This post is brought to you by Benchling. Thank you for supporting the sponsors of BPC!
Ever since my sophomore year of college when I got my very own hard-bound, very official looking lab notebook, I’ve enjoyed the process of keeping a lab notebook (maybe a little too much...). Print-outs of every gel I ran would be lovingly taped into the pages; so would protocols with dozens and dozens of steps. I would draw schematics of my experiments, draw big smiley faces on days my experiments worked, and sad emojis when things failed. Keeping up this methodical notebook took time. No joke, I must have spent at least two hours a week cutting and taping. And oh man, can I go through a paper lab notebook quickly!
So far in my research career, I’ve spent significant time in 5 research labs (oddly enough, four of these begin in a C: Cockett, Cochran, Chen, and Cremins!) and have had to leave my lovely lab notebooks behind. I kept adequate digital copies of protocols from all the labs I’ve been in, but if I ever want to take a walk down memory lane and look at gel images of yester-year, I’m out of luck. Even more important than science nostalgia, if I ever want to find a protocol that I used a few years ago to replicate an experiment, I have to comb through pages and pages in my dozens of paper notebooks.
I’ve been interested in the concept of a digital lab notebook for a while exactly because of this issue – I want to be able to access my lab notebook from my current lab and previous labs from anywhere and easily find a lab notebook entry or protocol in seconds. I’d known fellow graduate students who have used digital note-taking applications as a lab notebook and I had toyed with the idea a few times. Ultimately, I was concerned about how easily some notes could be deleted and how difficult it would be for other lab members to access my lab notebook.
I first heard about Benchling at a happy hour that they sponsored for grad students in my department. They passed out free t-shirts with their cool logos and made a pitch for their new concept for a digital lab notebook that streamlines the scientific collaboration process through easy search-ability and seamless integration with cloning tools. As soon as I got back to my lab after the happy hour, I set up an account and was instantly excited. (I know this might sound too enthusiastic, especially because this is a sponsored post – but I’m not exaggerating here. It was exactly what I was looking for!). I noticed that digital back-ups of my notebook entries were automatically saved regularly and that I could easily share my whole notebook or individual entries with my labmates.
Around the same time, I started transitioning from entirely wet-lab (experiments at the bench) to a substantial amount of dry-lab (writing code to analyze and model our data). I’m finding that Benchling is a great way for me to keep track of the directory I’m working from for a given task, what the goals/problems I’m trying to solve are, and relevant snippets of code. This would be literally impossible with a paper lab notebook (ok, not totally impossible, but so so tedious).
In short, I love the organizational capabilities of Benchling because it helps me keep track of multiple projects in a coherent manner, allows me to access my lab notebook from anywhere, helps me easily search through my colleagues’ lab notebook entries (without the risk of me modifying their entries), and offers a solution for keeping a record of computational lab work.
Stay tuned for Benchling’s re-design that has some awesome new organizational tools. One of the things that I’m interested in is ability to perform sample inventory, which looks like it will have awesome utility especially for tracking cell lines.
In case you needed any additional convincing, Benchling’s cloning tools are so cool that they deserve their own post, but I’ll give you a teaser. In the 5 minutes between writing paragraphs as I was thinking about what I wanted to say, I downloaded the gene in the specific assembly of the murine genome I want to edit, designed guide RNAs for the CRISPR nickase system to edit my locus of interest, selected the guide pair with the highest on-target score and lowest off-target score that fit my overhang criteria, and assembled the guide RNAs into my lentiviral puro-selection plasmid of interest – all without leaving the Benchling interface.