Research Notebook

[femamerica13]

So I'm getting pretty deep into my PhD program, especially since I am almost done with classes and general exams, so I will research more often. I noticed that I took notes for papers that I read; I prefer handwritten notes since I can go back later to review them and sometimes try to repeat the models or the experiment. I also have an in-lab notebook to record the experiments plus writing stuff in the lab, so I don't need to take everything off and on (and my advisor doesn't look at the notebooks and teach us how to research). I wanted to use my fountain pens in more work-appropriate and legible inks in the research papers and work outside of the lab, and I was wondering what I should get and how to organize it since it may also include notes with me trying to program something to make a model. I found for lit reviews and the bare bones notetaking; the best system is filling out Who, What, Where, When, Why, and How. A lot of grad school research for me is trying something and seeing if it fails, since my old advisor did say to have a research notebook and a good way to organize papers, unlike my current one. My current one does get the money, though.   

[WalterC]

Not fountain pen related, but for keeping track of the literature in your field and maintaining a bibliography,  a system like zotero (https://www.zotero.org/ ) is very useful. There are other computer bibliography systems, that is just one that I've used a bit.

        Maintaining good lab notebooks is essential in some fields, writing down ALL the details of experiments and results is important, even for failed experiments. My field is mathematics, so it is different from laboratory sciences, but maintaining a record of your efforts is still useful. Computers are so ubiqitous now that if you keep handwritten notebooks you probably want a system for pasting in computer printouts. Scanning your notebooks and keeping a backup copy in a second location is probably a good idea.

[El Gordo]

Who am I to judge your advisors ... I don't know these people. 

So I can't advice, just give my opinion. They each seem to focus on a valid aspect of research: 
performing high-quality research and getting funds to pay the bills. Learn from both.

My opinion(s) on research notebooks:
I am quite old school in this area: a decent research notebook is key in everything you do, 
not only during your PhD, also during the rest of your professional life if you stay in the
same business. You likely will have to manage (probably sooner than later) more than 
your own PhD project. Eventually lead a team, supervising research and follow-up research
by your team members (or as a team member) on a daily or weekly basis. How are you going to 
manage that in a decent way (ie not by having monthly review meetings were ony some 
highlights are presented). You and your team members will have to rely on their memory and,
much better, research notebooks.

WalterC is correct. You didn't mention your study field, I assume it is about labwork somehow. 
Doesn't matter what field actually. But choices are not always easy ...

Personally, I prefer, old school as I said, paper research notebooks. Note that not any notebook 
will fit. You can find requirements on the net, in short, there are several requirements to
real notebooks: binding method, pagination, signature fields, permanent inks, and everything readable
 (also the errors), ..., amongst others. They can be bought off the shelf at the right places.
 My experience with a lot of these, although they are supposed to be archival, is the poor quality
 of paper from a fountain pen point of view. Which pushed me in the IG ink direction. You can
 also find blogs on the suitability of inks for use in chemical labs (solvent resistivity etc).
 
 It is not only for yourself and being able to recall what you did so you can write a PhD thesis 
 one day. In your professional life, it will be records of what you did and how you did, so that 
 anyone in your neighborhood can repeat the experiments. You are in the USA, so before 2013 the
 research notebook was also key in the first-to-invent system, actually proofing that you were 
 the first to invent something and have the right to patent (provided that the notebook was kept 
 according to the guidelines). Also: only facts and observations go in a notebook, no opinions.
 If you write yourself that "this can never work", a patent lawyer from an opposer will gladly 
 say thanks and use it against you. I have the impression that a lot of people think that in a first-to-file system the research notebook is no longer of value.
 
Before the computer era, it was simple: the notebook was all and everything. Now there are electronic notebooks (ELNs) coupled to LIMS and laboratory management systems, document management systems, and whatever. Search around and maybe try some, depending on the specific fields of interest.

 

As said before: you probably will have to manage multiple projects, often with different degrees of confidentiality. So having one notebook per project is my preference over mixing projects in one notebook. Also for archival purposes or, beware, collecting by the funding party.
  
