Sciencemadness Discussion Board

How do you keep your lab notebook?

Felis Corax - 21-8-2019 at 22:36

With my new lab just about set up I've decided to update my note taking process. As such I thought I'd ask some questions about how other people here keep theirs.

What type of notebook or software do you use, and why?

Do you write in first person or third, present or past tense?

What sorts of information do you include as part of experiment design?

What types of things do you record during an experiment?

How do you designate and name your experiments?

Do you record reagent preparation, equipment calibration, and other non-experimental procedures you carry out?

What is your purpose for keeping a notebook?



In the spirit of reciprocity, and to give an idea of what I'm looking for, I'll go first.

What type of notebook or software do you use, and why?
I keep my notebook in Jupyter Lab because it lets me record normal text (with markdown and LaTex as needed), as well as python code, pictures, tables, graphs, and so on. I've tried a couple different purpose-built cloud-based ELNs, but none have been as well fitted to my use case. I even tried a paper notebook once... it was not an experience I would want to repeat!

I know some people here swear by paper. I swear at it. :cool: I doubt anything could change my mind on this matter, though if you do use a paper notebook I'd still like to hear about how you keep it. Even if it doesn't help me, it may help someone else who reads this in the future.

Do you write in first person or third, present or past tense?
I've been experimenting with using the formal third person past tense "passive" voice in my notes. It took some getting used to, but now comes easily enough that that's not an issue. That said, I'm not sure if it really serves any purpose besides to provide a tone of impersonal objectivity.

What sorts of information do you include as part of experiment design?
When preparing to document an experiment I set up a "notebook" (the term for a jupyter document) with a title, table of contents, and any python libraries I'm importing. I include a brief describing what I'm doing and why, followed by reference data, links to sources, lists of materials and equipment, and any initial calculations I've done. I also include any code that I've written for the experiment, usually either functions to simplify calculations or code to import and process/graph data tables. I follow this with a detailed procedure divided up into stages. Despite being first, the brief doesn't get flushed out till after the experiment design is complete.

At the beginning of each of these sections I include internal links to the table of contents for easy navigation, and often include them between related parts of the document as well.

What types of things do you record during an experiment?
I divide my notes up by procedure stage. I start each stage with a copy of the procedure for that stage and a link to both the procedure and the table of contents. I note down what I'm doing, with a timestamp for each entry (I have a hotkey set up for pasting in a timestamp). I take pictures as necessary and include them as well, usually with an annotation. I make notes in as much detail as seems useful, noting equipment settings (usually temperature and stir bar RPM, I don't have a lot of fancy equipment... yet), how I carried out tasks, and any difficulties or potential problems I encountered. If I need to deviate from, or modify, the procedure I note that down as well. Usually. Sometimes I just modify the procedure to fit how I'm proceeding and go from there.

Sometimes I'll write numeric data in the text entries, but often I'll put it directly into variables in code blocks, or in a referenced csv document for the purpose of making a graph or table. I use code for all my calculations, which means all calculations are recorded and, if necessary, easily updated. When it seems relevant I'll note that I updated or corrected an error, but often I don't bother.

In my last few experiments before I had to pack up my lab for moving I was using the uncertainties python library for calculating and tracking propagation of uncertainty. I include uncertainty listed on measuring devices, and take multiple measurements whenever possible... especially with my cheap analytical balance. There are probably more factors I should include but haven't, such as a margin to account for any measurement errors that I make.

After all my notes and such I perform any final calculations and write a section on the results of my experiment. I include problems I encountered, suggestions for improvement on the procedure, and my level of confidence in my results. I often leave this till the next day as I'm often quite tired and/or hungry after a long session in the lab.

How do you designate and name your experiments?
I designate my experiments by a brief descriptive statement, followed by a number for keeping track of which time this is I'm doing it. Something like "Stdzn of 1M NaOH soln via titrn of KHP T1". This is one of the areas I'm thinking about changing, though. I'm considering prefacing each experiment with a unique serial number rather than simply a number indicating the number of times I've performed an experiment with the same title.

Do you record reagent preparation, equipment calibration, and other non-experimental procedures you carry out?
If I'm making a preparation that's new to me I will generally keep notes on it just like an experiment, though most simple stuff I don't bother with. Certainly I don't track the frequent and finicky calibration of my analytical balance. ESA is my mortal nemesis there... even with a grounded mat, a wrist band, and anti-static somewhat-conductive gloves.

I'm strongly considering changing to recording all preparations and persistent equipment calibrations, albeit not in the same detail as I do with experiments. I'm not planning on keeping records on calibration for my balance... I do it every time I use the damn thing.

What is your purpose for keeping a notebook?
My main purpose in keeping a notebook is so I can look back at experiments, see what I've done, and learn from my mistakes. I'd like to think if I ever find myself in legal trouble over having a lab that it'd provide evidence that I have legitimate uses for my various chemicals and equipment, but I don't try to maintain it in the sort of legally relevant manner that one might find in an institutional setting.

