The electronic lab

Jul 26 2011 Published by under Careers, Things that go beep!

When I was but a wee undergrad all lab work had to be diligently recorded in a lab notebook. Not on a piece of paper, even if for later transcription into the notebook. Directly in the notebook. That was how it was done.

When I was a slightly older graduate student TAing (demonstrating we called it) in the undergrad labs, that was the mantra I preached. Thou shalt record all in the lab notebook. Thou shalt not write on pieces of paper. Writing on a filter paper is right out. And of course I obeyed these commandments in my own lab work.

When I was a postdoc, ditto.

So when I started my own lab, that was how things were to be done.

Times are changing. Many of the instruments we now use are controlled by computers, so the data is on the computer. Other data is entered into tables, plots, spreadsheets on lab computers. The people entering science now are more comfortable typing than writing. The days are numbered for the traditional lab notebook.

Hence the rise of electronic lab notebooks (ELN's). ELN's promise all kinds of wonders. Data from instruments ported directly into the ELN. Notes typed directly in and linked to the data. All data and notes searchable! This last is a BIG DEAL. Ask anyone who has had to search through an old lab notebook (theirs or someone else's) for something. A search function is invaluable.

I'd like to move my lab into the electronic era. Problem is, ELN's are expensive. Or use proprietary formats for saving the data. Or are designed for large organizations, not a small academic lab. Or all three. Yes, there are some free ELN's out there, but such are of uncertain future (not that any system is guaranteed to be around for ever).

So what to do? I've poked around and solicited opinions. Aside from ELN's, some people use database programs such as Filemaker Pro with a template designed for lab note taking and data integration. Bento, a no frills database program made by Filemaker, looks like a potential option for Mac-based labs. Of course these are more file management options than true data integration approaches. Another option is a wiki. Or even a WordPress site optimized for lab data storage and sharing.

Any of these could work, but of course I don't want to adopt an option that turns out to be a pain in the butt or is later found to be too limited. And yes, I am aware of potential intellectual property issues with "improper" lab notebook/data storage.

So I'm asking for input. What have you used or tried? What options have you heard about? Let me, and any interested readers, know by posting a comment.

26 responses so far

  • martini says:

    We use Evernote.

    The key is that no matter what, the electronic notes are printed out daily and glued into a regular notebook for posterity. Even if you lose the program that runs the ELN, the data is still in tact. If you are really paranoid, you can make PDF's of all the printouts since they will still be searchable.

    MediaWiki is also another option, and again, for posterity, simply print out the data. You can also use Semantic Media Wiki and Forms to make lab book "forms" for structured data sets. In theory media wiki can handle all types of files with no problem. If you own the server, then file size is not a concern. Just back up the SQL database to an off site loclation periodically.

    For large data sets, both Evernote does not work well, but a well organized file server does work well.

    • odyssey says:

      Evernote is an interesting idea, although I would be a little concerned about the security of all that data being stored in the cloud like that.

      You're right about a file server. I left that part out of the original post. In a way what I'm really looking for is a front end or GUI for the server that integrates everything.

      • Never thought of using Evernote for a lab notebook. The good thing with Evernote is that it's not stored solely in the cloud. A copy remains on the computer running it. When connected to the cloud, any differences between the cloud version and the version you're running are labeled as 'conflicting changes'. Plus you can back up as html or xml.

        Unless your concern about the cloud regards security of private data--the data is encrypted but I'm not techy enough to understand how secure the encryption is.

  • Sideshow Bill says:

    One thing to remember about your lab notebooks is the ability to verify in a court of law, the creation date, the author, any changes, etc. Unfortunately that gets really interesting for the lawyers, which means things get really clunky and difficult.

    At a previous company, we had a system where you could log onto a server and "print" to it. It created a secured .pdf, witnessed with electronic signatures by both the investigator and a witness. It was a PITA and few people ever used it. (Or documented things anyway.) Of course that was a couple of years ago and I'll be interested to see any responses and see what's new since the company lab I've built is now looking into ELN's.

    I'd also be interested in any combination ELN/LIM systems out there.

    • Bill, some of us in academia have bigger things than notebooks to worry about if we are called to appear in a court of law. Some ELNs are perfect for industry but can become a giant pain in the neck some of us academics that are just looking to record some notes and not ambitious enough patenting stuff.

    • odyssey says:

      As GR noted, these things are not always as important in academia as they are in industry. Nonetheless, I would want a system that records dates of creation and alterations.

  • Sideshow Bill says:

    also, anyway to set this up so that you get an email when the thread is updated?

