Lab notebooks

Lab notebooks

It is difficult to reproduce research when data are disorganized or missing,
or when it is impossible to determine where or how data originated. 

Alston et al 2021

Keeping a notebook in science lab class is required, and going forward in the business of science, expected. Traditionally we’ve used paper notebooks, and there remains good arguments to continue in that tradition. However, your official notebook in DrD’s lab courses will be a digital notebook or ELN (Electronic Laboratory Notebook) that you create and share with me. It is trivial to to upload decent images of your written notes to your digital notebook. (That’s where Office Lens app helps, see Digital lab notebooks.)

My teaching experience leads me to make the following request about your notebooks; feel free to write, scribble, draw in your paper notebook as needed to capture the work you do in lab class. I say this because students have a tendency to write too little, or worse, simply copy and paste from the published methodology instead of providing the details about what actually took place during a lab session. Thus, I prefer to stat from a place of “over-sharing” rather then under-reporting. The goal of a proper lab notebook is so that you, and potentially others, can recreate the work described, i.e., the lab notebook is an essential component of reproducible research (Alston et al. 2021).

For more details about the OneNote digital notebook please see Digital lab notebook under Digital literacy.

Other than how it is delivered, a science notebook is a science notebook. So let’s review expectations. Note that instructions on this page cover bound paper notebooks, but remain largely applicable to digital notebooks, with obvious exceptions (use of pencil, page numbers). Digital notebooks can contain more than text and images, so in addition to the items discussed on this page, see “Digital lab notebook” for additional to do lists.

Background

Lab notebooks are crucial in science and my guess is that you have had many opportunities at keeping a lab notebook (Wright 2009). It is also my guess that you gave had a wide range of experiences with the notebook. Notebooks represent a lot of work for you and for your instructors, so there must be a reason why we keep doing this, right? From Wikipedia

A laboratory notebook … is a primary record of research. Researchers use a lab notebook to document their hypotheses, experiments and initial analysis or interpretation of these experiments. The notebook serves as an organizational tool, a memory aid, and can also have a role in protecting any intellectual property that comes from the research.

Here are my comments and suggestions for improving your note books. You should be able to adapt the spirit of these notes to your OneNote lab notebook. I like to use both paper and digital; it’s trivial to get written notes on paper into your digital notebook.

  1. Setting up your notebook.
    • Use only bound notebooks like the composition books available from Office Depot.
    • Use only ball point pen to write in your notebook. Avoid using ink that bleeds through the page. Pencil should be avoided, although there are times when pencil is a good choice (e.g., field notes).
    • Write your name, course number, and semester onto the inside of the cover of the notebook.
    • Number all pages consecutively, front and back, starting with page number 1. I expect you to write on both sides of the page, giving you 160 to 200 pages of space to work with.
    • Reserve the first four pages (front and back of first two pages) for a table of contents (TOC).
    • Fill in the TOC as we go through the course; refer to the published lab schedule for lab topics. Add page numbers in your lab manual that correspond to each topic. Note that there is no reason to reserve consecutive pages for a given lab topic.
    • Make sure your name and course number are prominently displayed
  2. Keep your notebook current. Set aside time before lab (10-15 minutes?) to review what the lab is about, note what product is expected from you. Write what you believe the purpose of the lab is about. After a lab is completed, at home, write a brief summary of the day’s accomplishments and conclusions (if any), and what is left to do to complete the lab topic.
  3. For each assignment (sometimes there are more than one assignment in a week’s lab), write out
    1. What you believe the purpose† of the lab was
    2. Note down any changes to protocols; this applies to changes in procedures, but also includes materials used, materials not available, etc.
    3. If the lab is primarily observational, ask yourself — how are you going to recognize the item weeks from now during the Lab Exam? — The answer is to take descriptive notes, to draw, to note your observations back to discussions and descriptions provided in the lab manual
    4. Write a brief summary of the chief results for the day’s lab. It is important that you tie what you observed (or measured, or calculated) back to the purpose of the lab.
  4. Note methods used. If the protocol is provided for you, note the source of the protocol, state in your notes that you followed the protocol exactly. If changes to the protocol were made, write these changes in detail. These modifications to published protocols are what you write up in your reports. Together with the published protocol, your notes about what you did and how you did it will in principle allow others to repeat what you did! Do not rewrite published protocols into your notebook, this is a waste of time. However, do print out a copy of the protocol and place it into your notebook for your records.
  5. List materials used, list equipment used, list any software used.
  6. If software is used make sure that you write out why the software was used (what problem were you working on?) and how you used the software to complete your task. Again, if you are following a protocol, cite the protocol and note any differences so that others can repeat your work.
  7. Answer ALL questions posed in the lab manual. LabExam questions for this course are selected from these questions. Write out by hand your answers to questions.
  8. Note who you worked with and what each person’s role was for the experiment. For example, if one person does the calculations and shares the results, note this in your lab notebook.
  9. About calculations, show all of your work, not just the answer.
  10. Date all pages with the actual date that you write on it! It is OK, although not best practice, to write about a lab days after the lab occurred. After all what you remember about the lab may be imperfect that is still better than writing nothing at all. However it is dishonest to write about a lab that occurred October 10 on the 17th of November but write “10 October” on these pages.

