Starting a PhD, time to start a lab notebook?

April 28, 2008 8:56 PM

I'm about to embark on a PhD in cognitive neuroscience (imaging genetics, to be specific). It's going to be a long 4 years, is keeping a lab notebook going to ease the discomfort?

I know lab notebooks are very popular in fields that are heavy on biology, but my stuff won't be (apparently you have to keep human participants in one piece…). What do you put in a lab notebook? Is it really that useful?

I'll want to be able to run multiple projects at the same time and keep track of what is going on where (i.e., equipment required, what I still need to do to get the project going, room/equipment bookings, participant schedule, etc etc).

If keeping a lab notebook isn't really that useful, what other clever uses are there for my Moleskine (preferably something that will make the phd easier to tolerate).

posted by doctor.dan to science & nature (18 comments total)

I'm getting a PhD in ecology/conservation and I have a separate notebook that I use to keep notes at meetings (lab meetings and with professors), as well as at any talks I go to. It's great to go back and look through it to get a good sense of what people are talking about, and remind yourself of any ideas you thought you should pursue. I also use it to keep basic to-do lists, but anything more complicated (scheduling participants + room bookings) probably deserves its own place.

I don't know exactly how your research will go, so I don't know if a lab notebook would be appropriate for recording data/experiments -- generally I find data sheets pretty helpful if you're recording the same information over and over.

But yeah, just keep a notebook around and write stuff down if you think it's important -- you'll get a feel for what that is as you go along.
posted by one_bean at 9:05 PM on April 28, 2008

Congrats on getting in to grad school. I just wrapped up my PhD and started my postdoc in CogNeuro. My opinion? Keep detailed notes in multiple notebooks. I typically have one Moleskine for each research project and one for general stuff like lab meetings. Write everything in there - from experiment design ideas, data acquisition quirks, what stats you did, ideas for writing the paper, etc... You don't want to have to run downstairs to the scanner because you forgot what TR you used.
posted by prefrontal at 9:16 PM on April 28, 2008 [1 favorite has favorites]

In short, yes, you should keep as good a notebook as you can. I finished by degree in Physics last year, and I think I figured out a good system.

One usually wants to satisfy two mutually exclusive goals when making a nice lab notebook: you want everything to be chronological and totally complete, but you also want it to be factually correct and easy to read for later browsing and reviewing. I found it hard to make a notebook both complete and correct because a lot of my early assumptions were idiotic, and my methods and understanding only improved with time. Lots of time. I found it hard to make a notebook both chronological and easy to read because graduate students multi-task over the timescales of months: attend classes, work on toy problems, read and summarize papers, prepare for conferences, do experiments/simulations, record data, analyze data, write a paper, revise said paper over one year later, etc. etc.

The solution: multiple notebooks! Buy a set of notebooks dedicated to a chronological listing of what you did/studied/learned/thought that day. Write as much down as you can, especially your thoughts. Print miniatures of important graphs, tables, diagrams and paste them in. Every month or so, summarize the preceding pages to make sure the story is accurate. Leave the first five pages blank and write a table of contents when the notebook is filled. Label the spines, the fronts, and the backs, preferably using color. Moleskines are ok for this, but I always found it nice to be able to paste in a letter or A4 page. Serious commerical labs require each page to be read and signed by a colleague. Must you go so far? Maybe not, but maybe every 30 days you ought to try and summarize your month's efforts in a single page and talk to a colleague (at a group meeting perhaps?) about it over coffee or a beer.

In another set of notebooks, document your understanding of the bigger picture, tangential projects, research at other institutions, and outline thesis chapters, papers, posters, and presentations. I found it useful to sketch presentation slides into a notebook before even opening Keynote/Powerpoint. Ok, ok, I never opened Powerpoint. Moleskines are perfect for this: they come in ruled, square-ruled, blank, pocketed, and packs of three! When you head to a coffee shop, you can take just the notebooks you need for the project on the front burner, and the "official" chronological books are still in the lab/office where they need to be.

