Slashdot Mirror
Online Artificial Gene Design
massivefoot writes to tell us New Scientist is reporting that researchers at Johns Hopkins University School of Medicine have released a new software suite, GeneDesign, that helps to simplify the steps in designing artificial DNA. From the article: "These key steps include translating proteins and amino acids - the building blocks which make proteins - backwards into a DNA sequence. Or the software can manipulate simulated DNA "codons" which can code for an amino acid. DNA codons are made of sets of three nucleotides - the fundamental molecules which link together to form a DNA chain."
SimGene?
Here is a link to GeneDesign: http://slam.bs.jhmi.edu/gd/
I think you mean "rogue" countries ;-) "Rouge" is the red makeup women put on their cheeks. ("Whores use rouge. Ladies pinch...")
Does anyone know if they plan to release the source code? Indeed, it could prove to be a very useful resource to students studying bioinformatics, or other fields that combine biology and computer science.
Cyric Zndovzny at your service.
So who is going to sue me when I design a gene to make Avastin and Herceptin? This will be the real test of our obsolete intellectual property regime, when the medical establishment's equivalent of the RIAA/MPAA sues cancer patients for synthesizing their own drugs, like the music industry is now suing your neighbor's kids.
it's a blue bright blue Saturday hey hey
Hmm, is that a serious threat though? You would need a quite competent biotech programme to produce biological weapons, and, frankly, with the state North Korea's in I doubt that they have such facilities.
Besides, with their current suspected nuclear capability, would biological weapons really be that great an advantage? Remember the DPRK regime's main concern is warding off an invasion by the US, and in such a situation a nuclear weapon is a far greater threat than any biological capability.
The market will be overtaken by Microsoft Visual DNA++ in around five years.
With spending like this, exactly what are "conservatives" conserving?
Although it is mainly protein oriented, there are several molecular tools available at ExPASy that I use a lot.
Also, VectorNTI is now free if you join their user group. It's a really powerful suite for plasmid design and molecular analysis.
What exactly is the exciting news here? This type of software has been around for many, many years. Analyzing a gene sequence to determine restriction enzyme sites, or optimizing codon usage for efficient heterologous expression is absolutely routine, and is performed even in undergraduate level molecular biology courses. It's laughable that the ability of this software to "...manipulate simulated DNA 'codons' which can code for an amino acid" is being touted as an advance.
I can't even believe that New Scientist is reporting this, let alone Slashdot. There must be at least 100 other tools which perform the same functions, many of which are free (both as in beer and source code).
I just typed 'gattaca' into it, and it started doing non-complaining type things.
No idea what though... I'm a geek not a chemist.
Frankenstein built via wiki-style callaboration. A troll adds two dicks, somebody removes one, but the troll adds it back again...
Table-ized A.I.
The underlying science is pretty trivial, yeah. (Or at least "well-understood.") But having this tool in one place, as a reasonably well-designed Web app, is neat.
... I think the real thing that bothers me is, why is the biology field so devoid of computer people?!
On to the bigger question
Stereotyping here -- it's a bit of a culture clash. Until fairly recently, biology (with exceptions for some subfields such as ecology) was, to put it bluntly, the science you went into if you wanted to do science but weren't very good at math. And I think it's fair to say that most "wet-lab" biologists still think more qualitatively than quantitatively. They're very, very good at describing things; they're not so hot at putting those descriptions into numeric or algorithmic terms. And, still stereotyping, CS people tend to be exactly the opposite: "if you can't code it, it doesn't exist," and they're uncomfortable with the inherent, um, gooiness of living systems.
Computers are always supposed to behave predictably. Living things never do. It's really that simple.
You also have the opposite problem, overenthusiasm, which is born out of the same kind of ignorance: biologists who think that they can throw a bunch of random microarray or PCR data at someone's analysis algorithm and get The Answer, and computer scientists and mathematicians who take Bio 101 and think they know enough biology to interpret the answers they get. In both cases, of course, both sides are severly underestimating the complexity of The Other Guy's chunk of the problem.
Don't get me wrong; I do think it's getting better. But even someone like me, who's had one foot in each camp for a number of years now, has to admit that we've got a long way to go before quantitative biology really exists as a unified field.
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
Well the parent did mention North Korea. That would be a communist country. Sounds pretty 'rouge' (red) to me.