Keeping a Laboratory Notebook

This document describes the principles of keeping a laboratory notebook. It was written in August 2001 by John Altman for his laboratory at the Emory Vaccine Research Center. John has prepared a draft of a Microsoft Word template for keeping a notebook page that you can download and install in your Microsoft Office Templates folder (Notebook Template). It is archived in the zip format, and must be decompressed using StuffIt Expander or some other software.

The form of the notebook

There are many different ways of keeping a laboratory notebook. In the past, all laboratories kept their notebooks in bound volumes, ensuring the integrity of the sequence of data entry. This method still works for many investigators, and some labs and institutions insist upon it.However, as more and more essential data iares obtained in the form of computer printouts, bound volumes often become unwieldy, especially as large numbers of printouts are taped inside the volume. For this reason, some laboratories now accept the practice of keeping laboratory notebooks in looseleaf binders. Either way is acceptable in the Altman laboratory, but for any laboratory notebook, it is essential that each page be signed by the investigator and dated in hand writing.

Remember the audiences for the notebook

The quality and usefulness of your notebook will be greatly improved if you remember that every laboratory notebook should be designed to communicate to at least three audiences:

Your self. This one is a no-brainer. Everyone realizes that a primary function of the laboratory notebook is to record laboratory activities so that you can refer back to them in the future. With this in mind, it is tempting to save time through the development of “private” shorthands and abbreviations. It is also tempting to omit protocol descriptions that you use routinely and repetitively. However, this approach often neglects the other important audiences for you notebook.
Your immediate laboratory colleagues and advisor. These days, no one working in the biological sciences works in isolation. It is essential that your laboratory notebook is kept so that it is easily interpretable by your colleagues, who may require your notes for a number of purposes: 1) as a basis for future work; 2) as a basis for assisting you should you be absent; and 3) as a basis for repeating your work (or deciding not to!).
Your research institution and funding agencies. Remember that your research is funded by someone (often the taxpayers), who have every right to hold you accountable for how you are spending the money they have granted you. Any research laboratory could conceivably be audited, and accurate and complete notebooks are essential for documenting how you’ve used the resources provided to you.

Organizing Your Laboratory Notebooks: A Project Oriented Approach

If you have several distinct projects, I encourage you to keep separate notebooks for each project.

Organizing you laboratory notebook: Titles and Tables of Contents

Every laboratory notebook must have a Table of Contents (TOC). In order for a TOC to be useful, each experiment and activity of note must be given a sensible and descriptive title that is recorded both in the TOC, and on the notebook pages that describe the experiment or activity. Examples of sensible titles include:

“Phenotypic and functional (ICC) analysis of antigen-specific T cells from donors MZ, TK, and BV”
“Purification of BirA enzyme from E. coli transformed with plasmid pJS169”
“Preparation of biotinylated HLA-B*5701/HIV.gag.44-51”

In addition to these obvious examples, it is important to immediately record important and novel ideas in your laboratory notebook. These records are essential for establishing intellectual property. One example might be:

“Design of chemotetramer for analysis of cell surface expression of chemokine receptors”

Finally, if you routinely use non-standard abbreviations, or if you have developed a “system” for labeling of samples and data (see #1 in the section below), you should include a key describing the system in the front of the notebook.

A Template for the notebook page

Every experiment and/or activity should be described in one self-contained set of pages (this is another reason for using a looseleaf format, because some experiments take months) that I will refer to as an “Experiment Document”. Each Experiment Document must have a number of essential elements, listed below.

