Bench Press

During the past month’s global swine flu emergency providing health care professionals around the world with accurate information was critical to understanding and potentially containing the outbreak. The time sensitive nature of dealing with an emerging disease highlighted the importance of developing an effective communication channel that is quick, accurate, and accessible by numerous individuals. Traditional paper distribution channels, mailing notifications to primary care physicians, can delay the receipt of time sensitive materials by 72-96 hours. Thus, the question becomes how do you design a system that can be accessed quickly and easily by a maximum number of health care professionals, while still providing quality information.

A new web application developed by the Indiana Health Information Exchange (IHIE) interfacing with a service called Docs4Docs®, provided by the Regenstrief Institute, appears to have answered that question. The IHIE’s web portal allows electronic communication of public health messages to any registered health care provider. Registered users can also send messages back through the portal to be disseminated across the network. The web portal’s simplicity allows it to bridge the gap between paper-based and electronic-based medical offices thereby ensuring that even doctors in rural areas without advanced IT infrastructure can receive and contribute critical information.

Docs4Docs® also leverages the Indiana Network for Patient Care (INPC) which is a secure community health records system, providing patient data whenever needed. Dr. Shaun Grannis, a Regenstrief researcher, explains “[b]y working with our public health partners to seamlessly deliver public health alerts in precisely the same manner that physicians receive time-sensitive clinical information for patient care, we ensure that physicians have the right information at the time they need to see it”. This was exemplified by the first electronic health alert sent out across the Docs4Docs® network with regards to the emerging H1N1 crisis on April 29, 2009.

Last year Regenstrief scientists received a $10 million, 5 year contract from the Centers for Disease Control in order to continue working on developing electronic records and notification systems like those that make up the backbone of the Docs4Docs® service in Indiana. I for one believe that money is going to good use and look forward to seeing other states follow Indiana’s lead with regards to developing new electronic records and notification systems.

Cameron Neylon wrote a great post about the difference between recording and presenting data in an online lab notebook. The whole post provides a great analysis of the differences he sees between LaBLog, the UsefulChem wiki and the basic philosophies behind their use.

The end of Cameron’s post really got me thinking about the possibilities that a “presentation layer” could have in an online lab notebook. I envision a presentation layer that leverages recent innovations in webapp technology to automatically generate a flowchart-like view of all posts/data/experiments contained within one’s notebook. This graphic would be interactive, customizable, and could be coupled with methodology excerpts in order to provide a complete view of experiments over time.

Much like the grouping of messages by conversation in Gmail provides an innovative and more intuitive organization of e-mail, I feel that a graphic of this sort would be an intuitive manner to deal with the somewhat fragmented nature of online lab notebooks without too much editing after the fact. It would make it easy to visualize branches in experimental thought or dead ends. While also consolidating experiments for viewing by people with access to your online notebook. Ideally providing an accurate representation of work flow and thought process.

I suspect coding something like this wouldn’t be the simplest task and there’s definitely a fair amount of kinks that I’m sure would have to be worked out. Regardless I’m excited to be able to think about the possibilities that online lab notebooks will bring to science over the coming years.

Neil Saunders recently wrote about the the difficulty some people find in keeping an electronic notebook; over the past year, during my rotations, I’ve used both paper and electronic notebooks, and I’ve come to one conclusion: whatever you can make electronic, make it so. Trust me, it’s worth the effort.

First, a bit of context. I’m an experimental biologist, not a computational biologist (at least, not primarily computational), so I have to deal with the fact that not everything in my research can be “electronified.” I’ve got samples in the freezer, vials of things in the fridge, cultures going in the incubators, and so on. Thus, I’m not looking for a notebook where I can keep every single bit of my research; maybe when the Matrix Google finally digitizes all of reality, I can finally just plug into my computer and never leave my desk.

On the other hand, though I’m not a computational biologist, I am pretty comfortable with computers. I program, I know HTML, and I can use Photoshop pretty quickly. I’m fine with cobbling together my own electronic lab notebook of sorts from the tools I can find on the internet (such as making a wiki); others (such as some in my lab) might find even formatting a wiki post to be an intimidating prospect. So what I do might not work for you.

Right now, my lab has an internal wiki using the MediaWiki engine, and I’ve been using my wiki space as my lab notebook. The wiki is backed up regularly, is password-protected, lets me view and edit the wiki from any internet-connected computer, has full-text search built-in, and has an editing format lets me put in cross-references to other entries; this is all I generally need for a lab notebook.

How do I manage the offline stuff, like gel pictures, data sheets, and so on? Well, I can put a surprising number of things on the wiki (for example, the lab next door lets me use their UV transilluminator, which has a CCD camera that I use to save TIFF images of my gels onto my network account), but basically I keep everything in a giant binder, numbered in order by date, and then put a reference to it in the online notebook. That way, I can easily find a result; just search the wiki for the entry I’m looking for, look up the reference number, and then find it in my binder of results. I do something similar with my experimental samples; my initials, followed by an experiment number, and then a vial number (such as “EJS-109-10″).

Unlike some people, my note-taking philosophy is that the lab notebook shouldn’t necessarily be a dirty log of absolutely everything that I do or think about while I’m in the lab; I don’t put in routine calculations or procedures, such as cell culture maintenance, making common reagents, and so on. The whole point of a lab notebook is so that I can keep track of what I did, so if I, or someone else, needs to look up what I did, or what’s in a vial in the freezer, I don’t have to spend hours trying to remember what I meant with “RfMQ2-3a-4-5-07″ on a tiny tube cap.

Sure, it’s sometimes nice to have everything in one lab notebook, gels pasted in and so on, but frankly, I find that even just the organizational benefits of being able to read my own handwriting and being able to search and cross-reference my posts to be worth giving up the all-in-one solution. When I kept a paper notebook, I spent so much time flipping back and forth between pages trying to remember where I’d written the concentration for the vial in my hand. Now, I just search for the vial number and voila!

Not only that, but I like to organize my lab notebook by project, rather than chronologically, because I generally have more than one thing going on at the same time. Organizing that way is doable on paper if you use a binder and loose-leaf paper, but still quite a hassle, especially since some experiments don’t always fit cleanly in one project or another, making it hard to find later (“Did I file it under this project or the other one?”). I prefer the electronic notebook, which lets me organize by both time and project, and lets me put experiments under more than one lab notebook by simply putting a link to it from both project pages. Not only that, but if I’m repeating an experiment with slightly different conditions, I can simply copy-and-paste a previous experiment and change just a few things.

Paper just doesn’t cut it for me anymore. If I were keeping a paper notebook, I’d basically be doing all the same things as I do on my electronic notebook: a loose-leaf notebook organized by projects, numbered experiments, separate binder of raw data, cross-referencing based on page numbers or experiment numbers, and so on. My online notebook does all this and adds remote access, readability, copy-and-paste, and searching to boot.

Not only that, but because my lab notebook is online, if I’m writing a paper or making slides for a presentation, I can be lazy and work from home. Win for the web!