Open Source Electronic Laboratory Notebook Software?

Question

[Nico Adams]

Dear All,

Apologies for a somewhat fuzzy question, but a colleague asked me recently whether I was aware of any open source Electronic Laboratory Notebook (ELN) packages.

Personally, I am aware of the EMSL Collaboratory ELN and I know that people are trying to use Drupal (MyLabBook) and blogging software for this purpose. I wonder whether any of you are aware of any other offerings or even use some of those in your labs.

Thanks for the help!

[Nico Adams]

Not really Pierre. Open Notebook Science is about doing science completely in the open - e.g. blogging an experiment before you do it/as you do it, making your results completely available etc... I am asking for software - not a way of conducting science.

[Pierre Lindenbaum]

Possible duplicate? Any Open Notebook Science In Bioinformatics?

[Pierre Lindenbaum]

Ah, yes , you're right sorry for the wrong tags.

Answer 1

[Neilfws]

Very little available and what there is, frequently old and/or not maintained anymore. A few links:

• Open source ELNs from the ILA - don't know which are still active
• ELN at Sourceforge - has been the top Google hit for years; no longer maintained
• Discussion at MyLabBook - of alternative frameworks and why they chose Drupal
• A list from Atrium Research - again, may or may not be active

As Giovanni says, OpenWetWare is probably the best-known current option, although it is aimed (I believe) at people keen on public notebooks.

EDIT: Forgot to mention Laboratory LogBook and the labBlog from Southampton (not sure if the latter project has released any code).

[Pierre Lindenbaum]

And your answer allows you to reach 10K. Congrats ! :-) http://www.youtube.com/watch?v=V1j7lyRnxVE

[Nico Adams]

Thanks Neil. Some of those are the ones I was aware of as well...see above...but there really doesn't seem to be any more then at the time of writing. Thanks for the answer.

[Neilfws]

Right, I missed that the EMSL ELN is now just ELN. It's unfortunate that it's the top Google hit for "open source ELN".

Answer 2

[Simon Coles]

I think it depends a lot on what you mean by an "ELN". As mentioned above, a lot of the Open Source ELNs come out of the Open Science community. There's a lot of stuff being done in the UK by people like Jeremy Frey and Cameron Neylon.

One that hasn't been mentioned in the list above is http://www.myexperiment.org/ which may or may not fit a definition of an ELN.

Depending on what you are trying to do, you might find the following useful to investigate - all of which I've seen used in both Academic and Industrial settings:

• Blogging platforms, especially WordPress
• Wikis (especially Confluence, which isn't free but it can be cheap for small numbers)
• The standard Office tools
• Especially on the Mac, a whole host of smaller note taking and organising apps

I was responsible for the now-defunct OpenSourceELN which we wrote in Zope/Plone and was surprisingly popular given we didn't really put any effort into pubicising it. We looked at reinvigorating a while back it but frankly Wordpress is better than anything we could come up with.

If you focus on what you are trying to do (which is generally content management in some way) and can overlook some terminology differences, then there's lots and lots of things around. The ELN problem isn't that different from other kinds of tools that have grown up to support knowledge workers, with the exception that in industry you start to worry about Patent evidence - but that's mainly a record keeping issue, not a content management thing.

Answer 3

[Giovanni M Dall'Olio]

As for my knowledge, the concept of open laboratory notebook comes from the OpenWetWare community. If you register on their website, they offer a free notebook that you can make public and will be integrated with the other notebook on the same site.

BioMan is an alternative written in Ruby. However, I don't know if it is still being supported.

As I was saying in the other question, some people in my institute are developing Lab Service Wiki, an extension to WikiMedia to handle a laboratory and all its needs. It is designed to manage lab services but it can be used as an open notebook; they told me they are working on a public release and that they are preparing a publication.

In my lab, we use OpenAtrium. I explained that in a old question.

[Roman Valls Guimerà]

+1 for OpenAtrium on our lab too. Being based on Drupal looks very extensible and powerful from a developer side and very easy to use on the user side.

Answer 4

[Tony Yuan]

OLN, a chemistry and biology ELN, is free to individual and educational users: http://www.olncloud.com

Answer 5

[marko.petek]

Check the Kickstarter campaign for sciNote, a free, open source and easy-to-use scientific electronic notebook.

Official sciNote webpage