Will the iPad Replace Your Lab Notebook?

by on 5th of April, 2010 in Organization & Productivity
Avatar of Jode Plank
About Jode Plank
I earned my PhD in Biochemistry from Duke University, then did a postdoc at the University of California at Davis. I am now the Scientific Illustration Manager at American Journal Experts, where I continue to pursue my interests in visual communication of science and developing my ability to make data pretty.

The release of the iPad this week may bring the long-expected replacement of the paper-bound lab notebook by electronic notebooks one step closer. But are scientists, particularly PIs, comfortable with electronic lab notebooks?

The rise of the tablets
The concept of an electronic lab notebook isn’t anything new, and even the idea of implementing it on a tablet PC has been around for a while. However, as of six months ago, the only tablet PCs widely available were specialized laptops, with a swiveling touchscreen displays. The current crop of tablets, be it Apple’s iPad, Microsoft’s Courier, or any of the other offerings, brings us a lighter, cheaper, more ‘handle-able’ computer that many of us could see sitting beside us at the bench. The power of these machines is diminished compared to the specialized laptops, generally speaking, but still more than enough for the task. So will these technical advances usher in the demise of the paper notebook? It may depend on the software, and our expectations of it.

Physical versus electronic
The advantages of an electronic lab notebook are obvious:

  • You can search them. The information that you want is somewhere in the dozen lab notebooks of your predecessor – who wouldn’t want Google to help them find it?
  • You can copy them with the click of a button. Creating complete back-ups of paper notebooks is time consuming and laborious, which means it often doesn’t happen. Easy (or even transparent) back-ups of electronic lab notebooks allows storage of current copies off-site in case of disaster.
  • They are legible. Do not underestimate this point!
  • You can put some pieces of data in them that you just can’t put into a paper notebook. Current scientific data can take the form of movies or of an interactive, multidimentional interface (think genomic and proteomic data), that just can’t be taped into a paper notebook without the “loss” of data. (The data exists, just not in the notebook.)
  • Did I mention that you can search them? Just think how powerful that could be.

The advantages of a paper notebook are fewer but significant:

  • The book is a universal format. You can pick up a lab notebook from 1985 and read it. Try to read a 5½ inch floppy disk from 1985. Even if you pull the data off the disk, how many files from 1985 can still be read by today’s programs?
  • Lawyers love them. A prebound, handwritten notebook, properly signed, dated, and witnessed, is the gold standard for defending patents or concerns of scientific misconduct. Even though many of the high-end electronic lab notebook programs sold to pharmaceutical companies go to great lengths to ensure the integrity of the data, having cracked versions of popular mainstream programs available weeks after their release undermines confidence in these claims, at least to the non-computer science crowd.
  • They are cheap. No licenses to maintain, and no worries that the notebook will stop working if the lab has to go a year without funding.

Moving towards a universal format
Some of the electronic lab notebook programs out there have recognized that proprietary file formats worry scientists, and are moving towards more universal formats. The most popular choice seems to xHTML. This seems the logical choice – it can be read by many programs including the handful of web browsers out there. It can certainly handle images, movies, graphs, and even link to particular files when proprietary programs are required to look at the data (sequencing chromatograms, for example). And while it may evolve, the world is invested enough in it to give it the best chance of survival.

How rigorous do you need to be?
This may be controversial, but in an academic lab you may not be as worried about making patent lawyers happy as in industry. I know that academic labs patent things, and that rigorous dating and witnessing of lab notebooks can be important for other reasons, but the truth is that many labs are already violating these rules with their current paper-based system. Here is the range of paper-based notebook rigorousness that I’ve seen in academic labs:

  1. All lab notebooks used are prebound with numbered pages, any extraneous material (such as a picture or graph) is glued in, and all pages are signed and dated by the experimenter and a witness.
  2. All lab notebooks used are prebound with numbered pages, and any extraneous material is taped into the notebook. Dates are recorded for the experiments, but the pages are not signed or witnessed.
  3. Lab notebooks consist of binders, and experiments are recorded on pads of scientific paper, which are added page by page to the binder as they are used. Extraneous material may either be taped to the pages or may simply have holes punched into the edge and added directly to the binder.

