A digital notebook

When I first started graduate school, I kept an old-fashioned notebook.  A 4×4 quad ruled Roaring Spring Lab Notebook.

It had gridlines, it had carbon paper (The carbon sheets remain, unperturbed, at the back of the notebook), it had Thomas Edison on the cover scienceing it up.  It was everything I thought science would and should be.

As a tool for keeping track of what I did for later reference, however,it was a complete disaster.

I’m not an organized person by nature.  I work in spurts, I don’t keep careful track of what I’m doing.  I often have to go back and fill in the details.  This means writeups I would intend to return to later were buried under experiments I would go ahead with in the meantime.

I also am not a linear person (or perhaps science is not a linear endeavor).  One day I would work on project X, the next, project Y.  Science works that way, sometimes, project X needs a week to grow, sometimes project Y sits in the fridge while the primers are synthesized and delivered in the mail.

Both of these traits make for a messy, and extremely confusing lab notebook.  Sure, I could have kept one notebook for each project I was working on.  But what about when I’d perform an experiment that fit into two projects?  Sometimes I will perform an assay using two sets of mutants, for two separate reasons.  Would I double-copy the experiment?  Perhaps this is when I should have actually used that carbon paper.

No, instead, I switched to a standard 3-ring binder after my first year in graduate school.  I could re-define the boundaries of a given project easily, add and remove page dividers for each project, and easily add in printed pages.

Looking back on my research project (and looking forward to where I may be next), I think if I could do it again, I would keep a digital notebook first and foremost.  I did keep a digital notebook, using the app Mori.  Unfortunately, development on Mori ceased long ago, and I used it exclusively for digital notes.

No, I think the ideal thing to do would be to keep a purely digital notebook, with printed backups of results and summaries in a three-ring notebook.

A digital notebook is searchable.  It doesn’t have to be linear.  I can look for all projects with a given gene or technique, and pull them all out.  A good notebook is tagable (and hopefully well tagged.)  I don’t have to decide if an experiment goes in notebook A or notebook B.  It just gets tagged AB, and goes into the digital notebook.

I also don’t have to wait until my results are processed to add them to the notebook.  This is a big one.  Raw unprocessed data files (such as .nexml tree files that are a finished product, but need to be visualized, or microscopy experiments that take a fair amount of post processing effort) go right in the notebook.


A sloppily generated note on media generation gets filed away digitally.

Scanning in the above sheet, for example, lets me find it no matter what project I’m working on in the future, rather than digging through years of failed and succesful experiments in different notebooks when writing my materials and methods later.  Note that I added a minimal number of tags, but wrote out the key media ingredients (different forms of iron) for search purposes.

I’ll talk more about the best way to organize a digital notebook and tips for making the most of it (for example, sharing and compiling status updates for the boss).