Sulaiman - 21-8-2019 at 23:03

I use a hard backed A5-sized paper logbook because;

I like to record things as I do them rather than rely on memory later,
and I do not want my laptop near my experiments.

I cannot edit or remove notes as I used to on the PC or in a loose-leaf binder,
this means that I do not accidentally remove useful notes etc.

My reason for keeping a Lab notebook is to be able to reflect on previous experiments,
and to be able to correctly identify the contents of various flasks and bottles containing experiments in progress, or waste products.

Lately, I add the date to labels on diy chemicals,
this way I can quickly get a reference from my Lab Book.

If I had a perfect memory I would not keep a Lab Notebook.

karlos³ - 22-8-2019 at 00:49

I also use A5 paper, but transfer them later into .txt files, and sometimes without the paper part.
The digital stuff is more thorough than the ones on paper, which are usually only the calculated amounts and numbers and nothing more.

teodor - 22-8-2019 at 02:17

- What type of notebook or software do you use, and why?
- excercise book. Writing with a pen is more natural for me also I can mix text with drawings.

- Do you write in first person or third, present or past tense?
- I use different styles depending on my mood

- What sorts of information do you include as part of experiment design?
- Quantity and source of reagent, procedure, the picture of the apparatus I used

- What types of things do you record during an experiment?
- yield, everything I noticed unusual or new for me

- How do you designate and name your experiments?
- I name it by a date when I did. The same date I use as reference both in the notes and marking of bottles which will store results

- Do you record reagent preparation, equipment calibration, and other non-experimental procedures you carry out?
- Everything that will allow reproduce the experiment (all conditions I think are important)

- What is your purpose for keeping a notebook?
- Make experimental results reproducible, also collecting all unusual things to explain them later, possible with other experiments.



[Edited on 22-8-2019 by teodor]

Ubya - 22-8-2019 at 03:42

What type of notebook or software do you use, and why?
-i use an A4 4 ring binder. i like to write on paper just because i can write while i'm doing an experiment (my memory is really shitty, i don't want to forget to write something).

Do you write in first person or third, present or past tense?
-at the beginning i used to write in third person past tense, but as this notes are just for me to remember things i did in the lab and to think abount it later i now write in first person, more like a conversation with myself. if i'll ever write something here i'll obviously adjust my notes to be read by a public

What sorts of information do you include as part of experiment design?
-theory of the experiment, materials and math (stoichiometry etc), procedure, issues, drawings

What types of things do you record during an experiment?
-reagents i used, equipment i used, time i spent, any changes of a variable during the experiment (changes in color, temperature, smell, strange behaviours etc). plus a monolog of what i'm doing and why, mostly to solve issues if i encounter one

How do you designate and name your experiments?
-is it a synthesis? a workup? a separation? kinda generic. for example i needed to purify some commercial solvent, the titile is "separation of DCM from commercial solvents "name of the brands used""

Do you record reagent preparation, equipment calibration, and other non-experimental procedures you carry out?
-not always, but if something unusual must be done yes i write it down (extra precautions for dry solvents for example)

What is your purpose for keeping a notebook?
short memory, i do experiments that last for months, i get to work on things just for a few hours a week if i'm lucky, i could be doing nothing for months, and when i come back to something i did i need to know WHAT i did hahaha. often happens that i think of how to solve a problem i encountered in a procedure, i read my lab notes and notice that i already thought about it and didn't work, so it is pretty usefull to me

XeonTheMGPony - 22-8-2019 at 04:06

I use a black cloth binder with standard letter size paper, I use a #2 HD pencil that is well sharpened.

I keep it to the basics, technical detail and procedure used and I show each step of the math used

I will usually include a basic drawing of the flow path of the process and a drawing of the apparatus set up.

stamasd - 22-8-2019 at 10:38

Here's what I do. I don't claim it's the best method, this is what works for me.

I use a very advanced piece of software called Notepad. :)
The lab notebook is a directory on my hard drive. It's automatically backed up periodically. The name of the directory is very unassumingly "chem".

Under that directory I have a tree of folders by type of experiment. Organic/inorganic/mixed. Involving electrolysis or not. Step in a multi-step prep. All organized hierarchically.

At the last level, experiments are sorted by date. I record any detail that I think will be useful in reproducing the experiment later. Amounts, times, temperatures, pH, apparatus used if anything more than basic, voltages, currents, impedances etc. Observations about the state of the reaction at different times: color changes, precipitates etc. Photos if any go in the same folder, numbered and referenced in the text. By default all photos I take have the date/timestamp burned in, because metadata can be volatile.
For data analysis, graphing etc I use mostly LibreOffice, and occasionally SigmaPlot.

