April 28, 2011 | By: Nick Morris

Aa Aa Aa

To lab book, or not to lab book, that is the question? (I say no, what do you say?)

OK, this is not really an eLearning post, but it is an interesting question (and problem) - should students keep a lab book or not? My answer is, they shouldn't!

What is a lab book?

Well, in the question posed here I am taking it to mean a good ol' fashioned lab note book. You may (or may not) know the sort of thing I mean. I am talking about a lab book that typically takes the form of a bound book of pages (from which it is difficult to insert or remove pages) that is used to keep a journal/diary of experiments (methods and results).

The lab book - the good

Lab books are great from the point of view that they are highly portable, don't need power, and if you spill something on them (assuming it is not acid or something equally nasty) fairly resilient to life in the lab.

They are also extremely user friendly, and don't require much maintenance other than the occasional wipe down after a particularly nasty spill.

The lab book - the bad

Now this is why I think students should not keep lab books:

1. They are not searchable - Well you can't easily and quickly search a paper-based system. You can create an index of experiments, but I doubt that you would include details in the index of, say, the antibody batch you used.

2. They may be portable, but they are not 'shareable' - Well, yes, you can share a lab book with a colleague in the lab, but if they have it, and you don't, then you can't use it. Plus, sharing a lab book with a collaborator in another country is almost impossible, and when you leave a lab you tend to leave you lab book with your supervisor and so you leave all your data and methods behind.

3. They are ethically unsound - This is a tough one that a lot of scientists don't think about. If you are a scientist, just pause for a moment and think where your lab books are.... I suspect that some of mine are now in landfill, as previous supervisors would have thrown them out by now, or they are in storage. So, this means the data contained within the lab books is now (if it wasn't published) effectively lost. This raises an interesting question: How many billions of dollar, euros or pounds of research data have been lost as it is locked away in labs or is now in landfill? Is it right to have wasted all this money?

4. They are prone to errors - This is the old 'methods problem'. Say you are running a series of experiments over several months and you are copying (by hand), or referring back to, a previous method. It is very easy to accidentally make an error when copying over, or fail to track any subtle changes that may occur.

5. They can't be backed-up - Well, I suppose you could photo-copy every page. But with a handwritten lab book it is almost impossible to keep a back-up. So, if the lab burns down part of the fuel will be your lab book.

6. They can't be standardised - In fairness they can as you could have a special lab book that is printed with standard boxes and areas to fill in, but in general they can't be standardised, so, one person's lab book will look very very different to another person's lab book.

7. They are a source of potential contamination - If you spill something on your lab book then it is sometimes impossible to get the book truly clean, and if you are then carrying it around you risk contaminating yourself, and your work.

The lab book - the ugly

Most of this was covered under 'the bad' above. But lab books can be ugly. My old lab books were particularly ugly as I have awful handwriting, and some of my old lab books picked up some really interesting stains (film developer seemed to be the worst as it goes a really nasty brown colour).

The lab book - a solution

Go digital!

I went digital with my lab book way back in 1994. I kid you not!

The reason I went digital was my old paper based lab book nearly caused me to have a nervous breakdown when I was writing up my PhD. Essentially I faced two problems:

1. Recreating methods - If you have worked as a scientist (or tried to reconstruct a method from a paper) you will have encountered this problem. You look at an experiment in your lab book and it says "Method followed as outlined on 22nd December 2010 with the following modifications.....". You then look at the 22nd December 2010 and it says "Method followed as outlined on 18th December 2010 with the following modifications.....". Before you know it you have dug back through a year of lab books (or 10 years of scientific papers) to recreate the method for your paper or thesis (or to share). Nightmare.

2. Tracking data - This was a real problem in my PhD. On a given day I might start 3 or 4 experiments, each of which would finally produce results weeks later. I had a real problem linking the results to the method. If I used a date then this could be ambiguous as I could have three experiments all with the same date. Also, the result tended to end up 3 to 4 weeks further in to the lab book than the original write-up of the experiment. This was a real problem when trying to link results back to experimental method.

So when I started my post-doc I created a 'lab book database' using FileMaker Pro (if I was to do it now I would most probably use MySQL (see Do you speak my language: M is for MySQL, MAC address, Malware, MashUp, Metadata, Middleware) and php (see Do you speak my language: P is for PHP, POP, Program, Perl, Phishing, Python, Proxy)). If I couldn't afford FileMaker Pro I might go for Bento or I might even use Evernote - Software I use: More on Evernote - teaching, research and students?.

