Part of the “Self Reflection” series by and for early-career researches
After an hour-long search, you’re pouring over an old notebook from a previous post-doc in the lab, trying to recreate a protocol that your lab thought you would never use again. There’s an upside-down y with a squiggle over it, a drawing that looks like a box with a mess of circles inside it, and arrows pointing to different areas which are labelled with something that resembles a child’s drawing of water more than actual letters.
Working in a lab requires a conglomeration of different skill sets: management, research, and sometimes, what seems to be the equivalent of archeology and a foreign language. One of the simplest, yet most daunting tasks, to help a lab run smoothly is to keep your important documents organized. Recently there’s been a trend in lab management to take advantage of advances in technology. Digital databases tend to be “more stable, searchable, and sharable” (“The paperless lab” by Chris Tachibana). In this article I’ll be discussing some principles to develop a electronic database for you lab rules and protocols.
Save all your specifics
Save it all. Save your catalog numbers, save your plasmids, primers, and sequences, save your protocols, and save your rules and regulations. All of these have a place in a well-maintained lab, and in order for them to play their part, you need to be able to find them. I’ve worked with labs who have a beautiful system for cataloging their collected data, but when asked the expected product size of a pair of primers, theyare left scratching their heads and digging through notebooks from 10 years ago.
In our lab’s database, some of our folders include: a folder for each lab member to store our data, grants (current and previous), protocols, instrument manuals/warranties/service history/etc., plasmids/primers, record of previous lab members, software, chemical and stock inventories. Digital solutions today have more than enough space to store all this. Just make sure your files and folders are clearly labelled.
Be specific with the information you save, especially with protocols. It’s easy to write a familiar protocol in short hand (e.g. Grind sample, add 500 µL Hepes buffer, and centrifuge max speed for 5 minutes). But, give this set of instructions to a new lab member and several questions are going to arise. How much tissue should I harvest? How do I grind it? What molarity buffer? Does it need to be on ice? What temperature should I centrifuge at? Is it max speed on any centrifuge or only a specific one? Use the same principle for documenting lab rules as well. Instead of saying “check the eye wash once a week”, describe how you check it to know if it’s functioning and how to document that it was checked.
In addition to getting things in your database in the first place, make sure it stays updated. Document any changes to a protocol, who did them, and why. Record if you started purchasing a chemical from a different supplier. Word of mouth or scraps of paper aren’t the easiest or most reliable way to document these small but significant changes.
Making it similar helps make it searchable
Try to keep the formatting similar across your folders and files whenever possible. For protocols, develop a standard layout so lab members know where to find information they are looking for. For files, use a standard naming system so that documents are organized and easy to locate. For example, our file naming policy is Year_Month_Day_Description_Initials. The month and day always has 2 digits and the year has 4. Underscores are used to separate parts of the name. This allows us to find things chronologically, to know what’s in the file, and also to know who’s file it is.
One of the disadvantages of protocols only stored on paper is you can’t “control-f” to find what you’re looking for quickly. Using a database that has a search function- both for file names, but also for file content- can save a lot of time and frustration. That being said, I don’t like to read protocols from my computer, so once they are uploaded to the database, I print out my own copy. I have a binder that sits by my desk with all my commonly used protocols.
Make it sharable, but keep it secure.
Your protocols and procedures are now all beautifully organized. But, if you’re the only one who can see it, it’s not of very much use. Find a way to make this database accessible to all lab members. Everyone is going to need to use these protocols and it’s much easier if you have a shared database to track updates and changes (see #1).
But, at the same make sure your database is secure. You may have different requirements for this depending on how sensitive your data is, so make sure to follow any rules that are in place for that. Also, since you’re uploading your valuable data and protocols, you need to protect it. Limit access to current lab members. I also keep a back up of any data that I upload to our database on my personal computer. That way if someone accidentally deletes my folder, I don’t loose all my hard-earned data.
Getting years of protocols and modifications and rules under control may seem overwhelming. But time put in now is time saved from rifling through old notebooks and binders for one sentence of information you need.
Our lab has used OneNote by Microsoft and is currently using Dropbox. Another similar program is Evernote, which can be upgraded to their Business version. Other programs that I haven’t personally used, but have heard good things about include Quartzy (for inventory and ordering), Protocols.io, and LabFolder. (Note that if you are attending the Plant Biology 2018 conference in Montreal this summer, there is a workshop on the topic of reproducibility that covers some of these strategies – see image below).
For more resources on electronic notebook organization check out “The paperless lab” by Chris Tachibana and “Lab Organization Ideas for Life Science Researchers: How Technology Can Help.”
Find the rest of the “Self Reflection” series here.
Alyssa Preiser is a graduate student at Michigan State University in the Sharkey lab studying alternative carbon flow pathways around the Calvin-Benson cycle. Connect with her on LinkedIn or through the Sharkey lab’s Twitter.