In essence, it is best (or mandatory) to follow the rules and the structures in your organization.  Quite often however there are none. In academia, each PhD often has its folder, (non-) organized according to own insights. Ever needed some data from a graduated colleague that were not in a thesis or publication? Found an Excel file with a bunch of data and no clue of the meaning, or spent a lot of time tracing back the data on a graph from the graph itself? 

 

So if there is no structured approach: red flag next to poor lab management. But an opportunity to bring something extra to the lab. Expect some opposition, better arrange your own work, excel, and then inspire if you are not yet in a position to push decisions.

 

Back to computers and paper: the hard part imo is the timestamping and the fraud-resistant "connecting" the paper to a computer system. There all electronic ELNs, DMS, LIMS, etc might have the advantage of tracking and logging changes and all whistles and bells if compliance rules are necessitated.
  
In one company we had a DMS, so I asked my team to scan their notes of the day and upload them to the DMS in the appropriate project folder. The project folder had a standardized structure, used for all projects. Advantages: I could follow up on data on a daily base, even over different shifts per day. All notes are timestamped and use and modification tracked (and there is some "pressure" to keep good records). On uploading a pdf was generated and automatically OCRed (where possible ... some pressure to write legibly).
  
For literature: I also used / still use Zotero, "collections" organized by project. The fun part is that references for one collection (project) can be exported to a bibTeX file, which I can use when writing reports.

 

So the system I use typically contains the following:

•   paper research notebook: for what it is intended, stays locked in the lab
•   paper journal: daily companion on the road, anything that does not belong in the notebook, meetings, timesheet data, todo's, ...
•  zotero: project literature
•  document management system: structured electronic storage of project files
  •   amongst these: reports and internal notes. I use the Quarto and R combo. Maybe (certainly)  a steeper learning curve than Word, but way more interesting (and if you start early, you could be fluent by the time you write your masterwork). 

But as always: my opinion,  useability depends on circumstances  beyond my control and knowledge and YMM greatly V.

[Stompie]

There is a Philosopher chap on YouTube called Park Notes and he goes into a lot of detail with the notebooks he uses for his research, note taking, thoughts, journals etc, you might want to check out his channel.

 

For uniformity I would suggest you go for the Lechtturm A5 notebooks, called the 1917 although they also have ones with much thicker paper if you need it but the notebook size is identical except the amount of pages.

They have index pages, pages are numbered and lots of little add ons that can be quite useful.

They come in a variety of colours and are very fountain pen friendly.

They are also quite sturdy - one of mine has been in use since 2012 for a variety of notes and it is still going strong despite being quite badly abused at times.

And, as they are all the same size, if you stick with the 1917 model,  a collection of them would like nice on a book shelf.

 

Also, Leuchtturm make larger A4 and smaller pocket notebooks that match the larger notebooks in terms of features.

[El Gordo]

Leuchturm (not only 1917) would be my choice (and is my choice for private journals) as well. However it does not serve as a laboratory notebook. Some missing elements. In our region, a grey linen cover notebook (Aurora) is often used. Very flexible, not a research lab notebook either.

 

Bookfactory, Eureka Lab Book Solutions (previously without "solutions" and now without sewn versions I was told, did not check) and others show the specific page layout. Adapting the layout and using local printers was the way to go in companies I worked. 

 

Background and food for discussion: https://www.finnegan.com/en/insights/articles/don-t-throw-away-lab-notebooks-record-keeping-under-aia.html and https://www.datacc.org/en/best-practices/how-to-use-an-electronic-laboratory-notebook/laboratory-notebooks-between-paper-past-electronic-future/

 

 

 

[WalterC]

El Gordo's posts are very useful -- read and reread them. 

        It would be useful to read up on how people in your field maintain research records. Methods for maintaining lab notebooks and experimental records do very from field to field. You can likely find journal articles and web pages that give the options for your field.

        Good luck! Maintain your mental and physical health while completing your Ph. D.; it can be stressful, but it can also be fun.