Focus
Student Scene
January 21, 2002
 Alex Carter Photo by Graham Ramsay |
A S.L.I.M. Chance for the Evolution of Lab Research
I walk into the darkened lab and turn on the lights."Good morning, Slim."
"Good morning, Alex."
I sit at my desk to review the day's agenda. "Slim, show schedule, please." On my computer I see exactly what tasks I need to perform--and when--to complete the experiments I currently have going. Slim reminds me of a departmental seminar I want to attend at noon and a teleconference later with some collaborators in Africa.
As I'm putting on my lab coat, Slim inquires in its impossibly calm voice, "Would you like to begin an experiment?"
"Yes. Experiment number eight-seven-three."
"I'm sorry, Alex. That number is already in use." Pause. "Would you like to use eight-seven-four?"
"Yes." Today I need to purify synaptosomes from brain tissue. I instruct Slim, the Scientific Laboratory Information Manager, to put my synaptosome protocol on screen. Almost instantly it is displayed on my hand-held Palm device, and I begin to make up the solutions I need. As I weigh various chemicals I swipe the container's barcode in front of the balance's sensor. The balance relays how much I have measured of each chemical back to Slim, who records all of my actions in my electronic notebook. Similarly, as I make up solutions, the beakers and graduated cylinders report to Slim the volume of liquid they contain.
A warning chimes. "Alex, you have made solution C at twice the specified concentration. Do you want to continue?"
"Show history," I request. Slim lists on my Palm all of the steps I have performed in this experiment and, sure enough, I've only added half as much water to solution C as is needed. Good thing I É Slim caught that. The first time Slim corrected me, I told it to go run a diagnostic test on itself. I've since learned not to argue with Slim, but I do still check on it.
Many Birds, One Stone
My current project involves determining the biochemical composition of neuronal connections in the brain and requires that I measure the levels of dozens of proteins, the modifications they have undergone, and their interactions. I can't believe that when I was a graduate student I had to painstakingly analyze one protein at a time, hoping that I was focusing on the right one. Now, in the proteomics era, I can grab one of these little tailor-made protein chips and screen a hundred proteins at once. What used to take months can be accomplished in a couple of weeks. Of course, biotech companies are promising new chips that will screen tens of thousands of proteins at once. I'll believe it when I see it.All of my reagents are ready. I pull on my driving gloves. "Slim, switch to Cloning Mode." As I begin my experiment at my bench, two sets of robotic arms come to life in the automation chamber across the lab. I've loaded the chamber with all of the materials I'm using at my bench. By monitoring the motion of my sensor-laden driving gloves, Slim can direct the robotic arms to repeat the same procedures. Hence the Cloning Mode allows me to rapidly repeat my experiment in triplicate even though I'm really only doing it once. The marriage of virtual reality and robotics has finally brought us as close to being in two places at once as we're likely to get. Time is still of the essence in the race to publication. That has not changed.
I'll Wait for the Movie
My experiment is now running, and for the next hour I watch video abstracts of the latest literature in my field at www.VideoPubMed.com. As journal articles have become increasingly available online at no cost, research labs have had less of an incentive to renew individual subscriptions. The journals have responded by developing internet video channels sponsored by the big suppliers of scientific equipment like Nikon, Molecular Probes, and Fisher Scientific who are always looking for new ways to plug their products. The VideoPubMed newscaster announces after each segment, "The data in this study was brought to you by Zeiss" or MJ Research or whoever. VideoPubMed has become a kind of CNN for scientists, and video has proven quite useful for the presentation of data on dynamic processes that defy the static printed page.Managing the Data Diaspora
As I flip through the video abstracts, I download the most interesting research papers and use Slim's information visualization utility to stay organized. I simply draw a line between the icon for an article and any other files within our server. The next time I bring up the category Alzheimer's, for instance, I will see all the downloaded papers and all the experimental results that I have linked to this topic radiating from the Alzheimer's icon like the spokes of a strange bicycle wheel. When I click on any icon, it moves to the center of the wheel, and all the other files and categories associated with it move out to the periphery.There used to be a time when only astronomers, physicists, and computer modelers working with the most advanced supercomputers had to worry about managing huge data sets or complex experiment schedules. I remember when our Slim was first installed. Many biologists said we were wasting our time worrying about data and experiment management. Biologists thought they might just continue as they always had, cataloging every result with pen and paper, even though new technologies were generating data at an ever increasing rate. This denial was eventually crushed when a few pioneers made clever modifications to existing laboratory information management systems. These labs showed they could reduce human errors, increase productivity through automation, and provide researchers with new conceptual tools to manipulate and organize data in its various formats. Technology has opened the data floodgates and only the creative use of technology can channel that flood so information can be replaced with real understanding.
"Alex, the department's noon seminar will begin in ten minutes," Slim reminds me. I could watch it online, but instead I head to the seminar hoping to meet up with some of my colleagues from across campus. I also hope there will be coffee and cookies. Some things technology still can't replace.
--Alex Carter, an eighth-year MD--PhD student in the neuroscience program at HMS
For some examples of the technology described here, visit www.limsource.com for the state of the art in laboratory information management systems and www.thebrain.com and www.pnl.gov/infoviz for advances in information visualization utilities.