How to tell you’re living in the future: bacterial computers, HTML and RDF

Clue no.1. Papers like “Solving a Hamiltonian Path Problem with a bacterial computer” barely raise an eyebrow.

Clue no.2. Undergraduates did most of the work.

And the clincher, …

Clue no.3. The paper is shared nicely in the Web, using HTML, Creative Commons document license, and useful RDF can be found nearby.

From those-crazy-eggheads dept, … bacterial computers solving graph data problems. Can’t wait for the javascript API. Except the thing of interest here isn’t so much the mad science but what they say about how they did it. But the paper is pretty fun stuff too.

The successful design and construction of a system that enables bacterial computing also validates the experimental approach inherent in synthetic biology. We used new and existing modular parts from the Registry of Standard Biological Parts [17] and connected them using a standard assembly method [18]. We used the principle of abstraction to manage the complexity of our designs and to simplify our thinking about the parts, devices, and systems of our project. The HPP bacterial computer builds upon our previous work and upon the work of others in synthetic biology [19-21]. Perhaps the most impressive aspect of this work was that undergraduates conducted every aspect of the design, modeling, construction, testing, and data analysis.

Meanwhile, over on partsregistry.org you can read more about the bits and pieces they squished together. It’s like a biological CPAN. And in fact the anology is being actively pursued: see openwetware.org’s work on an RDF description of the catalogue.

I grabbed an RDF file from that site and confirm that simple queries like

select * from <SemanticSBOLv0.13_BioBrick_Data_v0.13.rdf>  where {<http://sbol.bhi.washington.edu/rdf/sbol.owl#BBa_I715022> ?p ?v }

and

select * from <SemanticSBOLv0.13_BioBrick_Data_v0.13.rdf>  where {?x ?p <http://sbol.bhi.washington.edu/rdf/sbol.owl#BBa_I715022>  }

… do navigate me around the graph that describes the pieces described in their paper.

Here’s what the HTML paper says right now,

We designed and built all the basic parts used in our experiments as BioBrick compatible parts and submitted them to the Registry of Standard Biological Parts [17]. Key basic parts and their Registry numbers are: 5′ RFP (BBa_I715022), 3′ RFP (BBa_ I715023), 5′ GFP (BBa_I715019), and 3′ GFP (BBa_I715020). All basic parts were DNA sequence verified. The basic parts hixC(BBa_J44000), Hin LVA (BBa_J31001) were used from our previous experiments [8]. The parts were assembled by the BioBrick standard assembly method [18] yielding intermediates and devices that were also submitted to the Registry. Important intermediate and devices constructed are: Edge A (BBa_S03755), Edge B (BBa_S03783), Edge C (BBa_S03784), ABC HPP construct (BBa_I715042), ACB HPP construct (BBa_I715043), and BAC HPP construct (BBa_I715044). We previously built the Hin-LVA expression cassette (BBa_S03536) [8].

How nice to have a scholarly publication in HTML format, open-access published under creative commons license, and backed by machine-processable RDF data. Never mind undergrads getting bacteria to solve NP-hard graph problems, it’s the modern publishing and collaboration machinery described here that makes me feel I’m living in the future…

(World Wide Web – Let’s Share What We Know…)

ps. thanks to Dan Connolly for nudging me to get this shared with the planetrdf.com-reading community. Maybe it’ll nudge Kendall into posting something too.

One Response to How to tell you’re living in the future: bacterial computers, HTML and RDF

  1. [...] This post was mentioned on Twitter by Dan Brickley, semanticaweb. semanticaweb said: “Solving a Hamiltonian Path Problem with a bacterial computer”: From those-crazy-eggheads dept, … except the thi… http://bit.ly/hWynpn [...]

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