October 27, 2005

Refreshing look at notebook management

HubLog: NotePress

I wish NotePress was available to me when I first started in grad school. It would have helped me tremendously. alf, as most of you probably already know, has been developing some amazing web applications and others that I dare not try to describe--I won't do it justice. As a user, I am very impressed with his work in making science more efficient, at least on the digital end. Don't just take my word for it, check out hubmed.org for yourself and start creating your own RSS or Atom feeds of any literature query you wish. Punch in those RSS feeds into your favorite RSS aggregator and feel the power of how to keep "current" with your field's literature.

NotePress, I gather without having yet tested it, is probably one of those applications that could be as useful as hubmed. Imagine being able to put NotePress behind a firewall, in your lab's intranet, and be able to pull up your experiments in your boss' computer without needing to physically be in the lab. It could really facilitate discussion and even planning: your mentor could make notes on each experiment at his/her leisure and direct the course of each experiment (so long as you follow them ;-). As alf has alreadly mentioned, however, experimental data will need to be organized using other tools. I wonder if somehow MS OneNote could be integrated to provide files via a remote interface?

Although a number of programs have been developed, notebook organization still does not have a dominant, highly recognizable player, like there is for bibliography management. The difficulty, I guess, lies in the ability to manage digital experimental data, as well as physical materials in a cohesive, coherent manner--there isn't really any good substitute for pen and paper. Add on top of this complexity the fact that labs do things differently, depending on where you're at and on the type of science, and you quickly realize why software companies would rather not get into that. I've always believed that the scientific community would benefit from developing widely recognized open standards that are easily implemented and understandable for digital lab notebook management. I figure as a start, one could begin with GMP and GLP standards and work on how each stage can be addressed digitally. It could also be rewritten for general lab practices, independent of the type of science performed. It's not yet clear to me the best plan of attack on how to accomplish this yet, but the end goal is to provide a framework where developers have clear ideas as to what the scientific community needs in a lab notebook. This will ultimately facilitate database design and management, interface designs, etc. And by being a widely accepted standard, it'll be easy for scientists to move from one lab to another, and to disseminate the information for more timely discussions--"real time science" discussion as my one thesis committee member liked to describe it. It's only a matter of when this will happen, not if. I'm sure that if I spent time looking up the literature, there probably are already a dozen proposals. alf may have already written something up that I haven't yet seen?

Finally (off-topic), I realize that I have not been blogging for quite a while now. Things were a little quiet on the science-front and I was pushing hard to finish up my PhD. I have defended and have now moved on to the final leg of my training in the program. So essentially from this point on, I will no longer blog as the "Struggling Grad Student." In fact, this is probably the last, if not next to last post (notifying you of a new blog, if I decide on doing a new one). It's been an interesting learning experience for me after writing this blog and after reading the tons of science blogs. Farewell for now, and happy hunting.

Posted by johnvu at 12:03 AM | Comments (0)