavior.

Allowed Image Formats

The commom image formats ( png , jpeg , ...) are supported. tiff images are currently not supported as they can feature multiple channels.

Step 3. Reference other items using hyperlinks

We now want to enrich our notes and reference the exact material that we have been using to prepare today's cup of tea/coffee. If you navigate to the Consumables | Other section, you will see that a number of public items related to tea/coffee making are available.

Publicly available consumables

Public items are visible when the ownership filter (boxed in red) is set on All

Similarly, the subsection Equipment | Other lists publicly available devices to make tea/coffee.

• Get back to the experiment Making myself a cup of ... and enter edit mode: Edit
• Click in the text where you want to reference the tea/coffee maker
• Click on the link icon available in the text editor menu (boxed in red on the picture), this brings up the Insert a link pop-up. The pop-up offers to navigate and find every registered item; for the moment, we want to insert a link to the consumable we use to prepare our cup of tea (or coffee)

The link plugin lets you reference any registered item

Click on the link icon (boxed in red) to bring the link plug-in interface

• Mouse over Consumables to bring the list of all available consumable types (as shown on the picture); click on Other. A search interface (the same one as featured on any list page) is available and let you locate the item you need in the Consumables of type Other. Note that if you do not see any item listed, double check that the All is selected in the ownership selector (right to the search box).

• You may for example type tea or coffee in the search box (boxed in orange on the picture below) to filter results (click enter or on the ).

• Select e.g. «Green Tea Bag» (or any coffee beans you like) using the checkboxes available on the left. Do not click on the item name as this would bring you to the detail page of this item.

• Click the Add Link(s) button.

Selecting the right item to link

The global search lets you narrow down items

The selected tea bag is now referenced in your notes as hyperlink (you need to exit the edit mode to enable the link). The Linked Items panel lists all items that have been referenced this way.

Linked items are listed in the Linked Items section

Linked items are listed in the Linked Items section; and are clickable links from the text.

You can also reference multiple items of the same type at once. Let's try it out with linking some consumables:

• Click in the text where you would like to insert the links and click on the Insert Link icon
• Mouse over Consumables and select Other
• Warning: if you used the search before, it may still be set. Make sure to remove it by clicking on the available in the search box (on the right)!
• Select multiple items e.g. one particular tea/coffee, one sugar type and one milk type
• Click the Add Link(s) button.

The items are inserted each on a new line. This way, you can easily format them e.g. into a bullet list. When a link is removed from the notes, it is also removed from the Linked Items.

• Save your work with & exit button

Soft-links vs Hard-links

Links inserted using the Insert link plugin are plain HTML links. Like any html links, LabID is not aware of them and it is not possible t e.g. "find all the experiments that link to the Green Tea Bag".

Inserting a html link with the link plugin

The link plugin can also be used to add a plain HTML link.

Step 4. Attach a document and online edition

As you already (indirectly) saw with images, you can attach documents to your experiments. Depending on the document type, LabID offers slightly different options :

• when the attached document is an image, you'll have the chance to insert it in your note using the image plugin (this means that you can first attach images and only later include them in the text using the image plugin as we did in step 2).
• when the attached document is an office type document (word, excel, ppt ...), LabID offers online collaborative edition.

We'll see an example now.

Attach an excel spreadsheet

After drag'n'drop of a file (red boxed zone), attached documents can be edited online by clicking on their name (orange arrow)

• In the data pack, you'll find an excel spreadsheet "Tea-Coffee_consumables.xlsx".
• Drag'Drop it over the Attachments section (red boxed zone)
• Once uploaded, click on the file name (not the symbol left to the file name) to open the excel spreadsheet in the online editor (orange arrow). Note that the document is first open in read-only mode.

An attached excel spreadsheet displayed in view mode

The parent experiment link is available at the top-left (orange arrow). Click the top-right edit button (boxed in red) to enter edit mode.

• Click the Edit on the top right to enter the edit mode (note the button then says Exit edit), make a few edits and click on the save icon (or select Save in the File menu). Warning: clicking on Exit edit without saving will not save your modifications nor warn you!

• Click on the experiment name to get back to the experiment view page.

An attached excel spreadsheet displayed in edit mode

Quiting the edit mode (orange box) without clicking the SAVE button (red arrow) discards your edits without warning.

Step 5. Deleting images

As you edit your notes, you may embed images and later replace them with e.g. a better version of the image. Here we explore how to properly clean up your experiments in such situation.

• Let's embed another image in our note. For this, follow step 2 instructions and use an image from the data pack (use one of the "pexel_..." image). You should have now embedded multiple images (say 2 but you may have a different number) in your notes and the Embedded images section should reflect this with a badge displaying the number 2.

  • You may open the section to gain details about all the images embedded in your notes.
  Two embedded images

  

• Remove the image we just embedded: in your notes, click on the image to select it and press the delete key.

• Scroll down to the Embedded images section. The image count still shows 2 together and a trash icon is now available in the section header hinting that something may be cleaned up.
• Click on the trash icon. A dialog asks you to confirm the clean up action, confirm it.

The embedded section with cleanup icon

• All images that are not referenced in the text have now been removed from disks.

Congrats! You now have completed this hands-on!