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Creating a DIY Mycology Lab Notebook

Learn how I created my first mycology lab notebook, what I track, and how I manage trade-offs with cloud-based solutions.

I’m currently growing five different species of mushrooms with multiple experiments running and new ones under development. Ensuring that I track all of this work is a must; for sanity and science.

In addition to the project management benefits of writing down the details of my work, keeping a good lab notebook is a necessity for an amateur scientist.

Here’s a brief overview of requirements for keeping a lab notebook, what I track in my own lab notebook, options for keeping a lab notebook, and some thoughts about how I plan to improve tracking my lab work in the future.

Adam Savage Writing Meme
Adam Savage Meme

General Requirements for a Lab Notebook

My Personal Requirements

Given that this is my first mycology notebook, I wanted to capture some information for myself that may or may not also meet the normal requirements of a commercial laboratory notebook (or maybe they do!).

My background in data and computer science has also trained me to see the potential value in tracking more data than I may seem immediately necessary. Here are some of the data points I wanted to be sure and capture off the top-of-my-head:

  • Date and time of procedures
  • Temperature and humidity
  • Detailed procedures with tools, methods & materials used
  • General observations
  • Side-effects of experiments that involved the procedures and materials I was new to or unfamiliar with
  • Related to the above: mistakes made and adaptations or workarounds as each step advanced
  • General inventory counts

What information did I hope to learn by capturing all of this meta data about my experiments?

By tracking all of the above, I could presumably finish a complete grow cycle of mushrooms and determine the following:

  • Total time from initial culture to the end of a grow
  • Total yields
  • Biological efficiency
  • Total costs and costs per unit of final product
  • Initial capital / startups costs per species
  • Most and least efficient techniques
  • Gross costs
  • Net profits
  • Return On Investment (ROI)

You can see how helpful it is to measure the feasibility of starting a fungi-related business if you track and interpret the data as you go along. I’ve seen a lot of new entrepreneurs across as businesses try to wing it and it usually causes them a lot of lost time and money, greatly reducing their runway and general chance of being financially successful in the long run.

Although learning the science of synthetic biology and genetic engineering is my first priority for EverymanBio, I do need to be mindful of how I spend my limited resources and eventually need to generate some kind of revenue to keep this dream alive. Having the detailed data tracking my moves gives me valuable insight into the return on my time and money.

Keeping a good lab notebook is just as much about ensuring the science you employ can be reproduced by ones peers. The same data used to ensure reproducibility also allows me to more easily and more efficiently keep iterating on what works and drop what isn’t.

Options for Keeping a Lab Notebook

My first inclination when logging anything, especially data I want to analyze over time, is to go electronic. However, several of the chemistry and biology textbooks I own recommend that students start with something written.

In my experience, writing the journal is faster and more convenient. It has a different psychological component to it as well that contributes towards my overall desire to keep pressing ahead with the work.

With a hand-written lab notebook, I don’t have to worry about bringing in my dirty laptop into my clean space and all that entails decontaminating it and myself as I go back and forth.

I also don’t need to worry about any technical issues. No internet connection is needed. I don’t need to expend mental energy on learning a new tool or customizing it to suit my needs. I can easily move my notebook between work spaces and not worry about connectivity or power constraints.

Excerpt From Hand-Written Mycology Lab Notebook
My Mycology Lab Notebook

But it isn’t perfect. There are real trade-offs that make it difficult for me to imagine using a hand-written notebook for everything over the long-run. I cannot, for instance, share my lab work easily on EverymanBio.com.

Trade-offs between Written Lab Notebook & Electronic Lab Notebook

The main trade-off is that if you want to do all of the calculations and analyses that I mentioned above, you would need to transcribe all of your handwritten data to something like an Excel spreadsheet, SQL or some other database.

And that’s a pretty big trade-off. Imagine writing notes about a grow-cycle that takes four months start to finish. At the end of the grow cycle is where mushroom growers are doing daily harvests, sometimes multiple times a day. It’s just not feasible with even a moderately sized grow to go back through all of the lab notes and manually calculate something like ROI when its just so much easier to use Excel to quickly perform calculations or plot graphs.

Looking Ahead

I’m still searching for the right balance of data tracking that accommodates my love of hand-written lab notes vs the loss of electronic analysis. There are many cloud-based lab notebook offerings, but they come with the overhead that I’m not entirely sure I’m ready to take on. For example, I’ve considered using Markdown in Git, Jupyter or eLabFTW, which can be displayed natively on GitHub. But there are massive trade-offs that result in added time and energy on matters which don’t add much value towards my core objectives. Have you ever tried to write out a large data table in Markdown? Not the funnest of exercises.

I may end up with a hybridized approach where I use a cloud-based solution for quantitative data and keep the written portion for qualitative data. Which solution I use for which is still up in the air.

Molecular florist and fellow diybio Sebastian S. Cocioba puts his lab notes in a Google Doc for all to see: https://tinyurl.com/yxzzfq2m

I really like this approach from an ease-of-use standpoint. It’s a plain document that he keeps appending to every day; however, I’m not sure how this approach would solve for the kind of quantitative analysis that I’d like to do. As of today, his notebook is over 500 pages long. Sebastian has several diy projects that I’d love to follow and reproduce in my lab, but it’s incredibly difficult to do that with such a large document because it requires that I scroll back through the entire history to find where the details pertaining to a specific project live.

Perhaps one day he’ll see this post and fill me in with his thoughts on this matter. I’m sure he’s tried many solutions over the years. If I were a bettin’ man, I’d say he landed on this format because of its simplicity and that is worth more than the problems the more complex solutions aim to solve.

If you have any opinions or suggestions on the matter, please reach out and let me know. I’d love to hear your ideas. For now, I continue to write things down and track them in my written notebook while simultaneously experimenting with different quantitative tracking options. And if I happen to land on the perfect solution, I’ll be sure to let you know.

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