Working on my thesis, I’m soooo grateful that I’ve kept good notes throughout my PhD! Here’s some notebook-keeping tips that have worked for me! The main thing that I’ve found key – great searchability! Also authenticity – I don’t shy away from putting in exclamation marks, frown-y faces, strange but descriptive descriptions like “gunky” etc. – though you might not be able to do this in industry… It helps put you back in the shoes of old you when you’re going through your notes and makes for some much-needed good laughs when you look back during the stress of thesis-writing! Some gems I found in the pics…

I keep hardbound & digital lab notebooks (I use OneNote for this) – the physical book is great for quickly jotting down experimental notes when your fingers are goopy (well not too goopy – at those times I write on a paper towel or glove or something and then transfer it over once I’ve deglooped!  But it’s hard to search through if you don’t know the date to look for (no command + F for paper). The digital version’s not always as detailed (but it is much neater…). A lot of it is bullet points of experiments I did, yields, etc. I include key terms so I can easily search & find the date I did something then cross-reference to physical book for more details. Speaking of dates, when writing dates, always include the year. It may not seem like you need to, but the years do go by! 

I also take pictures of my written notes and save them to my computer – this is also great for when you’re too exhausted at the end of a long day to type everything up nicely – if you wrote down all the potentially forgettable things on paper and you have the pics you can type them up the next morning – and go get some sleep. I take pics of other things too (like when a protein you’re purifying turns a funny color or something) –  and screenshots – Taking digital notes? Command + Control + Shift + 4 is your friend – it lets you take a screenshot of part of your screen and copies it to your clipboard. And, you know what they say, a screenshot says a thousand words! I take screenshots of things like my protein purification chromatographs. In addition to putting the pictures into my notes, I save them to a directory on my computer, where I have folders for each month.

You know how sometimes journal articles will have “key words” that search engines look for? Think about that type of thing when you write your notes – you want each page to have all the words that you might use to search your notes for the thing you’re looking for. So, for example, if you did a western blot, make sure that “western blot” is typed somewhere on the page. 

Speaking of pages, in my digital notebook, I have section tabs for each month and then pages for each day. I also have a “Literature” tab where I keep notes on papers I’ve read; a “paper thoughts” tab where I keep figures etc. for the manuscript (journal article draft) I’m working on; “sequences” and “sizes” tabs with info about the various proteins I’m working with; a “to do” tab; and, my favorite, a “results” tab where I keep results figures from the experiments I’ve done (different pages for different experiment types, with results ordered by date) – this is one of the most useful features I’ve found – it’s great for getting an overall look at what I’ve found, what I’m missing etc. and since I put the date on all the figures it makes it easy to get more information by going to that date’s page).

I make “paper-style” figure legends for my figures that are just for my notes (and potentially lab meeting) – This has come in really handy when I now need to put them into my thesis (and paper). Having the experimental details already written down there keeps me from having to dig through my notes from years ago to find out what the heck I did. 

note: when it comes to making figures, work with vector graphics whenever possible – this way you can scale without losing quality (I use Adobe Illustrator, but there are free alternatives like GiMP & InkScape). When you want to use them, you can then export different figure panels of that larger figure as separate images (e.g. using the asset export tool) you can mix and match and use them for different things (thesis, paper, slideshow presentation, etc.)  

A common theme you might have noticed is that I’m all about cross-referencing: I number my electrophoresis gels (gel electrophoresis is a technique where you use charge to separate molecules like proteins & DNA by size by sending them through a gel mesh that slows bigger things down more). I run a lot of electrophoresis gels, so I number them (e.g. SDS-page #81, agarose #40). Just ran page #487! I use this number on the sample tubes & when staining then save the results image with the date & gel number as the file name (and of course include these numbers in my notebooks) 

When taking notes, think in terms of “future you.” At the time it’s easy to think “There’s no way I could forget this” – yes, yes, you can. Write it down. Future you will be grateful (Think of all the times current you has wished that past you wrote something down…) –  Often I’ll go a few days/weeks working on 1 type of experiment (e.g. protein purification) then switch to a period working on a different type of experiment (e.g. activity assays). etc. Things that become 2nd-nature in 1 block may not stay that way…

