« Going Solar in the Snow | Main | Friday Catch-Up (12/23/05) »


bioroot.jpgIn Open Source Biology, what typically gets shared is information, whether manifest as the sequence of a microbial genome or a process for transgenic biotech. This is why sites like The Synaptic Leap and BioForge are so useful: they provide a medium for that information sharing, with clear rules and methods. This more or less parallels the world of free/open source software. But unlike programming, bioscience requires more than information and basic equipment: it requires materials with which to work. Antibodies. Plasmids. Microbial strains. And most of the time, these materials cost money. This is where BioRoot comes in.

BioRoot is a free online database service for biolabs with two primary goals: it provides a powerful web-accessible lab materials database, allowing scientists to better keep track of what they have and what it can do; and it allows participating labs to list what they have that they don't need, and would be willing to share.

As molecular biologist Bill Hooker observes, bioscientists are in a bit of a trap: very often, they can't be certain whether a given plasmid (etc.) will actually work for their experiments, but the suppliers nearly always sell the materials in relatively large quantities. You may only need one blot of a certain antibody to see if it works, but that antibody only comes in quantities that work out to 40 blots. If it doesn't work, the material gets stuck on a shelf somewhere, and possibly forgotten. With BioRoot, that material you can't use can become a valuable part of someone else's research:

When you enter a reagent into a BioRoot database and set it's visibility to WWW (as appose to Lab Mates or Private), everybody can see the reagent. It is effectively published. Folks will pull up tube #25pZyx in their searches and contact you to ask if you would be so gracious as to send the reagent along. Maybe an authorship will come out of the collaboration, maybe just a favor that could be returned when you are interviewing for a job. For the first time, your unpublished reagents have tremendous value and they will get the careful treatment they deserve.

This isn't quite the same as sharing programming modules on SourceForge, but it effectively adds a shared-material collaboration layer to bioscience research.

BioRoot is the creation of David Nix, a computational scientist at Lawrence Berkeley Labs and Affymetrix, and the author of a number of F/OSS applications for biological research. Nix clearly has feet firmly-planted in both the computer and biological science worlds, and sees where they can connect.

In my post about The Synaptic Leap, I suggest that TSL could be an early indicator of a broadening of the open source bio concept, with "smart bio mobs" not far behind. Open source bio pioneer Rob Carlson wrote to pursue the idea a bit further, noting that the material needs of bioscience give it a qualitative difference from software development. BioRoot both underscores that observation and suggests one kind of solution. Sharing reagents may not be identical to sharing code, but they both come from the same philosophical source: open collaboration can change the world.

(Thanks for the tip, Bill Hooker!)


Listed below are links to weblogs that reference BioRoot:

» Smart reagent swapping center from Smart Mobs
BioRoot.org provides laboratories with accounts that they control through which they can make it known that they have excess reagents available that other labs can put to use. This free service of a non-profit organization seeks to save time, increase... [Read More]


This page contains a single entry from the blog posted on December 22, 2005 2:17 PM.

The previous post in this blog was Going Solar in the Snow.

The next post in this blog is Friday Catch-Up (12/23/05).

Many more can be found on the main index page or by looking through the archives.

Powered by
Movable Type 3.34