The database approach overcomes a number of the limitations of the old paper-based lab book as it can:

1. Use a 'unique' numbering system - I will admit that I borrowed this idea from my industrial sponsor and modified it. By using a unique number for each experiment I could track and label all samples and results back to a given experiment. Marvellous!

2. Be easily shared - Well, they can. If you use a file-based system you can copy the files and send to a collaborator, or do a dump of the database. If you are using some 'web-based' approach then you can open up access to a collaborator. Another plus is you can take a copy with you when you leave the lab, and leave behind a copy for your supervisor.

3. Be backed-up - It is electronic so it can be easily backed up, and stored off site (so even if the lab does burn down you still have a copy).

4. Be 'internally copied' - This is a great bonus as it means you can copy a method from one experiment to the next, and then make any modifications needed. This means you are always working with the full complete method.

5. Be standardised - There are agreed international standards for how data should be stored electronically (for example see: Guidelines for reporting the use of gel electrophoresis in proteomics, which appeared in Nature Biotechnology 26, 863 - 864 (2008) - note one of the authors....). This has the potential for making data even easier to share, and for allowing data to be mined by computers.

6. Be easily searched - Well, it is a database. It can be searched. If you have you lab book in a database you should be able to pull out every experiment of a particular type in seconds, whereas with a paper lab book it may take you days to complete the same task.

7. Be made available online for other researcher - This solves the 'ethical' issue mentioned above as once a project is finished the whole lab book, methods, results and conclusions, can be made available on-line. This means other researchers can then build on your work and really make use of all the money and time that was invested in it.

Strangely, when I started using a digital lab book (I also had it set up so it could easily produce nicely formatted printed documents of each experiment) my supervisor was highly suspicious as he thought I was trying to 'hide things'. However, he finally came around to my way of thinking and really liked the fact that all data and samples could be easily tracked and searched.

The Next Step

At present most undergraduates I see working in the labs, and nearly all post-docs, still keep a paper version of a lab book. Why is this the case when nearly all students now have access to computers? One argument that is put forward in the UK is 'patent law'. Sorry, but I don't buy that.

I have tried to explain to undergraduates for years (as part of an informatics course I teach) the value of the 'electronic lab book', but they don't seem to get it, and/or are not interested.

So, how is this going to be moved forward? How can we get a mass adoption of the 'electronic lab book'? Please post your comments below as to how this problem can be solved.

Image: The image is from wiki commons, and it is not really a lab book!

12 Comments

May 07, 2011 | 01:21 PM

Posted By: Nick Morris

Thanks to @jobadge for pointing out her work at "Online lab books for supervision of project students" (https://lra.le.ac.uk/handle/2381/9112) on the use of Wikis in Blackboard as an undergraduate lab book.

May 07, 2011 | 11:09 AM

Posted By: Nick Morris

Khalil, you are right about following what your supervisor does, however, every so often there has to be a change (otherwise we would still be using quills and parchment in the lab, and no new methods would get introduced).

The 'writing at the bench' I addressed below, the solution is to create the experiment in the electronic lab book, print it out, and then make notes on it. Later, the added notes are transferred back to the electronic system.

The move will happen one day, it has to. Whether the move will be voluntary, or researchers will be pushed in to it by the grant awarding bodies, is the real question.

May 06, 2011 | 02:03 AM

Posted By: Khalil A. Cassimally

I think one of the main reason behind the non-adoption of online lab books is because, let's face it, not many of our supervisors actually do it this way.

It's all been paper-based for the last generation (supervisors) and the move to an online medium may not be that easy. Especially if they don't see the advantages.

Students tend to follow their supervisors' way of doing research. At least, that's my newbie's experience. We adopt a somewhat similar approach and mind-set. And suddenly, an online lab book may not seem as attractive a choice any more.

Also, many (if not most) students write in their lab books while on the bench during the experiments. Just pen and paper is required. But to write an online lab book, a laptop is probably required. Still cumbersome and a hassle for most people. Tablets may be an attractive alternative. But they are just too expensive and possibly not particularly suited for note-taking at this point in time.

Thoughts?

May 05, 2011 | 08:05 PM

Posted By: Nick Morris

Shortened the long URL in the comment by Rory to http://bit.ly/lpzmxQ

The presentation at http://bit.ly/lpzmxQ is interesting and worth a look as it describes the use of Wordpress (a blogging platform) for keeping a student lab book.

