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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.
Ooo man the floppy drive is broken. No wait. The computer is just upside down.
North Korea's in I doubt that they have such facilities. Like I said, substitute your favorite rogue (how's that mrpeebles ^_^) nation. Any country that lacks the expertise but has the will will eventually obtain the tech. How about a biological AQ Kahn network?
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).
Based on what I saw in the article, there's nothing this DNA does that hasn't been available in any number of DNA sequence manipulation suites for the last 10 years. 'Reverse translation', constructing a DNA sequence that could be transcribed and translated into actual protein is the sort of thing you might see in an undergraduate genetics homework assignment. Higher throughput versions, akin to what this article is describing, perhaps a masters level bioinformatics project. As to 'protecting' against potential evil-doers ordering proteins of mass destruction, viruses are quite a bit more complicated than proteins. Anyone who needs to order their custom gene from somebody else is not likely to be decades ahead of state of the art infectious disease researchers who, to the best of my knowledge, have been unable to generate a de novo infectious agent. Honestly, these algorithms have been around for quite some time.
At first blush, GeneDesign 2.0 offers nothing over the long-available, free, web-based or local-mirrorable Sequence Manipulation Suite 2 at http://bioinformatics.org/sms2/. When I start on a molecular bio project, I use a mix of SMS2, BLAST, NEB cutter, IDT's web-tools, and other free online tools to accomplish everything I need, and keep track of my thought process in a simple Word document. This suite adds no functionality I don't have free access to already elsewhere.
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.
There have been innumerable bioinformatics sites put up over the years by various institutions, but they've never been examples of refined usability. You could say that is because the focus has been on the underlying tools and not the interface.
Despite being highly educated and working alongside a great deal of computational effort, biologists in general are not anymore computer literate that your average office worker. Much of the computational side has been taken up by computer literate Mathematicians, Physicists and Comp. Scientists. Those that can bring together a multitude of tools (often rudimentary academia quality software) to solve a problem through programming, find many of their collegues cannot or will not do the same. The older generation directing the labs then ask those that can to design sites to provide tools for the illiterate but as is the case in research, these static tools generally do not provide the necessary power or flexibility. Many efforts end up being ignored in favour of simply casing down the programmer in question.
Ultimately, the best solution is to teach programming to biologists as a core subject. Our old categorization of the sciences is out-moded.
But Atlantis is in another Galaxy (and run by the U.S. Military). How can it be a threat?
I really wanted to change my sig to something witty, but all I could come up with is this.
Well the parent did mention North Korea. That would be a communist country. Sounds pretty 'rouge' (red) to me.
You're new to slashdot, huh? As a biologist/bioinformatics guy, every time I read articles on slashdot that involve my field of research, I see that 90%+ of the 3+ or better comments are crap.
This leads me to believe that in areas that are not my speciality, slashdotters are equally full of shit. Sure, it's just a hypothesis right now, but I'm sure with a little help I could gather convincing evidence...