As much I liked this system: I might switch over to an electronic journal system at my next project. Lab Wiki's are just so useful in big groups, and a lot of paper reading, data collection, analysis, etc. are done in software anyway. Also, the search, revision, tagging, and HTML linking capabilities ought to be a killer advantage. On the other hand, the last thing I want is more computer work, so perhaps the notebooks are still better after all. Best of luck.
posted by fatllama at 9:30 PM on April 28, 2008 [4 favorites has favorites]

I can't recommend Microsoft OneNote enough. I know, I know; Microsoft? Go to their website and download the trial and you'll be hooked.
posted by lockestockbarrel at 10:05 PM on April 28, 2008

A lab book was part of my assessment for my undergraduate thesis. I was a software engineer doing a pedagogical study.

As part of my professional life, I'm required to keep a workbook: thoughts, ideas, meeting notes, work hours, etc. Doing one for my thesis was good practice.
posted by ysabet at 10:20 PM on April 28, 2008

If you ever consider doing something with your degree, there are very real legal reasons to keep a lab notebook. In particular, patent applications are a lot easier with paper trail documenting your development of the invention. In addition, I find they are useful to formalize your thoughts into something you can actually work on.
posted by saeculorum at 10:24 PM on April 28, 2008

If there is any chance that your work might be patentable, then an unalterable, chronological record is invaluable for proving the date you first thought of key elements. Having a colleague read and sign each page is even stronger. There are software systems that will meet the legal requirements but an ink pen and a bound notebook work just as well. Even if you don't believe in patents, it is very helpful to have your documentation if some company falsely claims to have thought of your idea before you (depending on the country where you are working).
posted by metahawk at 10:31 PM on April 28, 2008

I'm also an ecologist. In addition to field notebooks, I also maintain a set of moleskine journals. I don't write in them everyday but on days that I do field/lab work [not writing], I write a short paragraph on what transpired. My data notebooks capture real data but there will be days when no real data gets collected [e.g. days when I set up experiments, try prototypes etc. but don't collect data]. These notebooks come in handy to look up and piece togather dates where nothing of note happened but provide the necessary context for other stuff. So when I write manuscipts, I use my journals to get the actual timeline of experiments.

In your case, you might use this to keep track of when/where you met what subject. Meetings where you are not actually testing that person may come in handy in future.

PS: I'm not a meticulous note taker so I rely heavily on these little entries/emails to place events.
posted by special-k at 10:32 PM on April 28, 2008

one_bean, thanks for all your tips. Lab/participant bookings are all done electronically so I guess I could always print a daily summary of that and stick in the lab notebook. The reason I was intrigued by the lab notebook idea is that, at the moment, I have stuff written everywhere. If an idea pops into my head while I'm reading a paper, I write it on that paper. Naturally, I only find this info again once it is of no use.

prefrontal, thanks, congrats to you on finishing! The one reason I'm (still) shying away from multiple notebooks is if one project fails completely, I'm left with a partially used notebook. I guess this would be avoided if I was consistent with documenting everything (and don't start projects that are likely to fizzle out).

fatllama, thanks for sharing your system. The summary tip is a great one, it'll definitely solve the problem of writing something down to do/think about later and not doing it. It'll also keep me on top of the project. The University through which I'm doing my PhD does offer the commercial grade lab notebooks, which require each page to be signed and witnesses. I don't really see this as being useful to me, I'm not working on a project that will result in patents or commercialisation. My motivation is to become more organised and spend a little less time in front of my mac.

lockestockbarrel, I did like OneNote before I switched to the Mac, although I felt that it was heavily geared towards tablet PCs. Circus Ponies' Notebook is very similar to OneNote. VoodooPad is great for those after an electronic notebook. I need to be able to write into the notebook while testing so I can't use something that is confined to the iMac on my desk (and there is no way I'm lugging a laptop with me every time I test).

ysabet, the reason I wanted to get into a lab notebook is that I noticed that a lot of professional careers do have a very strong emphasis on keeping track of everything. Its a shame my undergrad course made no mention of lab notebooks.

saeculorum, in Australia patents are awarded to whoever registers it first rather than who invents it first, removing that requirement. However, there is still a strong requirement to keep everything documented in case there was a patent dispute (every page of the notebook has to be dated, signed and witnessed).

metahawk, my research is in attention and emotion, I don't see anything patentable coming out of it.

special-k, testing individual particpants/subjects wouldn't really lead to too much being written in the notebook, as far as I understand it. The data (EEG, fMRI, etc) would be recorded by a computer, and I would then merely extract it when I actually need it.
posted by doctor.dan at 12:19 AM on April 29, 2008

Nthing notebooks.