May 05, 2011 | 07:21 PM

Posted By: Rory Macneil

Thanks, Nick. Re using an ELN as a teaching tool, you might also get some ideas from the following presentation by Dave Lunt at Hull, http://8736845395074351732-a-1802744773732722657-s-sites.googlegroups.com/site/davelunt/data-etc/Lunt_ELN.pdf?attachauth=ANoY7crKz_Yd2_knhd65o28BOFve1zv-WnaEZPK3p7lH66oFba4kWntuFy9BO_hs0dKRhxyp5KghHIJQ3lK6waG3_gLzmht3y2ly85QYQSq7dmUPl5T74Uj5MmE1rrLdCk4bYJMB4RKW2Ulo3A9BHHL7YrXi4vi6-xfI7JOAehhTxIaYejqZdWGTJ4V_GR0pewDZ2kGY_OVcnId8BaU5W0HZOQ1mYK7Orw%3D%3D&attredirects=0, and the following video http://www.axiope.com/electronic-lab-notebook/blog/product/?p=74.

May 05, 2011 | 06:42 PM

Posted By: Nick Morris

Thanks for the comment Rory, and thanks for the interesting blog post over at http://elnblog.axiope.com/?p=829. I like the idea of using an electronic lab notebook (ELN) as part of a course. I will have to think about that.... There might be something that can be done involving Evernote (http://evernote.com/), which although not an ELN as such could open up some interesting possibilities for collaborative lab notebook between undergraduates.

May 05, 2011 | 11:15 AM

Posted By: Rory Macneil

Thanks for the interesting post, Nick. It's sad to admit it, but there are very few days in the past 8 years when I have not thought about the question you pose! Your post stimulated me to think systematically about the question of adoption of electronic lab notebooks. I started to write my thoughts down in this comment, but they evolved into a full fledged post of its own, which is at http://elnblog.axiope.com/?p=829. Thanks for causing me to reflect!

May 02, 2011 | 04:16 PM

Posted By: Nick Morris

Thanks for the comment Mark. FigShare, http://FigShare.com, looks like an interesting project.

Any plans to implement data standards such as MIAPE, MIAME etc.?

May 02, 2011 | 02:21 PM

Posted By: Mark Hahnel

During my PhD, I got very annoyed that a lot of my research although real data and potentially useful for others to cite or use would never be seen outside of my labmeetings. For this reason I began developing http://FigShare.com

A lot of time and money is being wasted by groups around the world duplicating research that has already been carried out. FigShare allows you to share all of your data, negative results and unpublished figures. In doing this, other researchers will not duplicate the work, but instead may publish with your previously wasted figures, or offer collaboration opportunities and feedback on preprint figures.

In terms of lab books, each user has their own research page as well as an RSS feed for theire research. By plugging this feed into eg. a wordpress blog, a simple personal electronic notebook is created with all research citable. This is going to be developed further to make online lab notebooks accessible to all researchers, regardless of coding ability.

May 01, 2011 | 08:27 PM

Posted By: Nick Morris

Good couple of comments from Tom and Liz.

Great tip from Tom on the numbering. I use something similar, i.e. NMXXX, but I have added in the year, e.g. NM11/XXX. (I can't remember why I added a year in to the mix!)

Liz has a good point about the notes. I have worked around this problem by creating the experiment first in the database and then printing it out. I then add notes to the print out as I perform the experiment (the print out also acts as a check list as I work through the method), and then up date the electronic version with any changes once I have finished the work.

May 01, 2011 | 05:36 PM

Posted By: Tom Phillips

I'm starting a PhD next year and I've been thinking about an electronic lab notebook - you've convinced me it's the way to go! Probably go for a wiki-style notebook.

I'm in the process of writing up my MSci project and I've noticed all of the bad points you've mentioned. Contamination is something that especially worries me.

I would definitely recommend that everyone uses a numbering system rather than dates only, even with paper. I've found my initialsXXX, where XXX is an experiment number (e.g. TWP001, TWP002 …) works really well. Useful when organising data files too - just keep everything in a folder and prefix filenames with the experiment number.

April 28, 2011 | 10:44 PM

Posted By: Liz Ing-Simmons

The advantage of a paper lab book is that you can note things down as you work - when you're learning, this can be really important! I suppose you could just have rough notes and then copy them up, but that adds extra work. I can see the usefulness of an electronic lab book, but I think, as an undergraduate, I would still write things down on paper the first time I learnt them.

As for referring back to methods, I always referred back to the first version, rather than to a version that referred to another version...! I guess your computerised version is a bit like version control software for protocols rather than code? 'cos that would be great.

To be honest, what currently makes me unlikely to start using an electronic lab book is that I don't think I have the experience/expertise to set one up for myself. If there was a ready-made package available, for example if I joined a lab where they were already commonly used, I probably would. But I'd keep my paper notes for my personal use.