Actually, I lied. Even though 1 is the most proper (rigorous) way to keep a lab notebook, I have never seen a lab that handled their notebooks this way. I’m certain there are some that do, but I haven’t seen it myself. I’ve seen some labs which function with system 2, and most that I’ve seen use system 3. System 3 works great, but only if you trust the scientist that created it. So if your lab is using a relaxed paper-based lab notebook system, do we really need to get caught up in this aspect of the security of the electronic lab notebook?

How does free sound?
With the introduction of the new tablets, developers are creating a number of programs that we haven’t really seen before: journaling programs. These programs, in broad brush-strokes, are intended for people to use to record their thoughts, insert images, and link to other files (or web pages). Do these parameters sound familiar? While they certainly don’t offer all the features of commercial electronic lab notebook programs, they do 95% of what most of us would want them to do, and they are essentially free. (If you want an example, check out this video.) Alternatively, with a little work you can use a program you’re already familiar with – Word or an equivalent – to set up your own HTML based electronic lab notebook. These programs would have the lowest form of dated security, consistent with system 3 described above, but you can’t beat the price.

I would love to hear your thoughts. Do any of you work in a lab that uses an electronic lab notebook? What system do you use, and how do you like them? How long do you think it will be before we are all using electronic lab notebooks?

27 thoughts on “Will the iPad Replace Your Lab Notebook?”

  1. Roberto says:

    Hey Jode,
    I've witnessed (and used) a lab book that works by system #1.
    In France (at least in the CNRS), research lab personnel use a gorgeous official lab book created by the Ministry of Education. And by gorgeous, I mean to drool for. It's got clear instructions on how to compile it, including why, when and what, and it's even got a fancy cover made of original manuscripts by national scientists of the past. It's amazing. You can see a PDF here – it's in english too:
    http://www.cnrs.fr/infoslabos/cahier-laboratoire/docs/cahierlabo.pdf

  2. Jode says:

    Roberto,
    That does look amazing. One thing that electronic notebooks lack is the aesthetic of a nicely made and executed paper-based notebook. Somewhere along the line Calligraphy 101 fell off the 'required courses' list for scientists…

  3. anon says:

    I was involved briefly with a project to implement a custom electronic experimental management system but it was a nightmare attempting to write a generic piece of software that was flexible enough to cover any possible experiment across different fields from biosciences to chemical and engineering sciences. Electronic signatures have been around since PGP but I don't know if a court would uphold this kind of authentication compared with a paper notebook. Litigation will probably keep scientists using paper for a while.

    Personally I am waiting for the day when the likes of Microsoft's "surface" becomes integrated into laboratory benches so the lab itself becomes a data entry/management tool with the likes of the iPad used for carrying data between workstations, but this will probably remain the domain of Arthur C. Clarke for several decades yet.

    I have recently been using zimwiki and eJourn. Zimwiki works well and immitates voodoo notes on the mac, mapping a wiki type editor to a calendar. Wiki based lab notebooks are probably (in my opinion) the best way to go for centralizing lab protocols and maybe experiment data (if secure). I find a paper notebook is still the most convenient system to quickly make notes and record observations until electronic systems become more integrated into the lab and quicker to interact with. Not to mention avoiding spilling corrosive chemicals all over a £500+ iPad!

  4. Matt says:

    The lab I work in is currently in the process of implementing the CERF lab notebook software from Recentris (http://www.rescentris.com/). We haven't had a chance yet for a hands-on (at least, not at the user level), but from what I can see, it looks like it should work out pretty well. Then again, I've been keeping a largely electronic notebook for several years anyway, typing up my rough notes into a form that can actually be read by others and integrating data figures directly into the document. I'm not anticipating that the new software is really going to change a whole lot for me.

  5. Jode says:

    Matt,
    I've seen this program and others like it which seem to store individual experiments using templates. Is there a place in this system where the researcher has a narrative? For example, "The efficiency of reaction x has dropped from 80% to 40% in the positive control reactions, making me think that the substrate has deteriorated. This set of reactions will test the old substrate against a new batch from supplier A." Or does one extract the rational for a particular experiment from the fields and the context of the files (what the person did the day before and the day after)?

  6. Caroline says:

    Personally, I'm hoping that the guys at Mekentoj try their hand at it. One of the first programs they wrote was for a lab organizer, though they never put their full weight behind it.

