Research Data Service

Electronic Notebooks

Electronic Notebooks help you maintain reproducibility in your research and sharing of information.

There are many different notebook options available, either commercially or free. Some are oriented toward laboratory work (ELNs), and some are computational based. Each application has different features and will have different advantages depending on your needs.

There are a number of different applications already in use across the University. Check with your school or institute support staff if there are any preferred applications in use or already available to you.

Choosing an Electronic Lab Notebook (ELN)

You should make an informed decision about which application you choose.  Make sure you understand where you data will be stored when you use the software and how easily your data can be extracted for use in another application if needed.

Harvard University maintains an Electronic Lab Notebook Matrix which may help you compare the features of the different ELNs.

Harvard University Electronic Lab Notebook Matrix

RSpace (ELN)

RSpace logo

Information Services has completed a trial of the RSpace enterprise ELN platform, and as from 1 January 2019 RSpace has been added to its expanding portfolio of services for researchers. The University of Edinburgh-hosted RSpace service benefits from integration with local infrastructure, allowing researchers to log in with EASE, link to files on DataStore, and archive data in DataShare.

RSpace is a multi-faceted research tool in a single, secure system accessed conveniently through any modern web browser. RSpace is an electronic lab notebook that enables researchers to do the following:

  • capture and organize data
  • use as collaboration software for groups to organise and share data
  • use as a management tool for principal investigators to observe and manage lab workflows
  • use as a platform for institutions to capture, publish and archive data

The University has a discounted licence agreement with RSpace to provide the standard RSpace Enterprise edition. 

To sign up for a free two-month trial account email support@researchspace.com using your University email, and indicating the name(s) and UUN(s) of the user(s) in your group, or your own UUN and name if it’s just you.  For groups, please also identify the Principal Investigator (PI).

If you wish to purchase licences for your research group, contact Software Services at is.software.sales@ed.ac.uk.

RSpace licenses are available free of charge for classroom (teaching) purposes. If you need licenses to use RSpace for classroom (teaching) purposes, please email support@researchspace.com using your University email, and indicating the name(s) and UUN(s) of the user(s) in your class including the details of the teacher or class leader. 

More information 

RSpace enterprise platform website

University of Edinburgh Software Services RSpace Licence wikipage

Request a live demo of RSpace for your group by contacting support@researchspace.com.

Wikibench (ELN)

As an alternative to using a commercial package, researchers within the University have adapted the University's Confluence wiki service and developed a user friendly wiki template called "WikiBench" that can act as a simple ELN.

The WikiBench template offers:

  • an attractive lab homepage
  • researcher notebook layouts
  • templates for common tasks
  • wiki macros to enrich content, ease navigation and automate page creation and aggregation

Trying WikiBench can be a useful way to find out what functions your lab actually needs from an electronic lab notebook. The creators of the WikiBench template are happy to help you set up your own copy. If you are interested in trying WikiBench or have queries you can contact them bio-rdm@ed.ac.uk.

A short WikiBench demo presentation on Media Hopper

Example data in WikiBench ELN

Instructions for setting up a new WikiBench template

Jupyter Notebooks and Noteable Service 

Edina Noteable Logo

Jupyter notebooks are an open-source web application that allows you to create and share documents that contain live code, equations, visualisations and narrative text. Jupyter notebooks are an ideal platform for promoting open reproducible science by allowing you to share working versions of your analysis in varying computational languages. With the Noteable service, you can easily share working versions of your analysis with other colleagues within your lab via our hosted environments, allowing you to quickly collaborate on computational analysis. As well as giving access to Jupyter notebooks in a variety of programming languages, Noteable can also be pre-configured with additional packages and libraries to suit your needs. 

Jupyter allows you to: 

 

  • Document complex data analysis.

  • Create computational narratives, explaining your findings and method alongside code.

  • Include visualisations and data tables alongside code.

  • Work with remote data sets.

  • Create public access versions of your analysis to share with other labs or for public engagement.

  • Support can be added for over 100 language kernels.

 

Information Services and EDINA have developed and deployed a cloud-hosted Jupyter hub environment giving access to Jupyter notebooks without the need for installation. This service was originally piloted for use as a supporting learning technology but is now being developed to support research use cases.  The Noteable team is currently looking to work with colleagues to better support Noteable for Research use cases. If you would like to investigate using Jupyter notebooks for your research or currently use Jupyter and want to make use of our cloud service, then please contact the Noteable team: James.Slack@ed.ac.uk, Nuria.Ruiz@ed.ac.uk.

 

More Information :

 

If you have other requests about electronic notebooks, contact the Research Data Support team or IS Helpline.