  • docstymie says:

    We spend so much time printing stuff out from computers and pasting them into our regular notebooks that it makes no damn sense - except our attorneys are afraid the electronic ones won't stand up in a court dispute. So, we have to continue wasting time...

  • TheGrinch says:

    Lab notebooks are a pain in the ass, especially for us since we do computational work. Recording it in the notebook is like asking mankind to go back in the caves.

  • D. says:

    Digital pens in combination with Evernote/Onenote.

    • odyssey says:

      The digital pens are appealing since you get both the paper and electronic copies of your notes. Evernote however isn't optimal for large amounts of data.

  • Andrew Morton says:

    I'm in the same boat. Hate lab notebook and always on the lookout for an ELN alternative. I'm trying out the free version of this web-based solution: Axiope eCat ( Confess, I haven't fully migrated to it yet, but at least I can try this one out for free. I think there's a groundswell of interest now in affordable (or even free) ELNs for mere mortals for a properly designed system like this to take root. I can't be bothered hacking together an improvised solution with blogs/wikis or even Evernote. The lab next to ours have fully switched to using it, and swear by it.

  • odyssey says:

    Thanks for the suggestion. I'll have a look at eCat. Let us know what you think as you try it out.

  • Dr. O says:

    Bento looks really promising. I've been using word processors (Word, now Pages) to type up my lab notebooks for years, printing them out to create hard copies and using spreadsheets to compile the data. This seems like a nice way to integrate those older files into a database with newer files organized into projects...from what I've seen so far anyways. I'm downloading the free trial right now and will play around with it for the next couple of months to see what I think. Maybe then I'll write up my own blog post on the experience...

    • odyssey says:

      I'm kind of liking Bento right now. Simplish interface - very Mac-like - and very cheap (family pack of 4 licenses is only $99). There are also iPhone and iPad apps. The big downside so far is apparently only four computers can share a database. If it's literally four computers simultaneously, rather than four set users, that's probably not too much of a limitation since it's unlikely that all my (not much more than 4) peeps would be accessing the database at the same time.

      • odyssey says:

        Well, Bento won't work for me. Because of the way it links to files, you can't store the database on a central server and share it in a way that allows users to link their data files in a usable manner. Not really surprising since the program was really designed for home and limited small business use.

        It is nonetheless a very cool personal organizer.

  • tony yuan says:

    Odyssey - Try OLN Cloud, which is free to Academia, running on all platforms, including Mac, iPad, Android and Chromebook ...

    • odyssey says:

      It's free for 200Mb per person storage, but many labs would blow through that in a month. Or less.

  • It's not broadly applicable, but Seurat (now distributed by Schrodinger) looks like a useful tool for those doing a lot of small molecule screens. It allows users to link chemical and biological data to a structure and create customized reports. I've seen a brief demo for it and it seems pretty powerful for pharma, biotechs, or high-throughput screening/drug discovery centers in academia. That being said, I have no idea how much it costs.

  • [...] lab notebook This tops the list of recent searches. Not so long ago I had a post about electronic lab notebooks and a commenter noted Evernote was a possibility. One of my trainees talked me into trying it. So [...]

  • Paul Plotsky says:

    I have been following ELN and ELN-like solutions for small academic labs for years, but have yet to commit to a particular solution. Most of the commercially available ELN packages are really geared for commercial labs and are simply too complex and expensive for a single academic lab. My ideal would be to completely switch to iPads in the lab and have them linked to an in-lab server to host notes, general databases, etc, probably using Filemaker and Go. Has anyone tried this yet?

  • I am currently working on a solution to this problem which I hope you will find interesting. I am developing a website called labscene that will allow you to post all of your experimental data to our mediawiki based website completely for free. You can have your own profile and will be able to manage all of you data and even search other data that might be relevant to your research.

    We are currently in development but if you would like to keep track of our progress you can come sign up and give us feedback on. We could certainly use some beta testers throughout our development process.

    Thanks for the post and your interest in electronic notebooks!

  • Luisa says:

    in my experience, i would say stick to paper-based laboratory notebooks. it may be technically easier to transfer data among ELNS.. but aside from speed, paper-based notebooks help me collect and organize my ideas in my own way. Its a lot more flexible, and also, when using ELNS, it can be easy to become dependent on electronic systems, which can lose data instantly. Stick with what you feel comfortable with personally, attempting to adapt to new platforms can prove to be counterproductive in my experience 🙂 Good luck!!

  • Ryan says:

    Here's a review of the Labguru ELN in The Scientist based in the Mair lab at Harvard's experience.

  • […] team also highlighted that an ELN will enable scientists to work harder, smarter and faster.  We showed that this impacted the bottom line directly by first calculating an average hourly […]