Maintaining a laboratory notebook

Gratuitous advice on why and how to keep a written log detailing your science.

Why you might want to keep a laboratory notebook

1. To provide yourself with a complete record of why experiments were initiated and how they were performed. Your notebook also gives you a place to put the reams of data you collect and a place to paste the statistical outcomes and graphs that are generated from your analyses. Researchers who distribute their efforts across multiple notebooks, computer files, 3-ring binders, Post-Its, and scribbles on their palms are unlikely to be effective in the laboratory.
2. To encourage sound thinking. Keeping a notebook gives you a forum to talk to yourself, to ask questions, to jot down important thoughts about the experimental design, and how your results might eventually be interpreted.
3. To provide information to a person who is interested in continuing your research project. Other or future members of the laboratory may want to repeat and extend your experimentation if you die an early death, so you want a complete record of procedures, reagents, data, and thoughts to pass on to them. Notebooks that are kept solely for personal consumption are often illegible, incoherent, and  worthless to the broader scientific community.
4. To get rich! Not everyone sets out with the goal of patenting a process or contraption, but you might stumble onto something actually important and in such an event you must have a notebook that supports your claims. If you have not kept up a proper laboratory notebook, other researchers and their patent lawyers will beat you to the Patent Office and to the bank.

What to use as a laboratory notebook

• Purchase a notebook that possesses a stitched binding. Spiral-bound notebooks are undesirable because it is too easy too tempting to rip out pages out of frustration or error. Glue-bound notebooks are bad because glue doesn’t last over time, especially if the glue is edible (cockroaches will eat it). Ring binders and stacks of loose paper are equally unacceptable.
• Some laboratory notebooks have a “carbon copy” function that allows a duplicated sheet to be created and then removed to a second, safer location. These notebooks encourage bad notebook procedures and should be avoided. A proper notebook has a lot of glued-in information (printed graphs, datasheet templates, photographs, product labels, etc.) that simply will not show up on the sheet below, so the “carbon copy” notebooks are only good for archiving written entries. If you want a backup copy of your notebook, make a daily date with a Xerox machine. For the truly motivated and/or paranoid, note that you can periodically archive your pages with a scanner or (most easily) with a digital camera; then you can concatenate the compressed image files into a single PDF, then burn onto a CD.
• Notebooks come in a variety of dimensions. Those larger than a standard page are convenient because you can easily paste-in printer output without using scissors. Smaller notebooks cannot accommodate unmodified printouts, but are much easier to lug around in field conditions.
• More expensive notebooks have much nicer paper, so if you like a smooth, non-fibrous surface to write on, spend the extra money. Nothing beats smooth, expensive paper to boost creativity and productivity (but that’s just me).
• Also spend the extra money for a notebook that has pre-numbered pages.
• If your parents or mentor are springing for the notebook, you might opt for the really, really expensive variety that lays completely flat when open. It’s a small thing, but it grows on you.
• Here are some companies that sell laboratory notebooks:
  

  Book Factory
  Scientific Notebook Company
  Amazon.com (lots of links)

• If you want to keep a digital notebook, Rescentris.com is one option.

What to put on the outside of your notebook

• Put your full name and year of use on the front of notebook.
• I also suggest adding your last name and date span on the spine so that you can find your research when it’s on a shelf with lots of other notebooks that look just the same. (See a photograph showing both good and bad examples.) For writing on the spine, I recommend light-colored paint pens.  Or hot pink if you’re feeling wild. Paint pens also smell good, if you know what I’m talking about.
• Put your mailing address, phone number, and e-mail on inside cover.  This information is very useful when you foolishly leave your notebook at the bar along with your iPhone prototype.  Tape a $5 bill to the inside front cover with a note saying, “I’ll give you another if you find this notebook.” If you’re research is priceless, it’s money well spent.  Especially good to have wording like this if you do field research with your notebook. Of if you study mating behavior in bars, of course.
• Bling.  If the research and notebook are yours, take some pride in what you do and get crafty with the exterior, even if you just cover it with amusing stickers you peel off dangerous reagents.  But good science is an inherently creative process so I suspect most researchers have blinging talents, though probably repressed by medication.  By the way, decorating notebooks is a great bonding activity for the whole lab, so if you are the fearless PI, set an example or at least tell your underlings to do it.

