Aalto's Electronic Laboratory Notebook (Aalto Notebook): Quick Guide

If you are a researcher or student or teaching personal at Aalto University, you can register or begin to use Aalto Notebook by logging in using your Aalto ID credentials. Just visit Aalto Notebook (notebook.aalto.fi) and log in by following steps. 

1. When you go to notebook.aalto.fi, you will see that option "Aalto University" is automatically selected as an identity provider for institutional login. Please make sure of that. 
2. Press "LOGIN" button and this will take you to Aalto University single sign-on page. Enter your Aalto ID Credentials and press “Login” and you are good to go.

NOTE!Keep in mind that when you first log in to Aalto Notebook, you will be added to the team of your Aalto department or unit as default. In case you want to change your default team, please write to [email protected] for support. 

If you experience any problem with logging in using Aalto ID Credentials, please write to [email protected] for support.

Currently Aalto Notebook is only available for Aalto users. External collaborators do not have access.

If you have more specific needs to access Aalto Notebook or need more information about Aalto Notebook, please write to [email protected] for support.

New users need to register an account. This is performed automatically when using their Aalto ID credentials. 

By default, the new user is automatically assigned a team based on their Aalto credentials and Aalto profile. Also, by default, the group admin is the first registered person in the group, but the admin can be changed as needed.

1. Go to: https://notebook.aalto.fi
2. For "Select an identity provider" pick the option "Aalto University"
3. Click the Login button.
4. Enter your Aalto ID credentials.
5. After successful verification, you will be taken to the Dashboard page.

After login, you can create experiments and start recording your data.

1. From Dashboard or Experiments page click on the "Create" button.
2. Fill out the necessary experiment details.
3. Click "Save".

In order to save time during experiments creation, it is highly recommended to use the Templates for experiments you often do. They are a skeleton of a real experiment. To create a template, select “Templates” from the User menu.

1. Go to the User menu in the top-right corner of the page
2. Click on Templates
3. Click "Create", write a title and the fill in the template
4. Click "Save" when finished.

Tags

The tags allow you to easily group experiments together. You can think of it as folders, but more powerful because each experiment can have many tags, thus allowing you to cross-search efficiently! All experiments with the same tag will be accessible by clicking this tag or searching for it.

• To validate a tag, press Enter key or click outside the input field. It is saved immediately. 

The number of tags is not limited. Click on a tag to remove it (in edit mode). Tags are common to a team. Autocompletion favours the reuse of existing tags. See the animation below to see how tags are made.

Date

The date is today’s date by default, in the format YYYYMMDD. You can edit it as you wish. The real creation date/time is stored in the database in another column.

Status

This useful feature lets you set the ‘status’ of an experiment. By default you can have :

• Running (selected as default upon creation)
• Need to be redone
• Success
• Fail

These status can be modified completely by the admin in the admin panel.

Title

The title of your experiment. A duplicated experiment will have an "I" character appended to the title upon creation.

Experiment (Body)

This is where you describe your experiment and write your results. It is a rich text editor where you can have formatting, tables, colours, images, links, etc.

To insert an image in this field:

1. With the image open in any software program, copy the image.
2. Anywhere in the text field, press Ctrl+V to paste the image.
3. The image will be automatically uploaded and pasted into that space.
4. The default name for the image will be "image.png"

If you wish to keep the image name on upload:

1. First, upload it by dragging it in the ‘Attach files’ block. 
2. Then you will see a new block appear just below, with a thumbnail of the file, its name and size. 
3. Right click on the image and select «Copy link location». 
4. Next, click on the «Insert/edit image» button in the toolbar of the rich text editor (third button before the last). 
5. Paste the link location. Press OK. 
6. That’s it, you have an image inside your main text.

Make sure to right click on the thumbnail and not on the name!

Steps

Steps are a way to list the things one need to do during the experiment.

To add steps:

1. Edit a specific experiment.
2. Go to the steps section.
3. Enter a step and click Tab or Enter.
4. Click the Save button to save all of your changes.

So you can write several steps, and once they are done, click the checkbox to declare them finished. This is quite useful for long experiments spanning over several days, where the “Next step” will be shown in Show mode (index list), so you can see at one glance what is the next thing to do for this particular experiment.

Note that you can also declare steps in a template.

Steps will also appear in your Todo list.

Linked Items

This field allows you to link an item from the database. The number of links is not limited.

1. Type the name of what you want to link and you will see an autocompletion list appear. 
2. Select the one you want to link.
3. Press Enter. 

The number of links is not limited. This feature can also be used to link an experiment to a particular Project. If you have a «Project» Item Type and have a Project item in your database, you will then be able to see all experiments linked to this project by clicking the Link icon.

Attach a File

You can click this region to open a file browser, or drag-and-drop a file inside. The file size limit depends on the server configuration, and there is no limit on file type. If you upload an image, a thumbnail will be created. There is no limit on the number of files you can attach to an experiment.

When you are done, click the «Save and go back» button. You are now in view mode. 

Ellipsis menu (the three dots on the top right)

The Switch Editor entry will switch from the WYSIWYG editor (TinyMCE) to the markdown editor. And the Delete entry is to remove the experiment.

In the view mode, several actions are accessible under the date.

Edit

Go into edit mode.

Duplicate

Duplicating an experiment allows you to create a new item with the same title, tags, body and links, but with today’s date and running status. Uploaded files are not duplicated. A «I» character will be added to the title to denote that it is a replicate.

Lock

Once locked, an experiment cannot be modified anymore. Unless you unlock it. If it is locked by someone with locking powers (the PI), you will not be able to unlock it.