I finished my PhD (biochemistry) last year, and whilst I wasn't the best record keeper, the records I kept were a godsend when I was writing up my thesis.

Simply put, computer based notebooks don't offer the flexibility of paper based. Sure you can write up a whole Excel worksheet if you have a basic table.... or you can just do it in 10 seconds in your paper notebook.

I learned my lesson, and as a postdoc I am meticulous is keeping my notebook up to date. i keep it like a journal. Dating each page and stating my aims and my resultss

Your supervisor should also be keepiung an eye on you, and will be asking for your lab books every now and then to see what you have been working on.

These days I keep a separate notebook for each of my projects - Does it really matter if you have a half empty notebook by the end of it? There are much bigger issues you will have to worry about during a PhD :)
posted by TheOtherGuy at 12:50 AM on April 29, 2008

YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES YES

Keep a notebook. I finished my PhD a while ago (2006 in synthetic chemistry so everyone had a notebook) and the notebooks are incredibly valuable.

At the very least keep two, because your field is different to mine, the first should describe the experiment set up and should be detailed enough to allow anyone to repeat exactly the experiment that you ran. Without that book you have nothing but data points that may or may not correlate to each other.

I would also get used to carrying a moleskin or something like that to jot down notes when they come up. That means a small one just big enough to keep in your pocket and be sure to keep it on you at ALL times, even off at the pub or whatever, you never know when you are going to have an interesting idea that you might want to read further into.

Your first design of a lab notebook will not be sufficient, and no one except people in your speciality can help you with the design. My lab notebooks (well all 10 of them) were kept like my old prof wanted them to be kept, and with a couple of slight modifications I still keep them that way. Keeping the book will be an evolving process, the only suggestion I can really offer you is to go back every month or so and reread what you wrote and see if it is detailed enough. Find out what is unnecessary and trim it, and find out what you forgot and include that. Keep doing it for the entirety of the PhD, and you will have learned a really valuable skill in science. You will also have a nice set of what you have learned in the process of getting the PhD so assuming that your prof doesn't want to keep the notebooks they will be valuable to you later on.

-Koolkat
posted by koolkat at 2:41 AM on April 29, 2008

Yeah, a lab diary helps much. I'd also suggest a) CVSing (or something similar) all code and documents b) logging all computer activity. Nothing is worse than when Boss says "how did you make that plot?" "Hm, how did I make that?" (...an hour..) "HOW DID I MAKE THAT PLOT?!"

The other nice thing to do is just have a place for ideas. Because you'll have them and be someplace random.
posted by a robot made out of meat at 4:54 AM on April 29, 2008

Nthing everyone who says that yes, notebooks are a very good idea. I can see that it's not going to be quite as vital as it is in my field (second-year of a molecular bio PhD) but I try and keep a daily record of every experiment I did and what results I got with as much detail as possible on why and how I did them. I presume you won't have so many experimental results to deal with, but it's useful to be able to remember exactly when you did this analysis or had that idea. Supposedly my notebook should be witnessed and every page signed, but neither I nor anyone I've met here actually does that.

I got burned by not having detailed enough notes for my undergrad thesis, because I really didn't realise just how much I would forget about what I was doing a few months earlier, and that's motivated me to keep my notebooks up to date.

I'd also suggest getting organised about papers and books read: start up an EndNote database or similar, keep electronic or paper notes on them once you've read them, then the references are all to hand when you start writing a report. You might want a separate notebook for taking notes of seminars/lectures/courses you went to, particularly if there's some requirement to demonstrate you've been going to them.
posted by penguinliz at 6:09 AM on April 29, 2008

The one reason I'm (still) shying away from multiple notebooks is if one project fails completely, I'm left with a partially used notebook.