  7. Kurt says:

    The software is a lot more interesting than any hardware solution for electronic lab note books. Touchscreens have many disadvantages in a lab, it's better to lift the expensive screen from the bench and use a liquid protected keyboard instead.

  8. Ponzonha says:

    I have my (paper) notebook next to my laptop and by looking at it the answer is straightforward:
    NO.
    ¿Reasons?: Acid spills, burns and too may falls. I doubt the iPad would resist a normal lab use.

  9. Jode says:

    Interesting – I guess my notebooks are leading a blessed existence!

  10. Bonnie says:

    I love the idea of a searchable lab notebook, but it would take some serious effort to switch over at this point in my career. I still use a paper planner because I can't be bothered to open up google calendar, so I'm surely not going to want to wait for an ipad to wake up and open up my notebook program every time I want to write a number in it.
    Bonnie
    http://www.stem.ws

  11. Matt says:

    Jode,

    From what I can tell, CERF functions primarily as a database linking the various documents for an experiment together. For instance: a word document detailing the protocol, an image of the resulting gel, and an excel file containing the quantification. All of the files get stored together with a date/time stamp, which serves as the verification of when you actually did the experiment. So, the information that it contains regarding purpose/hypothesis and results will ultimately depend on what the researcher making the entry puts into the associated files. (I think I got that all correct).

  12. Jode says:

    Matt,
    Thanks for the explanation – that helps.

  13. Rob Day says:

    Matt and Jode,

    I am head of business development at Rescentris. We hope that Matt will enjoy using CERF and we invite him to contact us if he has any questions. Jode, CERF does function somewhat as you say, but it is more than just a database. The interface allows you to arrange files from absolutely any source, in absolutely any format, along with your notes, annotations and comments from reviewers in a way that really tells the story of your research from start to finish, regardless of what kind of data you generate. The finished product can be printed, yielding something that looks a lot like the lab notebook you use today, but with no cutting and pasting. Finished experiments can be instantly converted to templates that make your next experiment faster and easier. Data can be be automatically gathered from instruments, emailed in from any location, or drag and dropped right onto the virtual notebook page. We already have some functionality for the iphone and ipad and we are pushing quickly ahead with the development of our dedicated ipad client, that we believe will revolutionize the way scientists work and record their lab data.

  14. Rob Day says:

    To see some screen shots of the iphone / ipad functionality that the CERF ELN has today, check out the "mobile access gallery" at:

    http://www.rescentris.com/Screenshots.aspx

  15. Chen says:

    Well, I am almost a year into my PhD program and I am using word as my lab notebook, period. Even though it's a time consuming process, it's the only way I am willing to work. At the bench I am scribing all my notes on a draft paper and then copy it into a GLP-like template of word while on the road back home. it's also helping me process the day at the lab and the obtained experiment's results. I have numerous backups, I usually find anything I need in a matter of 10sec (using google desktop, which also digs PDFs). The ppl at my lab think I am crazy…
    Oh, and of course I am also printing and archiving every journal entry in a Binder for the meetings with my PI.
    Chen

  16. JQP says:

    "You can search them. The information that you want is somewhere in the dozen lab notebooks of your predecessor – who wouldn’t want Google to help them find it?"

    WRONG, sort of…Google can't find a thing if the information was never entered. Two, you can search paper notebooks, the process is called "reading"

    The notebook is SUPERIOR to any electronic format for this reason, archival reasons. You can search anytime, anywhere, you don't even need electricity to use one! The language will remain the same, no programs, no converting, nothing.

    Electronic media is only as good as how often it is backed up. Even then it is not perfect. As long as your building never burns down, you will NEVER have to worry about your paper notebook. Electronic has so many unsafe variables. Plus, it takes longer to use it.

  17. Jode says:

    JQP,
    I think you missed the point – Google could be used to search them if they were electronic, and reading is required for either format. And you cannot read a physical notebook anytime, anywhere. You can only read them in the lab where they live (unless you have made copies). However, electronic formats can be taken anywhere required, provided the PI has given his or her blessing. On top of that, fires (and subsequent water damage) occur with disturbing frequency in research buildings.

    Electronic formats have their issues – as I detailed – but not these issues.