Timestamp

An experiment can be timestamped if its status can be timestamped (the default ‘Running’ status is not). Once timestamped it cannot be edited anymore.

What happens when you timestamp an experiment :

• a pdf is generated
• a sha256 sum of this pdf is generated
• this data is sent to the Time Stamping Authority (TSA)
• they timestamp it
• we get a token back

More info here: https://en.wikipedia.org/wiki/Trusted_timestamping

elabid

In the bottom right part of the experiment, you can see something like: «Unique elabid: 20150526-e72646c3ecf59b4f72147a52707629150bca0f91». This number is unique to each experiment. You can use it to reference an experiment with an external database.

Comments

Users who have visibility to your experiments can leave comments on your experiments. As the owner of the experiment you will receive an email if someone comments.

Same as experiments for a lot of things, except there is no status, but a rating system (little stars ⭐). You can store any type of items inside, the admin can edit the available types of items. You can store any type of items inside, the admin can edit the available types of items. In view mode, click the link icon to show all experiments linked with this item. 

Examples of database items types:

• antibodies
• microscopes
• plasmids
• drugs
• chemicals
• equipment
• projects

This page presents the members and some statistics about the team. You’ll also find here a scheduler.

Scheduler

First you need to set some item types as bookable from the Admin Panel. After that you can select an item from the Scheduler page and use the calendar to book it.

The user panel is where you can adjust preferences for your account. You can access it by clicking the link in the bottom left of every page, or through the user menu in the top right.

General tab

From here you can select a language, adjust the display settings, change the keyboard shortcuts, modify the PDF settings, select a different text editor and set the default permission settings.

Account tab

This page allows you to modify your email/password, activate multi-factor authentication and change your name or add your ORCID if you have one.

Templates tab

Manage your templates. Once a template has been created, you can add tags, steps and links to it. It will then be available from the Create menu.

Api keys tab

Create an API key for your account from this page. An API key is like a username+password for your account. It allows you to interact with platform programmatically, through the REST API. See API documentation.

Notifications tab

From here you can adjust notifications settings.

You can export experiments in .zip. If the experiment was timestamped you will find in the archive the timestamped pdf and the corresponding .asn1 token.

You can also export and import items from the database (it can be several items).

On paper notebooks, there was this idea of having another lab member signing every page of a notebook before the page would get plastified to prevent modifications. This was seldom done properly.

With Aalto Notebook, you can have this workflow, but it is much easier to achieve:

• User A finishes an experiment
• User B, that has locking power (Admin + Lock user group) can go on that experiment and click the lock icon

This prevents user A from modifying the content (like plastifying), and it keeps a log of who locked it and when (like signing the page).

An Admin is a User in a Team with Admin rights, and access to the Admin Panel (from the top right menu or the bottom left link). A Team can have several Admins and must have at least one.

How to become Admin?

A user is automatically an Admin if they are the first user in a Team. An Admin can promote another user to Admin from the Admin Panel > Users tab.

What can an Admin do?

An Admin:

• Has access to the Admin Panel with settings impacting only their team
• Can validate/edit users of their team
• Can edit available Status for experiments of their team
• Can edit available Items Types for the database of their team
• Can edit the default experiments template
• Can manage groups of users amongst the team
• Can change the rightmost link in the main menu (default is Documentation)
• Can archive users. Archiving users means disable login for that account, and lock all experiments.

For more information on the Admin role, please refer to this admin guide. 

If you would like to become an Admin, please ask the current Admin of your team to promote you to the Admin role, or contact [email protected].

Aalto Notebook is designed to contain research data and data describing the research process, classified as public, internal or confidential. Aalto Notebook is not suitable for storing research data classified as secret, in particular sensitive personal data (racial, political, religious, trade union membership, genetic, biometric, sexual orientation, and health details of individuals).

For storing internal and confidential research data, users should check and adjust the 'Visibility' and 'Write' access permission settings for their experiments and resources on Aalto Notebook, in order to limit access to only required person(s).

Aalto Notebook is secure and has been approved by Aalto IT Services for use. The system setup is:

• Authentication based on Aalto IdP/HAKA login credentials
• TLSv1.2 browser encryption when travelling to and from the server
• Running on Aalto servers
• Automated backups of experimental data
• Automated server updates and reboots for deployment of latest security patches

Aalto Notebook is a stable platform. Maintenance breaks are informed in advance to the users by email. During maintenance breaks, the system downtime is kept to minimum. 

Yes, Aalto Notebook is regularly upgraded with new eLabFTW releases every few months. New releases are informed to users by email. For the latest release information, please check eLabFTW change log: https://doc.elabftw.net/changelog.html      

You can contact [email protected] to request training for your research group.

You can contact [email protected] to request new features.

You can contact [email protected] to submit bug reports.

 Yes, there is no site/maintenance/other license required for usage of Aalto Notebook by Aalto researchers. Simply log in and start using it.

Aalto Notebook is recommended, primarily based on user testing and interviews with different research groups. The main issue of most other ELN platforms is the price (good for a small group with a few experiments, but quickly becomes expensive for larger groups with more users and experiments and for long-term use). Aalto has a site-license for Office 365, so cost is not a factor there, but usability was found to be the main issue (folder-based, multi-device support mixed, no common interface, sharing still cumbersome). Aalto Wiki was explored as an option. There are some groups who like the wiki-style environment, but for growing (and established) groups, it is insufficient. It lacks easy scheduling and booking of equipment, in addition to lacking time-stamping. Aalto Notebook offers an easy to use interface to record experiment information and metadata. It is open-source, based on eLabFTW with an active user community. Also it is regularly upgraded and improved with new features, and it is maintained by Aalto IT services.