This is why binders are great - just use as much space as you need, and you can add tabs and tables of contents and such as they are needed. Short, related experiments can all go in different tabs on the same binder if that makes sense. They also make adding computer print outs look much neater. I've used binders and notebooks, and I greatly prefer binders. I also recommend making another binder detailing all the techniques you've learned how to do. But DEFINITELY keep good documentation - you'll forget a lot over the course of 4 years!
posted by fermezporte at 6:31 AM on April 29, 2008

Yes! 4th year PhD student in Chemistry here. (and physical chemistry where most of my work is not done in the lab, rather it is data analysis on the computer)

I am also recommending multiple notebooks -- I have one for professor/group/seminar meetings (and part of this is sectioned out solely for professor meetings -- VERY helpful!), a notebook for sample preparation, and a notebook for experiments on my instrument. This basically covers the three rooms I work in most often, of course, YLLMV (Your Lab Layout May Vary)

I found this blog post on Getting Things Done in Academia to be interesting, that blog also covers many note taking/record keeping software options if you want to go the computer route (which almost seems easier these days?) But I would vote for both. Start with a simple system that just allows you to keep track of what works, what doesn't, important data, and what experiments you're doing next and let it evolve from there.

You may also want another notebook for reading materials, although with journal articles I find notes in the margins to be more helpful there (or electronic notes on the PDF with a program like Skim (mac)) I have tried this with limited success, but I am also lazy about reading papers of late.
posted by sararah at 7:13 AM on April 29, 2008

I'm something of a dinosaur around here (Ph.D. in 1988), so my grad school experience may be outdated. But I'm a working scientist and in my field (biochemistry), lab notebooks are still absolutely essential. There's no way to survive without writing stuff down, since you'll soon forget the details of what you've done. Whether your goal is to publish, or patent, or simply not have to repeat stuff that you did 6 months ago, you'll need a written record.

Whether that's on paper or disk is a matter of preference, but paper is more convenient in many cases. In academia we used looseleaf binders, in industry we always use bound hardcover notebooks (for the unalterable record), but either is easier to carry around than a laptop. Sometimes you need your notebook at the bench, and if you do wet work (not sure if cognitive imaging would involve this), a laptop is at risk from spills and splashes.

It almost sounds like you're describing a sort of diary, since I can't imagine a standard lab notebook would have any effect on the pain of grad school (especially since I can't imagine anyone could do science without some sort of lab notebook). A separate place to record ideas, meeting notes etc, is a good idea. It would be too hard to find that stuff if it was interleaved in your research notebook. A third notebook just for recording your methods, techniques, etc, would be good too. You will probably have to leave your data with your grad school supervisor when you graduate, but it would be very valuable to have a "cookbook" of your methods that you can take with you to your next position. Believe me, not all the technical details will be recorded in your thesis or publications. I still occasionally refer to my old cookbooks!

Your cookbooks and records of thoughts don't have to be beautiful (I personally think Moleskines are a little too intimidating to be useful). In the tightwad companies I seem to end up at, we usually have the cheapie composition books used in high schools and they work fine. But definitely write everything down somewhere, and good luck in graduate school!
posted by Quietgal at 7:40 AM on April 29, 2008

YES! I'm a 4th year in cognitive neuroscience (mid level vision). I wish I'd started keeping a notebook years ago. Right now my "notebook" is mostly my extremely detailed checkin notes to my SVN repository, which is nice because it's not decoupled from my actual workflow.
posted by dmd at 1:40 PM on April 29, 2008

I'm in my second year of grad school and only started my lab notebook at the beginning of this year. Like dmd, I wish I'd started earlier: the notebook keeps my scattered ideas, activities, and questions together in one place, unlike the scattered hodgepodge of word documents and scraps of paper that I've used in the past. With my lab notebook I can easily page through my notes, going from idea to idea and day to day rather than scratching my head to recall if I filed one idea in "orals" or "prospectus" and the like.

They're also great if you have a wet lab, which means that you can easily take notes without interrupting your workflow.
posted by RachelSmith at 2:44 PM on May 23, 2008