Experiment-ing can be fun and/or stressful. So here’s some advice on how to maximize the chance your experiments are fun and successful! Today I planned out a big exhausting experiment I’m dreading but hopefully now well prepared for. Here’s some tips & thoughts about how I go about planning, performing, and taking note of my experiments so I hopefully stay in calm and in control – and remember all those experimental controls!

text a mis-mash from past posts with a bunch of links to more, video new

When doing an experiment, you don’t need to know all the details, but make sure you at least know the purpose of each step in a protocol, especially if you’re working from a kit. In addition to just being important to “know what you’re doing,” this will help you troubleshoot and optimize. If you’re looking for info about commercial products (kits, etc.) you’re using, patents are often where the good stuff’s hidden! And despite the dry language they’re often surprisingly understandable because they have to make their stuff understandable to the law folks.

You can make tedious experiments more fun by thinking about what’s actually going on at each step and visualizing the molecules interacting. If you imagine what the molecules are doing as you do “boring” things like minipreps, it makes it a lot more fun. And it helps you really appreciate why you’re doing what & this is especially important when you’re working from a kit. if you aren’t sure if you are doing something right, ASK! It’s way easier to learn something the right way from the beginning than to try to re-learn it the right way once you’ve gotten used to doing it the wrong way

Sometimes the “hardest” experiments are those that are just repetitive enough your mind can wander but not repetitive enough you can let it! Or you can have the “opposite problem” – I often get really stressed running experiments, and that makes me brain-foggy too – so I try to do all thinking I’ll have to do before stress messes w/my head. I write out my experimental plan beforehand in a *super* specific way (almost to “open tube x” point) & double-check it before starting. Then I can focus fully on manual work. And remember that experimental plans typically seem less ambitious on paper then they really are…

To help me focus even better, I put on active noise-cancelling headphones without anything playing – I can still here if anyone’s talking to me, but the active noise cancelling reduces distracting background noises

I find I’m more prone to making calculation errors in the stress of an experiment, so I get all those down ahead of time whenever possible – speaking of calculating things – I write out the recipes for common formulas and solutions I need to make (buffers, etc.) on post-it notes and stick them on my shelves. I also keep “cheat sheets,” buffer recipes, details about protein construct sizes & pIs etc.

Some other random experimental advice…

• Color code whenever possible 

• Take time to double check your data before you get deep into analyzing it. It can be tedious BUT it’s super important & can save you lots of pain later on! You want to make sure you can trust your analyses & if you find an error later on it’s MUCH harder to fix

When it comes to life in the lab, things don’t always go as planned. Be prepared to adapt and try not to be too discouraged. Scientific setbacks happen to everyone. That being said, there are some problems that can be avoided and I hope to help you avoid them!

Whatever you do, make note of what you did!

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 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. 

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!

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.  

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!  

more about lab notebooks: https://bit.ly/labnotesorganization & https://youtu.be/JGzSUz88S-g

more lab tips: http://bit.ly/bblabtips 

more on figure-making: https://bit.ly/makeexperimentfigures & https://youtu.be/AccUD9os7wI

more about those kinase assays: https://bit.ly/kinaseassays & https://youtu.be/qG2iGtbAhw0

more about other types of experiments: http://bit.ly/labtechniques 

more about experimental design: http://bit.ly/experiment-ing 

more about all sorts of things:  #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0 or search blog: https://thebumblingbiochemist.com        

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