†Note that the purpose of the lab in a lab course is about the science, rarely just about the technique or skill introduced. So, for example, any lab that uses a microscope? The purpose is not to learn how to use the microscope (a skill). The scientific purpose will be something like “Identify and compare tissue types that characterize different kinds of organisms.” This would then require you to understand WHY the different organisms were part of the lab!? In other words, the purpose statement lends context to the hypotheses asked in the lab.

Grading your notebook

If the objective of a lab notebook is to document what you did, in a way sufficient for you (or others!) to recreate what you did in the lab eve years later, then you should be able to figure our what I expect from your notebook. While every lab has it’s own expectations, there are several key elements that notebooks must have.

For each lab, for each element, I use a Likert-like scale (Sullivan and Artino 2013) to assign assessment scores.

Strongly
disagree		 Disagree OK Agree Strongly
agree
1 2 3 4 5

where “Strongly Agree” implies the element was present and developed sufficiently so that I can tell what you did on that day, and would, therefore receive a 5 out of possible 5 for score for that element.

For each lab, the following elements in your Lab NoteBook are evaluated:

  1. Key identifiers, including date and names of your lab group members
  2. Purpose: Brief description of what the lab was about and what outcomes/products were created. Note that this can be about learning a method, but that usually is not the main purpose of the lab! I expect to see from you what were the science question(s) and hypotheses tested.
  3. Methods & protocols: Usually you are provided these so all you have to do is reference the proper citation; In some cases, modifications to protocols are made — you must document these changes to protocol!
    • List of resources used (wet lab: supplies, stock solutions; Bioinformatics: software and or databases). For supplies, list vendor, catalog number, and if available, lot number.
    • Importantly, if solutions are made, any calculation, no matter how basic, must be included in your notes.
    • For Bioinformatics, note whether default settings were used, or note changes from basic settings.
      • If a script was used for an analysis (e.g., R software), then a copy of the code should be included.
  4. Results: Don’t just write numbers in your notebook; you must always include the context, i.e., the metadata, of any results you obtain.
    • Include observations. It’s a good idea to take pictures during a lab to help you keep tabs of the goings on. Include a brief narrative to explain why the image was taken.
    • If a gel, a properly labeled gel is expected — don’t just paste in the image without identifying the contents of each lane.
    • If results from a spectrophotometer, then both the raw results and basic descriptive statistics are expected;
    • If Bioinformatics, then screenshots of results pages, at a minimum.
    • Units for any measurement must also be reported.
    • If you create a spreadsheet, then include the name of the file.
  5. Analysis: Most labs expect you to evaluate results, test hypotheses given sets of data. Like the results, you must include enough information about how the analysis were conducted so that your steps can be recreated. This, too, is metadata,
  6. Summary: Always include a lab wrap-up. What did you/we find? What are the next steps, if any?

References

Alston, J. M., & Rick, J. A. (2021). A beginner’s guide to Conducting reproducible research. Bulletin of the Ecological Society of America, 102(2), 1-14. https://doi.org/10.1002/bes2.1801

Higgins, S. G., Nogiwa-Valdez, A. A., & Stevens, M. M. (2022). Considerations for implementing electronic laboratory notebooks in an academic research environment. Nature protocols, 1-11. https://doi.org/10.1038/s41596-021-00645-8

Sullivan, G. M., & Artino Jr, A. R. (2013). Analyzing and interpreting data from Likert-type scales. Journal of graduate medical education, 5(4), 541-542. https://dx.doi.org/10.4300%2FJGME-5-4-18

Wright, J. M. (2009). Make it better but don’t change anything. Automated experimentation, 1(1), 5. https://doi.org/10.1186/1759-4499-1-5