Confluence as scientific lab management tool or lab notebook (alternative to Labguru, etc.)

[Tobias Beck]

Dear all,

I am looking into using confluence as a lab management tool. I would like to manage projects, milestones, new ideas, but also experimental data such as pictures, plots and other data, similar to a lab notebook.

Is anyone using confluence for this purpose and has some advice? For example which plugins would be good to have (currently I am on a Confluence demand, but might change later this year), which (self-made) templates are handy, ... ?

In more detail, I have one specific question:

1.) What is the best way to handle scientific publications? Do you start a new Wiki page for each? Is there a way to import metadata such as journal name, authors into the wiki page? How do you link to the publication, e.g. in an experimental procedure? Any automatic way to include a new publication into the Wiki library?

I am aware that there are other (commercially) available solutions such as Labguru (not so flexible and customizable), but so far I have not found a good alternative. Or maybe someone has another suggestion what they use?

Many thanks, tartrate.

[Arthur Mack]

We have been using Confluence along with JIRA as an ELN for about 6 years now (Orginally Server but now cloud). We do use some plugins that help out and use JIRA to place workflows on the pages. We also use JIRA for our LIMS system etc etc. Basically we use the Atlassian platform to manage all our lab functions.

[Adrian Smith]

Hi Art - that's sounds really interesting.  I've just started thinking about using Confluence and JIRA for our labs. I would love to hear some more about how you have things set up.

[Arthur Mack]

@Adrian Smith  Thanks but that would take a lot of explaining. I can give you a few pointers:

LIMS logins for analysis we use JIRA Service desk with proforma to collect requests for analysis. We have a lot of custom fields for analytical data and use exporter to export reports for internal customers. We also use JSD for a lot of other support functions in the lab and in general.

We have many confluence spaces with custom templates for creating and filling in experimental data that are linked to various projects (software projects). Each experiment has a JIRA issue linked to it which shows its progress and we can charge time to using TEMPO.

We use a metadata plugins to help us collate and find all this data as well as CQL etc.

LIMS and ELN's solutions can be very expensive but time spent customizing an Atlassian Confluence/JIRA instance gives you a much more powerful tool that  will do this and a lot of other things as well. Our technical team can do all their work in one place.

[David at David Simpson Apps]

This is something I've considered in the past as the lab notebook options that I saw at the time were simply shocking.

One thing I'd say is that you'll want to modify some of the behaviour and add functionality that is lab notebook specific. This sort of thing is much easier with a download version of Confluence. It's possible to write plugins for OnDemand, but that stuff is just beginning.

You could likely build some plugins that search Science Direct and the likes to populate pages with lists of publications. Shaun Hare has done something similar at a Science Hack Day: http://porkandpaws.tumblr.com/post/729626682/sciencehackday