A notebook and “page” number. I have always labeled my notebooks with my initials, followed by a Roman number (e.g. JDA-VIII), and each experiment within that notebook is assigned a number (e.g. JDA-VIII-26). Usually, experiment 26 will contain multiple pages, which I record as follows: JDA-VIII-26.3.
As noted below, I find that this scheme provides me with an excellent way to label samples that I archive, such as plasmids.
Title. See comments above about suggestions for titles.
Hypothesis (or purpose). This is essential for communicating why you performed a certain experiment. In some cases, the hypothesis will be replaced by a “Purpose” (e.g. “purification of BirA enzyme”, or “construction of a plasmid for expression of protein X in E. coli”).
Background. You should record some brief notes describing previous experiments that you’ve done that constitute a foundation for the current experiment. This is also the place to record references to the literature, if appropriate.
Experimental protocol. This should be given in sufficient detail so that the experiment can be repeated. You are encouraged to provide cross-references to standard protocols (e.g. “electro-competent E. coli were prepared following the method described in Unit 1.12.4 of Current Protocols in Molecular Biology, with the exception of the following details....” I often organize experiments in Excel spreadsheet format (e.g. descriptions of FACS antibody panels, or compenents of restriction enzyme digests), and include these in my notebook (usually I paste them into a Word document).
Ideally, you should record catalog and lot numbers for important reagents. I remember attending a seminar given by a crystallographer who had prepared beautiful crystals of an important elongation factor and then found that she could not repeat the crystallization for 18 months. Eventually, she traced her problems to a change in the lot of PEG (polyethyleneglycol) that was used in her lab.
Documenation of archived samples. If your experiment results in the production of samples that are archived, note them here. It is essential that every sample be labeled with the following information:
1. Your name or initials
2. The date the sample was produced
3. What the sample contains
4. The concentration of the sample
5. A reference to your notebook page
It is often helpful to develop a “system” for coding of archived samples. One important component of this is the development of a set of standard “extensions” that immediately tell you (or your colleagues who find your samples at the bottom of the freezer!) what they are. Here’s a suggested, non-exhaustive list:

Extension	Type of sample
.mp	Minipreps
.pcr	PCR Reactions
.rd	Restriction digests
.ol	Oligonucleotides
.cdna	cDNA
.rna	RNA
.btm	Biotinylated monomers
.tet	Tetramers
.pbmc	PMBC
.mab	Purified monoclonal antibody
.hybdm	A hybridoma

Here’s an example of a label that uses this set of extensions: JDA-IV-17.3.mp.12. In this example, IV is the notebook, 17 is the experiment, 3 is page 3 of experiment 17, and 12 indicates that it is the 12th miniprep.

Raw experimental data. All notebooks must contain raw experimental data. Good examples include: 1) printounts from a radioactivity counter; 2) pictures of agarose gels or SDS-PAGE; 3) chromatograms from a protein purification; or 4) printouts of UV spectra of a purified protein preparation.
If your raw experimental data are kept on a computer (e.g. FCS files containing FACS data), it is essential that you record the file names and where they are stored. If you store data in a temporary place, record where that is, and then go back and amend your Experimental Document when you have prepared permanent archival copies of your data. You should always prepare at least two archival copies of your data, usually on CDs. You should store your CDs in a consistent location and describe where that is in your notebook; this is essential should it become necessary to access your data after you have left the lab, or while you are away.
Data analysis. Many experiments will require you to transform your raw data into a format that is more intelligible. This could be something simple such as reformatting the data from a radioactivity counter into a new table, or something more complicated, such as preparing graphs for a 51Cr release experiment.
1. FACS data analysis. FACS data are easier to manipulate to achieve the desired result and to hide flaws than almost any other type of data. For this reason, it is essential that your notebook include an analysis “trail”. I will soon require that all analyses of FACS data include documentation of the gating history for every sample. This is easily accomplished using the “Show Ancestory” function present in the Layout Editor contained in FlowJo. My recommendation is that you prepare two copies of your analyzed FACS data for every experiment—the first will contain the gating histories, and in the second copy you can omit or delete these to make your data easier to read at a glance.
2. Population frequencies in FACS data plots.Make certain that frequencies of populations on your FACS data plots are in a font that is large enough to read. If you find that they are not, my suggestion is to go back into FlowJo and regenerate the plots with a larger font size, rather than attempting to wrestle with the font sizes in Canvas or PowerPoint.
Generation of Publication Quality Figures. Notebooks are easier to read if you generate near-publication quality figures that include both appropriate and highly legible labels on axes that are appropriately organized.
Data interpretation and conclusions.Don’t forget to record your interpretation of your own data (e.g. “the fact that the frequency of IFNg+ cells present after stimulation with RAK peptide is the same as the frequency of B8/RAK-tetramer+ cells present with no peptide stimulation, even though the B8/RAK-tetramer+ population is evenly split between CCR7- and CCR7int populations demonstrates that the CCR7int population is capable of immediate effector function, which is not consistent with the hypothesis of Sallusto and Lanzavecchia”.)
Suggestions for future experiments.The data produced by most experiments will raise new questions that must be addressed in future experiments. These suggestions should be recorded here.

