In Development: An Open Source Language For Cell Programming

hessian writes with a story at Wired (excerpt below) about a project from Drew Endy of the International Open Facility Advancing Biotechnology, or BIOFAB, to standardize a programming language connecting genetic information from DNA to the cell components that DNA can create. "The BIOFAB project is still in the early stages. Endy and the team are creating the most basic of building blocks — the 'grammar' for the language. Their latest achievement, recently reported in the journal Science, has been to create a way of controlling and amplifying the signals sent from the genome to the cell. Endy compares this process to an old fashioned telegraph. 'If you want to send a telegraph from San Francisco to Los Angeles, the signals would get degraded along the wire,' he says. "At some point, you have to have a relay system that would detect the signals before they completely went to noise and then amplify them back up to keep sending them along their way.""

PS3

[tepples]

So with the PlayStation 4 coming out, is Sony bringing Linux back to the PlayStation 3?

Oh wait, wrong Cell.

Good job, Slashdot, your SSL is expired

[Anonymous Coward]

Try it and see [slashdot.org]. Expired about an hour ago. Glad everyone is on the ball.

Re:Good job, Slashdot, your SSL is expired

[Trepidity]

Everyone seems to be screwing up their SSL lately. Bing is broken too [bing.com], because the cert seems to point to some akamai domain and isn't valid for bing.com.

HTTPS is subscriber-only

[tepples]

Slashdot forwards HTTPS to HTTP for non-subscribers. I wonder whether this has anything to do with Google not making AdSense available over SSL.

Because he's got fairy godparents.

[tepples]

So why is the shit timothy the only allowed poster ?

Timmy is a basement dweller that no one understands. Mom and dad and Soulskill always giving him commands (Bed twerp!) The doom and gloom down in his room is broken instantly by his magic little fish, they grant his every wish cuz in reality they are his... [CUT OFF BY VIACOM]

Please no Java or C#.

[Impy the Impiuos Imp]

Please no Java or C#.

Please no Java or C#.

Please no Java or C#.

Please no Java or C#.

"Your comment violated the "postercomment" compression filter." Oh yeah?

Re:

[Pseudonym]

If biologist-designed file formats are anything to go by, both Java and C# are likely to be an improvement over whatever they come up with.

Re:

[VortexCortex]

If biologist-designed file formats are anything to go by, both Java and C# are likely to be an improvement over whatever they come up with.

Java and C# are VM languages.... Have you seen the bytecode they output? It actually disproves the Intelligent Designer hypothesis.

Re:

[Pseudonym]

I don't know about C#, but JVM bytecode makes a lot more sense if you write the theorem prover first.

Re:

[Rich0]

Have you seen this or [rcsb.org]this [nih.gov]? Those are actually fairly well-defined at least, but they read like something that was supposed to be punched into cards.

Re:

[Pseudonym]

Yes, I've seen those. PDB is admittedly hard to screw up thanks to the fact that it's just a matrix. I actually had FASTQ in mind when I wrote that.

Re:

[ikaruga]

Why not C#? I understand the hate against .Net/Mono because of the framework nature and MS influence but C# as a language is a pretty damn good one(the best IMO). If someone developed a native C#-like programming toolset with openCL/GL and Qt support alongside other popular libraries for both ARM and x86, I'd never look at C++ again.

Re:

[Spy Handler]

yup, C# is what Java should've been in the first place and what Java wishes it was.

Slashtards are down on it just because it's from M$.

Re:

[gigaherz]

Native code wouldn't help much for this. A compiler that outputs to a decent intermediate code allows the output to be later translated and optimized to the specific details of the target platform, which has greater chances of optimizing better than direct-to-native compilers. What makes VMs slower is memory management, RTTI, and the consistency checks that go along with a type- and memory-safe language. C# already has bindings for OpenGL/CL and Qt, alongside with many popular libraries, at least for x86.

The Science Article in Question

[RandCraw]

http://www.sciencemag.org/content/early/2013/03/27/science.1232758 [sciencemag.org]

Amplifying Genetic Logic Gates

Abstract

Organisms must process information encoded via developmental and environmental signals to survive and reproduce. Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes. We developed a three-terminal device architecture, termed the transcriptor, that uses bacteriophage serine integrases to control the flow of RNA polymerase along DNA. Integrase-mediated inversion or deletion of DNA encoding transcription terminators or a promoter modulate transcription rates. We realize permanent amplifying AND, NAND, OR, XOR, NOR, and XNOR gates actuated across common control signal ranges and sequential logic supporting autonomous cell-cell communication of DNA encoding distinct logic gate states. The single-layer digital logic architecture developed here enables engineering of amplifying logic gates to control transcription rates within and across diverse organisms.

Re:

[VortexCortex]

If you let these researchers keep going, their sentence structure will become self aware.

Microsoft has a dna computing proposal

[FithisUX]

The site is http://research.microsoft.com/en-us/projects/dna/ [microsoft.com] I wish it was open source. Damn you MS.

Can't patent natural phenomena

[pchimp]

I'm think that 'cell programming' has been about as open source as anything can be for a long, long time...