  18. Avatar of Jode Plank Jode Plank says:

    On another post, Rory wrote:
    "An observation about your ealier post is that both you and the people who commented focussed on the utility of electronic lab notebooks for the individual researcher. Its obviously the case that ELNs have to be easy to use and attractive to individuals (or they will never get adopted), but the real utility of ELNs is in the value they add to the group, by making it easier for people to share and search for the full range of types of information dealt with by the lab, including experimental data. It would be interesting to get your views and those of your commenters, on this aspect of ELNs."

    I completely agree with your point about the collaborative power of ELNs, and I think this (along with greater financial resources) is the reason why industry has been quicker to adopt ELNs than academic labs. While there are certainly exceptions, I think academic labs are less collaborative. When the lab is full of trainees, be it grad students or postdocs, there is an inherent focus on individual achievement rather than the completion of a project, as it is in industry. Some of this may be by design – you will never master the nuances of protein purification if you don’t do it for yourself, even if your labmate could get the job done faster and better. The other aspect is purely the nature of the system – the first-authored papers that a trainee produces are taken as the evidence of their training, so spending a significant amount of time advancing other’s projects wouldn’t likely be a wise career move. That is why I think the aspect of the collaborative power of ELNs that would most appeal to the average academic lab wouldn’t be the lateral exchange/management of information (between current members of the lab), but rather the linear exchange/management of information (between a previous member of the lab and the trainee(s) that are continuing the project). Admittedly, I have an academic perspective on the world (since that is where I currently ‘live’) so I don’t think I gave the collaborative aspect of ELNs enough of a discussion in the post.

  19. Avatar of Matt Plantinga says:

    We've had a little while now to use our electronic notebooks, and overall they're working out quite well. In reference to the title of this article, we are somewhat eagerly anticipating the release of the iPad app for the software so we can actually take our electronic notebooks to the bench. It will be quite nice not to have to print out all the planning sheets, which should save a good many trees over the years.

  20. The prerfect thing to get, even on Mac OS X, would be the E-Notebook sold by Cambridgesoft. They only have the version for windows. It can be centralized on a server, all the computers connected to it. It has "tabs" to put the NMR spectra of your compounds, the IR. It has a wonderful tree structure. I can write a reaction saying what are the reagents and the products, the catalyst, the equivalents and then I obtain all the necessary data. It is very neat.

    Somebody know some cheaper equivalent ? the commercial version for windows is way too expensive I don't mind to pay a resasonable price for a piece of software like this.

    1. CERF includes optional livescribe integration.

  21. Avatar of poorpostdoc poorpostdoc says:

    Personally, I've gone to using Livescribe notebooks (http://livescribe.com) after being left with a paper copy of my 14 graduate notebooks, which are fun to search through. Though my handwriting could be better, the Livescribe does a decent job at searching it. When I leave – originals go to the boss (if I'm nice, a searchable PDF version too). Drawback – it's a spiral bound notebook, and things pasted in – gel images and such – aren't in the electronic copy.

  22. Avatar of Matthew Matthew says:

    I'm a molecular biologist in a University-based lab. After searching around (a lot) I've now settled on using Evernote (http://www.evernote.com) as my lab notebook. I've been using it everyday for the past few months and I really like it. Whilst I was looking around the options for ELNs I found they fell into two main categories, they were either too structured and designed more for biotechs or else they were too simple and effectively just a glorified word document. I liked Evernote because it was intuitive, cross-platform (I use a mac at my desk, an iPad on my bench and a PC at home) and it has all the features I need. There are some things which will always be easier to just scribble on a bit of paper, but now I can just take a picture of those scribbles and Evernote's text recognition function will work its magic.

    For the past few months I've happily been using the free version, but am now considering upgrading (£2.50 a month for academics) as it increases the number of file types I can import.

    I am in no way connected to Evernote, I just think it fits my needs really well.

    And more generally, ELNs are a great improvement over traditional lab notebooks. The ability to search, make templates, tag and generally to organise your experiments has been really useful to me and I don't think I'll ever go back to a written lab book now.

    1. Avatar of Brian Brian says:

      I have thoroughly enjoyed this discussion on ELN, and wanted to pick some brains here. I teach high school science and have been tasked with setting forward the schools progression to ipads as digital textbook and other uses.

      I wanted to pick Matthew's brain about using evernote as that seems like the easiest and cheapest way for a school on a limited budget to implement an ELN. I look at CERF but that is obviously far beyond what we could implement.

      My e-mail is bkays@stlucys.com

      Thanks,

      Brian

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