As for what goes in those notes…

for each experiment, I make an overall summary where I put

  • a one-sentence overall description
  • the goals of the experiment
  • what samples I tested and when, if applicable, those samples were purified 
  • what concentrations I used
  • what temperature(s) I used
  • even if you personally didn’t purify it, when you buy things like antibodies or enzymes they’ll have batch numbers and you want to write those down 

I keep all my detailed calculations for reference (e.g. in a spreadsheet page) but then I also nicely format for easy reading my (double-checked) results of those calculations that tells me how much of each thing to add – when I’m doing the experiment, I work from this “final recipe” and it avoids confusion with all the extra numbers in the calculations. But it’s important to keep the calculations so that you can adapt them if you want to change concentrations for future experiments, etc. (and so you know why you did what you did!) Speaking of making changes, it’s important to make note of anything that you did that was different from how you typically do it. It’s also important to include *why* you did it differently, so you don’t look back and think “Why in the world did I do that?!” Plus, you never know what minor details will make experiments go better or worse, so making note of any experimental deviations can help you notice trends and optimize! 

If something goes wrong in the experiment (like I messed up a lane or something) I write a note in red. And if I realize at a later that I made a mistake with something I did or there was a contaminant in the sample, etc., I add notes to my notes in red with the date of the update. Even if it’s embarrassing, it’s important information (especially if your results turn out “interesting”!) and it might prevent you (and/or a future grad student from making the same mistake) 

For experiments that involve a lot of calculations, I keep spreadsheets for each experiment, adapting them as needed. I also keep spreadsheets of my protein constructs (different proteins or different versions of the same protein). I do a lot of protein making & purification, so I have lots of protein constructs, all at various stages of prep/purification. To keep track of them, I give each construct an inventory number like “15786” and “15787” (the actual numbers correspond to their spot in a lab database). These numbers are super helpful until you forget that other people can’t know what you’re talking about without you telling them what construct they correspond to…

I have a spreadsheet w/each construct identified by numerical code & description & I update it w/the current status (i.e. 3L Sf9 expression 3/8/21 or 3mg frozen 3/30/21). I also have a spreadsheet with all the slot blots I’ve done (an experiment I use to measure protein-RNA binding that I’ve done >450 of…). I also have a spreadsheet with my PCR primers (sequences and purposes). And I have spreadsheets for my x-ray crystallography work. 

X-ray crystallography is a technique that can be used to look at the structure of proteins, but the proteins have to crystallize to be able to look at them that way, and proteins often don’t want to crystallize because it means having to sit still and they’re too antsy (they want more entropy). Therefore, you have to do a lot of screening of different crystallization conditions in plastic multi-well plates. I set up 123 plates in my PhD and got some crystals, solved some structures, and – well, they weren’t very useful for my project so I moved on, but I learned a lot! Problem was, I moved on before I’d really polished any of the structures and made nice figures and stuff. So now, as I’m having to put those figures and discussion into my thesis, I’m having to go back and put myself in the crystallography zone mentally. Thankfully, finding the actual data and experimental conditions hasn’t been too bad because of all the notes I took! Including on gloves :). 

For my crystallography work, I have a spreadsheet with details on all of the plates I set up (the crystallization conditions, set-up and harvest dates, etc.). And then I have spreadsheets for the pucks holding the crystals after I harvested them. And spreadsheets on the data from when I collected diffraction data from the crystals in those pucks. You don’t need to know all the details, but hopefully you can appreciate that spreadsheets have been a major help – both then and now. 

Your notebook is mostly about the past, but it’s also very much about the future. I like to periodically make a “to do list” of experimental plans. Instead of just a list of tasks, I specify *why* I want/need to do each thing – what am I hoping to learn and/or show? Sometimes, to do lists can stress me because I see there’s so much to be done – but the important thing is to remember it’s flexible and subject to change! 

Some other things in my notes: in my “cheat sheets” section I have formulas for buffers and procedures for various experiments

In addition to my “lab notes” notebook, I  also have a digital OneNote notebook with background notes on my project, most of which I did when I was preparing my thesis proposal and having to really immerse myself in the field for the first time. 

sorry if my note was kinda rambly and unpolished – it’s back to thesis writing now, but you can find more details about crystallography and stuff if you search my blog. 

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