How to maintain a laboratory notebook

• If your notebook is not already equipped with page numbers, add them.
• Devote pages 1 and 2 to a Table of Contents (which you will fill in as time passes). Have 2 columns, one for experiment name and one for page number where experiment #1 starts, etc. If you come back to your notebook after 20 years, you will be able to quickly find the appropriate section of your notebook. This Table of Contents is also crucial for others who might want to use the notebook to reconstruct your brilliant activities. Your table of content will never be perfect, but it will be a huge help even while you’re using it.
• Never, under any circumstance, should you remove a page. This directive is to prevent unscrupulous researchers from “losing” data that might not have been favorable to their research objectives. If you rip out some pages you thought were unnecessary or had unfavorable caricatures of your colleagues, others might view the gaps, and your stories, as suspicious.
• Some researchers insist on reserving the left-hand page for “cryptic notes to self, and quick calculations,” and the right-hand page for “real” entries. Do not do this. This strategy undermines the more important goal of keeping a notebook. If you have made “calculations and notes to self” without proper narrative explanation and justification, you, too, will probably find the left-hand page unusable after several months have elapsed.
• If you make a mistake, draw a thin line through the word or number rather than obliterating the entry with a blob of ink. In some cases you may decide, upon reflection, that your original entry was actually the correct one, and you will be glad that you can still read it.
• For the same reason, never use correction fluids (e.g., White Out) or strips of white laboratory tape.
• Write legibly! If you ever use your laboratory notebook to reconstruct experimental details, you will be miserable if you haven’t been reasonably neat. Your notebook does not have to be a work of art, but it should be easily readable by another person of average intelligence.
• Provide the full date whenever you make an entry. Always use the international standard format: YYYY/MM/DD (e.g., 2011/12/25).  If you grew up writing dates a different way, change your ways.
• There’s a fad in some fields to “recopy” notes into a different notebook at the end of the day.  I think doing that is a profoundly stupid idea.  Sure, you might have fresh insight when you’re recopying data and such, but you’ll also introduce copying errors (yes, even you).  If you really think recopying is going to help your science, I suggest you record your “field” notes on one side of the notebook and then recopy and add insights to the facing page.  However, if you do fieldwork were it is likely that you’ll lose your notebook or it will be stolen by roving bands of thugs with machetes, recopying into a secondary notebook might make good sense.

What to write with

You should use a pen that can stand up to the dangers of the laboratory (or field) and also to time itself. Obviously, you should avoid felt tip pens and watercolors, but that leaves a lot of options out there.I did a quick experiment to compare the suitability of a sampling of pens (see them in all their glory). Briefly: I subjected test writing on strips of paper to various conditions to see how the ink behaved. Test conditions were soaking (water, ethanol, methanol, or acetone), erasing, and baking (while moistened with water). These treatments are of course a minute subset of conditions, but I only gave myself a day for the experiment since it’s not really earth-shattering science.  Photograph at right shows how the ink is removed by methanol.  After treatment, strips were removed and pressed under filter paper to dry flat.  Then lined up in their original orientation and photographed:

Here are some conclusions:

• The following pens seemed to perform well under the conditions I used: Pentel Hybrid Gel Roller, Sakura Gelly Roll (this company also makes Pigma Micron pens, which are great), Sanford Uni-Ball Gel RT, Sanford Uni-Ball Vision, Sanford Uni-Gel RT, Zebra Sarasa (this writes this best, and comes in a pleasing “blue/black” tint). I have a fondness for the Gelly Roll in part just because of the name, but they are becoming one of my favorites (I own probably 30 in various colors and ink types).
• Avoid the “Pilot G2″ line (they bled extensively in the organic solvents, and even bled when incubated with warm water).
• Do not use Sharpie (or equivalent) permanent markers for notebook entries: these markers were very good at resisting water spills, but were removed by many solvents. More importantly, permanent markers tend to bleed through to the underlying page, which makes for rather sloppy, illegible laboratory notebooks. Sharpie ink also fades over time, especially when used on plastic (like microfuge tubes or plastic plant stakes).  I’m not sure whether the fade is sublimation or interaction with some wavelength of light.
• Do not use pencils (e.g., like lead photo!). Although graphite is wonderfully resistant to many solvents, it is famously prone to being erased, which can be terrible if you erase something that, in fact, was rather important. Also, if you decide to patent a thought or protocol, you need to show the laboratory notebook to the patent office, and they will laugh their heads off if you show up with a pencil-filled notebook.
• Do not use fountain pens, which usually have water soluble inks that will be compromised from even minor beverage spills or rain (for those in the field). Also, if you fall asleep and drool on a page, you’re in trouble.
• Ball points, despite heated opinions to contrary by many researchers, are absolutely terrible at resisting most solvents and smears. If your mentor insists on ballpoints, snear knowingly.
• I didn’t test Crayons, unfortunately.  If you use them, just be sure to stay in between the lines.
• If you work at a nuclear power plant, at the International Space Station, or are constructing a dirty bomb, please be aware that radiation can affect ink.  For details, read this article (pdf).
• If you are a fountain pen addict like I am (see my favorite pen, if you’re curious), you can use your pen in the laboratory if you buy yourself Bulletproof Black ink from Noodler’s. I haven’t tested it extensively, but it seems to be fabulous, and is actually guaranteed to be permanent until the End of Days.
• In my youth I used a Koh-I-Noor Rapidograph.  But I didn’t take care of it and it died.  But it was fantastic, and I feel bad about not including one in the above experiment.  Give it a try if you are at an art store and can afford it.  Also, Space Pens might work well, especially if you’re in orbit.

What should go into your notebook:

