Can your lab book do this?

When I was a student I used to be a disaster at keeping lab books. Possibly because they weren’t terribly useful to me since back then I had an encyclopedic memory for experimental details or possibly because I never was much of a paper guy. As I grew older my memory started to shrink (oh god, did it shrink!), I started transforming data into manuscripts and as a consequence I began to appreciate the convenience of going back 6 months in time and recover raw data. Being a computer freak, I decided to give up with the paper lab book (I was truly hopeless) and turned to digital archiving instead. As they say, to each their own!. Digital archiving really did it for me and changed enormously my productivity. One of the key factors, to be honest, was the very early adoption of sync tools like Dropbox that would let me work on my stuff from home or the office without any hassle.

As soon as I started having students, though, I realized that I needed a different system to share data and results with the lab. After a bit of experimentation that led nowhere, I can now finally say I found the perfect sharing tool within the lab: a blog content manager promoted to shared lab book (here). This is what it looks like:

A screenshot of our lab book in action

This required some tweaking but I can say now it works just perfectly. If you think about it, a blog is nothing less than a b(ook) log and so what better instrument to keep a lab book log? Each student gets their own account as soon as they join they lab and day after day they write down successes and frustrations, attaching raw data, figures, spreadsheets, tables and links. Here some of the rules and guidance they need to follow. Not only can I go there daily and read about their results on my way home or after dinner, but I can quickly recall things with a click of the mouse. Also, as bonus, all data are backup’d daily on the Amazon cloud and each single page can be printed as PDF or paper if needed. As you can see in the red squares in the above picture, I can browse data by student, by day, by project name or by experiment. That means that if I click on the name of the project I get all the experiments associated to it, no matter who did them. If I click on a experimental tag (for instance PCR) I get all the PCRs run by all the people in the lab.

Except for the protocols, all contents are set to be seen only by members of the lab. However, inspired by this paper, I decided that the project will be then flagged as public as soon as the results will be published.

12 Comments

  1. Reply
    Anon 1 November 2011

    I would love to do this, but my universities policy on cloud computing prohibits it.

    • Reply
      gg 1 November 2011

      Maybe you could work around it installing the content manager on a local server?

  2. Reply
    CassGroup 1 November 2011

    How well did the students adopt this method of record keeping? I set up a wiki on the college intranet for group members to share protocols, but data would be great as well but I still find it difficult to get everyone to use it. 
    Additionally I find it useful to have records there for reference as I am working in the lab, has this been an issue for your students?

    Ben

    • Reply
      gg 1 November 2011

      They seem to like it. I notice they still keep a paper record for themselves as it is easier to carry it around and scribble notes down on the bench. They then digest and transfer entries into the blog at the end of the day.  I guess WordPress is way more user friendly to use than any standard wiki platform as they can do rich text editing and copy and paste tables directly from excel.

      It obviously becomes a big advantage for them when time comes to write their final report, given that all the raw data are well archived.

  3. Reply
    Anonymous 5 November 2011

    When you showed this to me in person, I was really impressed, and I’m still thinking about trying it in my lab. You write above that you did some tweaking. Do you mean installing all the WordPress plugins that you have listed on the about page, or was there more you had to do to get to the stage of perfection? If so, what?

    • Reply
      gg 5 November 2011

      Hi Andrew, it’s pretty much all about the plugins. I also had to modify a file in the core so that the calendar widget would show the posts flagged private (I am attaching the patch to the about page of the labbook). It may also be a good idea to restrict access to at least the wp-admin section of the blog using apache’s .htaccess policies or to keep the actual entire wp secret and private and mirror only the public contents as static files somewhere else (S3, for instance).

  4. Reply
    Anonymous 16 November 2011

    Hi gg,

    My solution for the lab I’m in was to modify mediawiki, the back end to Wikipedia. I like how it keeps track of revisions so that no data can be lost, erased or changed without a record.  Otherwise I would worry about data being accidentally lost by newcomers or undergrads. Also, because Wikipedia is so popular, there is lots  of documentation for all different skill levels.

    Have you been able to modify Word Press easily so that entries cannot be deleted or changed arbitrarily after the fact?

    Have folks had an easy time getting Word Press to do everything they want  (uploading all sorts of files, keeping important information sticky and persistent)?

    My friend and I ended up packaging our mediawiki install with some hardware and selling it to other labs that expressed interest. We also distribute the GPLd source for free. See http://innoboxdevices.com/ if you are interested.

    • Reply
      Giorgio Gilestro 16 November 2011

      Hi Andrew, I knew about innoboxdevices. I must have seen your service through hackernews some time ago. The idea of having a dedicated physical service would probably help you with universities and companies that have restrictions against the clouds. How’s the start up going?

      We seem to do great with WP. The interface is obviously easier to use than a wiki site; I’ve boosted a bit the rich text editor and it’s pretty much like using word so students have no problems with formatting and tabling; images upload is done through the WP interface which is easy to use and yet allows for some basic manipulation (for instance images can be rotated, resized and cropped during the upload); if an information is sticky you just have to create it as a page instead of post or under a category with higher visibility; access to WP is password protected and only the author or the admin can change contents: in case of mistakes there’s a built-in version control with automatic save; I do automatic daily backup of all contents to S3 too.

      If you want to add WP to innobox (you should!) and need some feedback write me via email. Cheers.

      • Reply
        Anonymous 16 November 2011

        Cool! Well that sounds really nice. I’ll be sure to pass this along to others!

  5. Reply
    Greg 6 December 2012

    Hi Giorgio,
    Really nice, I will adopt something similar for my lab.
    However I just wanted to warn you that using the cloud for this is dangerous: actually what is on the server of Amazon, Blogger, Google whatever or even Dropbox does not entirely belong to you only. Thus you might loose intellectual property on your findings. You may ask IP people from your University, just to check.
    Best,
    Greg

    • Reply
      gg 7 December 2012

      Hi Greg, nice hearing from you again. I don’t think that is an issue: see point 8.1 here and point 6.a here

    • Reply
      Giorgio 7 December 2012

      Hi Greg, nice hearing from you again. I don’t think that is an issue: see point 8.1 here  and point 6.a here

Leave a Reply

Your email address will not be published.