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BioDASH and BioHacking
Jamais Cascio, 16 May 05

biodash.jpgBioForge.

Systems Biology Markup Language.

Open Source Biomedical Research.

We are rapidly moving into a world where biology can be as manipulable as data. After all, DNA is code; life is information. The new tools and methods we're developing for bioengineering reflect this parallel, and the philosophies underlying the "hacker" ethic (in the original sense of someone devoted to exploration, invention and discovery) are being absorbed by the biological disciplines.

But whereas the original software hackers had to settle for the primitive tools of the 1970s and 1980s, today's biohackers can take advantage of far more sophisticated networks and collaboration tools. The latest example of the infusion of the information society into biological engineering is BioDASH -- "a Semantic Web prototype of a Drug Development Dashboard that associates disease, compounds, drug progression stages, molecular biology, and pathway knowledge for a team of users." As the announcement notes, this is the first step of a work-in-progress, and the developers hope that as people get more familiar with using the Semantic Web for life sciences, more applications will emerge.

(What is the Semantic Web?

The Semantic Web provides a common framework that allows data to be shared and reused across application, enterprise, and community boundaries. It is a collaborative effort led by W3C with participation from a large number of researchers and industrial partners. It is based on the Resource Description Framework (RDF), which integrates a variety of applications using XML for syntax and URIs for naming.

"The Semantic Web is an extension of the current web in which information is given well-defined meaning, better enabling computers and people to work in cooperation." -- Tim Berners-Lee, James Hendler, Ora Lassila, The Semantic Web, Scientific American, May 2001


...That is, it's an emerging standard making information sharing and collaboration across disciplines and organizations simpler and consistent.)

Why is this important? Because, as Rob Carlson notes in the current Wired, the tools for doing sophisticated biological research are getting incredibly inexpensive, and more people -- in the West and in the leapfrog nations -- will be experimenting with biohacking. And standardized ways of sharing information and applications greatly reduces the risk of accident.

Carlson writes: "The advent of garage biology is at hand. Skills and technology are proliferating, and the synthesis and manipulation of genomes are no longer confined to ivory towers." The development of information systems like BioDASH will make that garage biology simpler -- and safer -- than ever before.

(Via Open Access News)

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Comments

I hope "we" are not accelerating scientific research without also accelerating ethics, conflict resolution and politics:

The open politics web also "integrates a variety of applications using XML for syntax and URIs for naming." It focused originally on links and tags as opposed to categories, but there were some top-down terminology decisions:

It has had some success for instance at advancing Green URIs reflecting naming conventions for international Green Party policy, and the many naming conventions mostly pioneered at Wikipedia and other GFDL sources. We would like ultimately to define naming conventions for international simultaneous policy,

"The Semantic Web is an extension of the current web in which information is given well-defined meaning, better enabling computers and people to work in cooperation. ...That is, it's an emerging standard making information sharing and collaboration across disciplines and organizations simpler and consistent." This is what the open politics web attempts to do for parties and citizen political movements. It is most effective when employed by an open party committed to organization protocols suitable for wide open debate on wide variety of contentious topics.

A paper is being drafted on the first years' experience with this model at en: livingplatform.ca: Living Platform in Practice. Any questions raised on that page, I'll do my best to answer in the final version.

Better faster biology research is nice, but, without better politics, we're all quite dead. Perhaps as a result of the "better" biology as abused by bad politics that uses it to build weapons. So I don't see how a sane person can favour accelerating scientific research without also accelerating conflict resolution and real political position resolution.


Posted by: Craig Hubley on 17 May 05



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