Policies on removal of notebooks from the laboratory

All of your notebooks are the property of the laboratory (Emory University?) and will remain with the laboratory after you leave. This is one reason you might want to keep your notebook in a looseleaf format, with printouts of your Experimental Documents that are kept as documents on the computer; this way, you can easily make a copy of your notes and take them with you.

Some laboratories insist that notebooks never leave the lab, even if you just want to take them home for the evening, or to the library while you work on a manuscript. I recognize that some of you may not find the laboratory to be a conducive environment for writing, and therefore you may need to temporarily remove your notebooks from the lab. I strongly encourage you to make copies of materials that you will need to work outside of the lab, and to leave the original notebook in the lab at all times. I haven’t completely made up my mind on this one, and I’d appreciate your thoughts.

Catalog of your notebooks

Eventually, I will construct a master database that will serve as a catalog for all notebooks generated by persons working in the Altman laboratory. Until I do, please keep a catalog of your laboratory notebooks, perhaps in the front of every notebook.

This is somewhat akin to the inclusion of the complete Table of Contents in every volume of multiple volume laboratory manuals (such as the Current Protocols series).

Making copies of you notebooks

You are entitled to make copies of your notebooks to take with you when you leave the laboratory. If you keep your notebook in a loose-leaf binding and use a computer application for your write-ups, this will be a very simple matter. Otherwise, you will have to photocopy your notebooks. You might want to consider doing this every day as you prepare your notebooks, so that you don't have to copy all of your notebooks at once when you leave the lab.

Guidelines for Preparation of Graphs (to be completed)

The following notes provide a non-exhaustive set of guidelines for preparation of graphs for your notebooks, for publicaiton, and for slide presentations.

One figure does not fit all. In general, you should prepare graphs with different formats for notebooks, publication, and slide presentations
1. Notebooks. Graphs should have white backgrounds. Color can — and should—be used, provided you have access to a color printer.
2. Publication. Graphs should have white backgrounds. When possible, avoid color to reduce publication costs.
3. Slide presentations. Graphs can have white or black backgrounds (I tend to prefer black). Use color to convey differences, as opposed to shades of gray or stipling. Also use color for line graphs. For an example, see the following figure:
Figures should be clean, uncluttered, and carefully annotated. Use large, legible, non-serifed fonts. I prefer Arial bold.
Axes should be clearly labeled. The following are important:
1. Parameters and units. In the example above, the x-axis is labeled "ng/ml". Even better would have been "MHC ng/ml".
2. Numbers or categories. In the scatter plot above, note that I have not used more significant digits than was necessary.
3. Major and minor units are sensible and no more than necessary. In the figure above, the "major" units are spaced out and do not run in to each other. In addition, although the "minor" units on the y-axis are probably superfluous, when log-scales are used, it is best to explicitly include tick marks for the minor units, offering an immediate visual cue that the data are plotted on a log-scale.
4. Do not mix units. For example, an ELISA standard curve and serial dilutions of unknowns cannot be plotted on the same x-axis; in this case, use two graphs (perhaps one as an inset).
Titles. Always give a figure a title. When possible, titles should convey the conclusion of the experiment and not just a description.
Flow cytometry figures.