[Edited on 22-8-2019 by stamasd]

CharlieA - 22-8-2019 at 15:16

Five minutes googling laboratory notebooks will give a plethora of papers discussing this subject, including many university requirements for keeping a notebook for specific courses.

mayko - 22-8-2019 at 17:17

I use a bound paper notebook. A digital record is great for backups or after-the-fact writeups but IMO paper is best for benchwork. A couple of reasons are the flexibility (word processor, drawing program, and LaTeX rendering, in a single app called a pen!) and chemical hygiene (you're either taking gloves off and on every time you need to jot something down, or you're smearing on your keyboard the stuff you didn't want on your hands. A dedicated lab computer would solve this, and isn't a bad idea generally, but is also more costly than a dedicated lab notebook and lab money is usually better spent elsewhere). Also, I tend to think that any analysis/calculation/visualization that can't be done with paper and a scientific calculator is best left for later, when you can sit down with a cup of coffee and really mull things over. (When I do this, it's usually as an R markdown which I render to PDF).

* What sorts of information do you include as part of experiment design?
A brief overview of what I'm trying to do and why, followed by a table of important data (molecular weights, boiling points, etc). Sometimes an apparatus diagram or taped-in clippings from The Literature.

* What types of things do you record during an experiment?
Step-by-step procedure, amounts used, measurements taken, observations made, mistakes to avoid next time.

* Do you record reagent preparation, equipment calibration, and other non-experimental procedures you carry out?

I try to; I like to have a trail I can follow back to raw materials, and it works well into my labeling/organization scheme


*What is your purpose for keeping a notebook?
Quote:


I have to believe in a world outside my own mind. I have to believe that my actions still have meaning, even if I can't remember them. I have to believe that when my eyes are closed, the world's still there. Do I believe the world's still there? Is it still out there?... Yeah. We all need mirrors to remind ourselves who we are. I'm no different.
















Metacelsus - 23-8-2019 at 02:45

Back in undergrad, when I was doing organic synthesis, I kept a hardbound lab notebook to record all my experiments. I would record all the relevant experimental procedures and data, except for spectroscopy files which I kept on my computer.

Now that I'm doing stem cell biology research, I'm generating so much data that it's infeasible to use a physical book. Instead, I make a new text document for each protocol, which I can link to the data files I generate. This has worked pretty well for me. For data analysis I use an unholy admixture of Python, R, and bash scripting (it's not pretty but it gets the job done).

My number one piece of advice: don't let your lab notes grow organically. Have a plan.

mayko - 23-8-2019 at 17:42

Quote: Originally posted by Metacelsus  
For data analysis I use an unholy admixture of Python, R, and bash scripting (it's not pretty but it gets the job done).



When I have very involved computational analyses to do (mostly for work) I also use the r/sh/python gumbo. Something I've found very useful is a pipeline manager called Snakemake, which really keeps me organized and helps things run in an automated & reproducible way. It's still a mess but at least I no longer have folder after folder of files helpfully titled "data.v3.txt" and "script.sh" xD

Felis Corax - 24-8-2019 at 20:33

Thanks for all the responses! :)

I know there's a lot of information out there on this subject, but it's all geared towards students or professionals. It's good to hear what other amateurs find useful/important.

I have to say I'm a little surprised how few people are keeping their notes electronically. I wouldn't know what to do without my lab computer. Along with taking notes I use it to do research on the internet while I'm working, make calculations, and provide entertainment while babysitting long reactions. I have a couple of instruments that plug into it, too, including a digital thermometer that I stuck in the end of a glass tube and attached to an Arduino for I/O.

I do worry a little about contamination, but I swap gloves pretty often when I'm working with anything nasty. Besides, wouldn't that be a problem with a traditional paper notebook as well? Paper is a lot more absorbent than plastic keys.

What little data analysis I do is all in python. I use pandas for tables and graphs and such, numpy for some semi-specialized calculations, and uncertainties for tracking uncertainty. And that's about it. I'm still very much a noob with gobs and gobs to learn.

egret - 25-8-2019 at 12:06

For lab logboog I preffer paper workbook. It is reliable you can make notes any second even in no so clean eviroment, Udualy this record is a pard of some ptroject. Then the impotant findingd together wihth pictures and discusion ase writen ín nword file in PC.

deadpool - 4-9-2019 at 01:07

I use a Fujitsu laptop pen input, it will complete the math problems for me as I write them (stoichiometry) (like this https://youtu.be/pcP1OO-88RM?t=89 ). It' transfers my notes to a raid back up via wifi, which is then again sync to a remote location.

Don't get suckered into an android/ipad or something for note taking; use a tablet-pc one the screen spins around and closes. :)

Sturge11 - 4-9-2019 at 02:36

I take all of my direct notes in the lab in a college ruled multiple subject notebook on a plan clipboard. I am partial to the Pilot G2 series of gel pens and keep them in stock. I do transfer things to my laptop once I'm done, but I just feel that it flows better if I am physically recording things during doing.