Question: How Would You Use Open Source Tools For Laboratory Notebook System ?
gravatar for Roland
9.1 years ago by
Roland40 wrote:

I am a chemoinformatics researcher looking to find user experiences and feedbacks on methods to keep laboratory notebooks on a computer. (using wiki, blog, open office, etc ...)

Thanks for your help.



open • 5.1k views
ADD COMMENTlink modified 4.9 years ago by marko.petek0 • written 9.1 years ago by Roland40
gravatar for Fabian Bull
9.1 years ago by
Fabian Bull1.3k
Fabian Bull1.3k wrote:

Using a wiki in this situation is pretty much the best you can get. Mainly for these reasons:

  1. It deals great with every media.
  2. It can be distributed to the web for colleages.
  3. It can be upgraded with thousands of plugins.
  4. It makes organization of your data easier than the other solutions.

This list could go on for ever but in the end its personal taste.

ADD COMMENTlink written 9.1 years ago by Fabian Bull1.3k

I agree w/ the positives listed here. However if you have a lot of staff turnover and those staff members don't have a lot of computation experience (think rotation students), wikis can be difficult. Not only do you have to teach them what you are doing in the lab, but you also have to teach them how to record what they are doing. This can be overwhelming for a new person.

That said, I prefer wikis to my current system with Wordpress. Wikis offer increased flexibility with fewer bugs.

ADD REPLYlink written 9.1 years ago by Laurakat50
gravatar for Dave Lunt
9.1 years ago by
Dave Lunt2.0k
Hull, UK
Dave Lunt2.0k wrote:

I use WordPress as a blog electronic lab notebook (ELN). I'm really happy with it. I always found wikis annoying without a crib sheet of codes in front of me. WordPress, like a wiki, is versioned- you can compare and go back to the version before you messed it all up! I have nothing against wikis, but WordPress is easier, more productive for most people (and more beautiful). Its also open source and there are a truly phenomenal number of community written plugins to help you.

Lastly, I think there is a big difference what different people want to do with an ELN. This is often forgotten. Some people are mostly interested in data logging, others assembling different media into a truly readable history of the experiment, others to share the record and have an active embedded conversation with collaborators. Think carefully what you want and play with different options. For me the test of what to adopt was whether I could get students to start using it. I couldn't with several options (wikis, Google Docs), but they took to WordPress quite easily- the thing I think did it was the ease of inserting pictures and the ease of the blog commenting system for collaborations and supervision.

I once wrote some stuff about why I chose WordPress in my blog, its not too recent, but its only got better in WordPress3.

Best of luck, Dave

ADD COMMENTlink written 9.1 years ago by Dave Lunt2.0k
gravatar for Pierre Lindenbaum
9.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

See Jean-Claude Bradley's blog/notebook usefulchem:

ADD COMMENTlink written 9.1 years ago by Pierre Lindenbaum131k
gravatar for Leszek
9.1 years ago by
IIMCB, Poland
Leszek4.1k wrote:

In my lab we have been using google docs for >1 year now. I know, that some people prefer to stay independent from big corporations, but beside that I don't see many bad points.

ADD COMMENTlink written 9.1 years ago by Leszek4.1k
gravatar for Alaw
9.1 years ago by
Roslin, Edinburgh
Alaw90 wrote:

This is a very complex area and the answer depends very much on what you are wanting to achieve. You mention that you work in cheminformatics. I've seen several presentations from commercial companies pushing their LIMS systems in that field where the processes that go on in the lab are modelled very well in the electronic system. If that is the case, then one of those systems will be your ideal (albeit probably expensive) solution. And it won't be open source.

If you are thinking more in terms of flexible, free-form note-taking then the Marketing spin that the commercial companies put on their ELN solution falls apart. You will have to find something more open-source and adapt it to your needs.

And then you have to consider what stuff you want to share and how widely you need to share it. Science funders are often very big on sharing, but equally big on putting an onus on you to protect and exploit any IP that may arise. Obviously these are fairly conflicting requirements. I note that you have tagged your question with "collaboration" and "open-notebook science" so I guess that you are not concerned about IP (or haven't been told that you should be).

My personal preference is to use a helpdesk/ticketing system to track individual pieces of work (virtually no two tasks that I work on are the same and none fit into the conventional sample-assay-result LIMS paradigm) and then to make public data that arises from the experimental work via a separate controlled mechanism. Our "collaboration" usage thus only operates inside of our tent, but that works for us.

For the record, we use RT from ( I have no affiliation with them, but their software is useful in our hands.

ADD COMMENTlink modified 9.1 years ago • written 9.1 years ago by Alaw90
gravatar for Vimalkumar Velayudhan
9.1 years ago by
Vimalkumar Velayudhan200 wrote:

When we required a documentation system for our lab, I suggested Python Sphinx. Sphinx is mainly used for documenting Python projects but works well as a general purpose documentation system.

The source files are written in plain text using the reStructuredText syntax. It outputs HTML by default but PDF and other formats are supported.

We have been using it for over a year now and it appears sufficient for what we need - documenting lab protocols, software, scripts etc.,

Sphinx is well documented and you will find a primer on reStructuredText syntax here.

ADD COMMENTlink written 9.1 years ago by Vimalkumar Velayudhan200
gravatar for Nathaniel Street
9.1 years ago by
Nathaniel Street0 wrote:

I have been using openatrium, which is based on Drupal. We have found it fits our needs but is not perfect. However, compared to a a standard WIKI it has some distinct advantages.

ADD COMMENTlink written 9.1 years ago by Nathaniel Street0

Could you name some advantages?

ADD REPLYlink written 9.1 years ago by Fabian Bull1.3k
gravatar for jean-claude
9.1 years ago by
jean-claude0 wrote:

As Pierre mentioned we do use free hosted public wikis (specifically Wikispaces) for lab notebooks. These are ideal for making research public quickly. However for raw data we usually use Google Spreadsheets and link to the sheets from the wiki, which is useful more in organizing links to content rather than hosting content. If you are interested in cheminformatics applications, Rich Apodaca and Andrew Lang have written a bunch of Google Apps Scripts that might be useful. For an analysis of using these script for an organic chemistry lab notebook see here.

ADD COMMENTlink written 9.1 years ago by jean-claude0
gravatar for marko.petek
4.9 years ago by
marko.petek0 wrote:

Check sciNote, a free, cloud-based, open source and easy-to-use scientific electronic notebook:

ADD COMMENTlink written 4.9 years ago by marko.petek0
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