• Include detailed notes on all discussions and thoughts on the experimental goals. This means, of course, that you should start making dated entries immediately rather than waiting until you get your experiment(s) started. Because some information might come via e-mailed suggestions (from your mentor or colleagues) or from online sources (PDFs or web sites), you might paste “miniaturized” versions of relevant passages directly into your notebook rather than spending the time to transcribe.  If it has a scrapbook feel, that’s what you want.  Post photographs, too!
• Eventually, include detailed experimental protocols that could be easily followed by another researcher. If you have typed out a detailed protocol in a computer file, print it out (shrinking it to make it fit nicely) and glue it into your notebook (it is worthless if you file it elsewhere). Give each experiment a name so that you can refer to it quickly in subsequent entries. All experimental protocols should be accompanied with clearly worded hypotheses and goals, and indicate exactly what measurements are going to be taken.
• Provide full justification of all experimental details (species used, temperature, reagents, etc.). Justification might come as simple logic (stated, in your own words) or as references to other published research (e.g., voltages applied as per Frankenstein 1818, with full citation given).
• Annotate all calculations so that all numbers, concentrations, etc. are fully explained and would be interpretable by another researcher. Remember to include units.
• Give full details for all experimental organisms. Who provided seeds, plasmids, etc., and what information did they give you? Were seeds the result of open pollination, or were they from controlled crosses? Have lines used been subjected to thousands of generations of laboratory conditions or are they truly a wild strain? If you bought organism yourself, give source, delivery conditions, etc. Include catalog number (e.g., Burpee LE-23001) when possible.
• For greenhouse experiments, write down details of potting media (brand, type) and pot (shape, dimensions, color, brand). Also record when plants were watered, fertilized, repotted, or repositioned. If other people are asked to care for your plants, ask person to keep a detailed log of when plants were watered and fertilized.
• Record reagent details. Details include vendor (name, address, phone number; in case you want to buy more in the future) and product information (brand, product number, chemical structure, purity grade, lot number, date of mixing/production, expiration date, etc.). Whenever water is used, specify de-ionized, distilled, tap, cold, hot, sterile, etc.
• Record equipment details (brand, model number, sensitivity). In some circumstances it is important to record serial number, just in case there was something unique about the item you used. For growth chambers, always record bulb type and wattage (and brand name).
• Record field, greenhouse, laboratory, and growth chamber conditions such as temperature (in Celsius!), humidity, barometric pressure, light levels, light/day cycle (hours of each, and when night starts), wind speed, wind direction, etc. Note that conditions sometimes change, so record these parameters often if variation is likely to affect your results.
• Sometimes, personal information should be noted. If you are interested in observing behavior of nearby wounded bulls, it might be good to note whether you are wearing a red shirt. Similarly, behavior of mosquitoes might be inadvertently changed if you smell bad or are wearing perfume. Strange details like this can be important down the road.
• Record names of people providing assistance with data collection, techniques, statistical advice, equipment loans, stipend support, supplies funds. Write this information down immediately so that you remember to include it in your future “acknowledgements” sections. Keep notes about phone conversations and e-mail interactions.
• Make quick drawings of experiment set-ups, location of experiment in laboratory or greenhouse, etc. For field experiments, include a sketch of where field site is situated. These sketches do not have to be works of art.
• Attach photographs that document key experimental details.
• On the day you first enter data into a statistical program, write down the file name and where the file is stored (e.g., DVD on shelf in room 101; backup on laboratory computer in “Backup folder”). Give your file an informative name (e.g., “Heat_exp1_2011-12-25.dat”) rather than “experiment1.dat” or “stats_hell.dat.”
• Make daily entries, even if to say just “checked for mortality in Heat Exp 1; no mortality yet.”
• Specify purpose for each entry, and reference an experiment name. If you just wrote, “Censused” for a particular date, you wouldn’t have a record of which experiment you censused or what specific data you were collecting.
• If you happen to record some data directly onto datasheets (e.g., Excel spreadsheets that exist on computers or within ring binders), include dated entries for all such occasions: “entered data onto heat.xls spreadsheet.” Ideally, construct your spreadsheets so that you can paste them into your notebook, perhaps right after your experimental details are explained: you could “mark” this page with a flag so that you can easily add data to these pages.
• Detail all mistakes, problems with procedures, and lapses in data collection so that you can fully explain “odd” results at the end of your experiment.
• Use military time for all time entries.
• All entries should be un-obscured by attached graphs, data sheets, photographs, etc.
• When you include datasheets, photographs, graphs, product labels, etc., use glue to cleanly and permanently attach all edges. Do not use staples (they poke through to the other side) and do not use tape (it becomes brittle and yellow).
• Avoid making entries that are wholly unrelated to your project (e.g., “Don’t forget to mail presents”).
• Include the full names and contact information for all collaborators (in courses, this translates to laboratory partners). You will sometimes have, “see X’s notebook for further info,” and these entries will only be useful to other researchers if there is good contact information at the start of a particular experiment.
• At the conclusion of your experiment, or at the end of your course, write or print out a full directory of all electronic files that relate to your experiment.
• Describe the locations of all computer media, data binders, seeds, samples, etc., so that items can be located by others in the future. This information is best in tabular form (perhaps as an Excel or Word table printed and glued into your notebook). All seeds, DNA samples, etc. should be fully labeled with your name and date so that it is clear which notebook should be checked to learn more about the history of the sample.
• Typically, the laboratory notebook should stay in the laboratory where the experiments were conducted (i.e., with your mentor or employer). If you can’t part with it, make yourself a Xerox.
• Digital cameras are really cheap, so if you do expensive, important science I recommend that you have 1 camera per project and equip the things with a clear label (“camera for archiving Joe’s notebook”) and Eye-Fi memory cards.  At the end of each work day the researcher should take a photograph of each page (would take just 5 seconds per page).  Eye-Fi card would then automatically beam high-resolution JPG of each page to some secure server, or even multiple servers.  Then when your experiment blows up the laboratory in big mushroom cloud, you still have a copy of the nifty protocol (you wouldn’t be around anymore, potentially).  Also, when your trusty lab technician steals are your notebooks (like this person), you have a backup.  Sketchy researchers in your lab will think twice about doctoring past entries if they know a JPG history is on a server somewhere.  An additional benefit is that Principal Investigators can log into server on their iPhones to see laboratory activities even while sipping cocktails on the beach.

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