Electronic Lab Notebook

By C.Du @snail123815 & Joost Willemse @Karivtan

Leiden University is hosting an ELN server that provides a web application called Research Space (RSpace) . Using RSpace ensures compliance with data management policies and provides a sustainable solution for our research documentation needs. This page serves as a guide to help you get started with RSpace, including how to apply for an account, set up autosharing within your group, and find tutorial videos.

Adopting an ELN can feel awkward if you’re used to paper notebooks. Take it slowly and try things out with your group. Start by using the ELN simply as a cloud notebook: create entries, add text, and attach images.

Practical tips:

• Begin with basic, frequent entries to build the habit; don’t try to move everything at once.

• Use the mobile app to upload photos of plates, gels or notes, but do not record or process sensitive or confidential data on personal devices — prefer institutional devices for that.

• Use templates, tags and clear titles to make notes easy to find later.

• Ask colleagues or ELN support for demonstrations and share experiences within your group.

Warning

Do NOT contact RSpace support. Please always contact our faculty level support for assistance.

Faculty level support (login required) can be found in FWN-IM-Electronic Laboratory Notebook (ELN) documents and RSpace ELN&Inventory QRCards. Or you can approach help via ISSC helpdesk → “Research support” → “ELN” → “Report an issue/Ask a question”. This way we can track issues and questions, and provide better support to everyone. If you contact RSpace support directly, they will refer you back to us, which will cause unnecessary delays.

For Benchling users, you can still use it for molecular cloning. But please migrate to RSpace for all other journaling. Please keep a complete, repeatable record of your cloning work on RSpace as well. Check below for how to do that and reasons why we do not recommend Benchling as a general ELN.

ELN direct access URL

ELN (RSpace interface) - https://leiden.researchspace.com/

Application entries

Check Intro-application for the application process. After your ELN account is activated, you can log in to the RSpace web interface and start using it.

There are three application entries and one deactivation entry in ISSC helpdesk → “Research support” → “ELN”

• ELN PI account activation: for PIs to request a group account (equivalent to PI account) if it does not exist. Group name has to follow the convention: IBL-[CLUSTER NAME]-[FIRST LETTER PI][Last name PI] for example:

  • IBL-MBH-GvanWezel

  • IBL-SCS-TAivelo

• ELN account activation: for all employees including PhD/PostDoc/Labmanager to request. Fill in the “PI team” field correctly, so that the account can be linked to the right ELN lab group. If you are not sure about the group name, please ask your PI or contact IBL RDM support.

• ELN student access: for employees to apply for student access. Consider to set up the end date a bit later in case of any delay.

• ELN account deactivation: for lab managers to request account deactivation for users who leave the group.

More details about how to fill in these forms can be found in the FWN-IM-Electronic Laboratory Notebook (ELN) Quick Reference Cards (login required).

Usage policy

FWN-IM-Electronic Laboratory Notebook (ELN) Usage Policy (login required)

Please read the usage policy carefully before using the ELN. Most important points are:

• Every account will be disabled after 6 months of inactivity

• ELN is not meant to be used as a bulk storage

Setup autosharing within group

• Go to Universiteit Leiden RSpace and log in with your ULCN account.

• Share all lab journals of all users with everyone in the whole group.

• Go to My RSpace and activate autosharing; then all items you create will be shared with the whole group.

• Share a single notebook with all users in the group.

• If you only want to share a single notebook with everyone in the group, please create that notebook in the shared folder of the group.

• Share a single notebook with users or groups within or outside the current group.

• If you want to share a single notebook, select that notebook and click the share icon. Select the user or group and save the changes. Here you can also share it with all users.

Tutorial videos

For ELN tutorials, see FWN-RSpace ELN Inventory Training Videos

Benchling is not recommended as a general ELN

Benchling is widely used for molecular biology workflows such as sequence design and analysis. You can continue using Benchling or similar tools for those tasks if they fit your workflow. However, Benchling should not be used as the primary place for lab journal content. The institutional record should be kept in RSpace.

Moving content from Benchling to RSpace

If you already have lab journal content in Benchling, you should move the required research record into RSpace. If a full migration is not immediately practical, record all new content in RSpace from now on. The goal is not to reproduce every Benchling feature there. What matters is that the information needed to understand, verify, and repeat the work is stored in the institutional ELN. For export instructions, see the “Export projects, folders, and data” section on the help page of Benchling. When moving content from Benchling to RSpace, pay attention to the following:

1. The sequence of the construct can be exported in GenBank format and attached to RSpace.

2. The cloning strategy can be copied as text and recorded in RSpace. You can set up a template for this purpose.

3. The primers used can be exported in CSV format and attached to RSpace. You can also create them as “Inventory” items in RSpace.

4. Sequencing results, for example in ab1 format, can be attached directly to RSpace or, if they are large, stored in Research Drive and linked from RSpace.

5. Alignments can be exported, for example as PDF files, and attached to RSpace. The same principle applies if you use other cloning tools such as SnapGene or Geneious.

Why Benchling is not recommended as a general ELN

Benchling is a strong scientific tool for sequence-centric workflows. However, we do not recommend it as the primary ELN. This recommendation is based on data management and continuity. The major concerns are:

1. Benchling is vendor-controlled with no on-premises option, which means that the University does not control the hosting environment.

2. Benchling exports are limited, which makes future migration and long-term portability more difficult.

3. Benchling is optimized for sequence-centric workflows, so it is less suitable as a general record for the broader range of research activities carried out in the institute.

RSpace is the University’s supported ELN and is hosted by Leiden University. That makes it more suitable for general research documentation, group continuity, and long-term stewardship of research records. Therefore, we strongly recommend using RSpace as the general ELN for all research documentation, including the record needed to understand and repeat cloning work.

(Disclaimer: the above points are based on the current state of Benchling as of March 2026, and may change in the future.)