Monday, February 15, 2010

Keep your lab notebook in a private blog

In my previous post about Q10 a commenter suggested a software called "The Journal" by davidRM for productively keeping track of experiments, datasets, projects, etc. I've never tried this software before, but about a year ago I ditched my pen and paper lab notebook for an electronic lab notebook in the form of a blog using Blogger, the same platform I use to write Getting Genetics Done.

The idea of using a blogging platform for your lab notebook is pretty simple and the advantages are numerous. All your entries are automatically dated appear chronologically. You can view your notebook or make new entries from anywhere in the world. You can copy and paste useful code snippets, upload images and documents, and take advantages of tags and search features present with most blogging platforms. I keep my lab notebook private - search engines can't index it, and I have to give someone permission to view before they can see it. Once you've allowed someone to view your blog/notebook, you can also allow them to comment on posts. This is a great way for my mentor to keep track of result and make suggestions. And I can't count how many times I've gone back to an older notebook entry to view the code that I used to do something quickly in R or PLINK but didn't bother to save anywhere else.

Of course Blogger isn't the only platform that can do this, although it's free and one of the easiest to get set up, especially if you already have a Google account. Wordpress is very similar, and has tons of themes. You can find lots of comparisons between the two online.  If you have your own web host, you can install the open-source version of Wordpress on your own host, for added security and access control (see this explanation of the differences between Wordpress.com and Wordpress.org).

Another note-taking platform I've been using recently is Evernote. Lifehacker blog has a great overview of Evernote's features.  It runs as a desktop application, and it syncs across all your computers, and online in a web interface also. The free account lets you sync 40MB a month, which is roughly the equivalent of 20,000 typed notes. This quota resets every month, and you start fresh at 40MB. You can also attach PDFs to a note, and link notes to URLs. Every note is full-text searchable.

And then of course there's the non-free option: Microsoft OneNote.  Although it will set you back a few bucks, it integrates very nicely with many features on your Windows machine. I've never used OneNote.

8 comments:

  1. Particularly given that you work with human genetics data, I wonder whether the privacy & security aspects are strong enough. Depends on what you record in your lab notebook of course.

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  2. Good point. I should have brought up this point. Even though you can password-protect your blog and keep search engines from indexing it, it may not be the best idea to store results, or identifying information online. In my own work I only post in my notebook-blog the filename and location of this sort of information stored on my own computer, so I can easily find it later.

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  3. actually, some of the best software i've used in this regard is here: http://sourceforge.net/projects/eln/

    unfortunately, active development ended in late 2009 -- but, imho, it remains the best cross-platform lab notebook replacement around.

    getting it up and running on your own server is pretty easy and is as secure as your webserver... ;)

    i like many of the features that do not allow 'erasures', and also admin priveleges that allow a supervisor/collaborator to review documents.

    lots of room for improvement, seems to me that integrating with genomics/bioinformatics tools would be fairly simple as well...

    i'd rather see things progress along these lines than just using basic blogging software or, gasp, evernote...

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  4. Great post. I have my lab book on WordPress on a private server. I went with WordPress partly because of the size of the community making plugins. I also like the open source aspect.

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  5. I invite you guys to try out the Documents>Notes features on LabLife (www.lablife.org). You can put notes in your private workarea, or in shared lab space. Notes are dated, and versioned, and searchable.

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  6. OneNote now syncs across computers easily just like EverNote. I believe its worth the cost and wish I had it when I was in grad school. Its just so easy to use.

    OneNote is still really nice to have as a professional that comes across a lot of data that I need to look up once every blue moon.

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  7. You have got to try OneNote. I like listing ideas and stuff around the house but I always lose them. OneNote helps me organize them all.

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  8. great post Stephen! I actually prefer to stick to my paper-based laboratory notebook :)its a lot more personable and flexible in contrast to ELNs in my experience

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