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Online Artificial Gene Design

Posted by ScuttleMonkey on Sat Feb 18, 2006 04:58 PM
from the outdated-already dept.
Biotech Software
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."
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  • Game (Score:5, Funny)

    by fozzy1015 (264592) on Saturday February 18 2006, @04:59PM (#14751615)
    SimGene?

  • For those who care (Score:5, Informative)

    by xirtap (955611) on Saturday February 18 2006, @05:05PM (#14751638)
    Here is a link to GeneDesign: http://slam.bs.jhmi.edu/gd/ [jhmi.edu]

  • Will the source code be available? (Score:4, Interesting)

    by CyricZ (887944) on Saturday February 18 2006, @05:07PM (#14751654)
    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.

  • Intellectual property (Score:5, Interesting)

    by quokkapox (847798) <quokkapox@gmail.com> on Saturday February 18 2006, @05:10PM (#14751677)
    So who is going to sue me when I design a gene to make Avastin and Herceptin [nytimes.com]? 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 [p2pnet.net].

    • Re:Intellectual property (Score:2, Insightful)

      by Anonymous Coward
      Sure, most college grads trained in molecular biology can cook up their own bio-cocktail of Epogen, Herceptin, Enbrel, etc.

      But the big question is
      1) would you use your own untested (or minimally tested) cocktail if your life depends on it? ie if you have a cancer that can be treated by the real drug, would you trust your basement concoction to actually save your life?
      2) All of the biologic drugs are injected in to skin/muscle or infused by vein. Would you trust injecting your cocktail into your own body? Do
    • The thing about drugs is that generics often have slightly different
      performance than brand names since they are not made by the same
      facility and often even with deviations in manufacturing protocols.
      Your home-made version will likely differ even more. Now the prescribed
      dosage will become uncertain. It becomes tricky when a tiny tweak can
      cost someone their life.
      One can flip this problem. Herceptin has a known side-effect of cardiac
      failure (esp. in older people). Now, who do you sue if your relative has
      died d
    • Even a drug with a simple-looking molecular structure, like aspirin, is the product of dozens of genes, each of which produces an enzyme with a specific catalytic activity. To enzymatically synthesize a drug in your basement, you'd have to 1) figure out the chemical steps needed to synthesize the drug, then 2) calculate the exact 3-dimensional protein structure needed to align the precursor molecules in the right way to catalyze each of those reactions, then 3) synthesize the DNA to make that protein, and
    • Good thing that what you are proposing is not actually feasible, it would be sad to see the pharma-corps lose potential money in this way. On the other hand I don't see any reasons to allow people, even those who can't pay in any case, to just infringe on patents of laboratories that invent these drugs. Darwinism at its best - you've got to survive somehow and if it includes being able to make enough money for the drugs you need, well then you've got what it takes.
  • The article discusses how much of the software available today lacks safety checks on the DNA sequences that are produced.

    That's really not much different than what we have with many programming langauges today. While most widely used C and C++ compilers today do offer numerous helpful compilation warnings, little is done to verify the safety of the emitted code. Many of the security problems we're dealing with today are due to buffer overflows, and other matters such as that.

    It is often quite expensive to
    • Speaking of DNA compilers, does this software have one? Does it have one for each of the organisms you would model DNA against?

      I find it hard to believe, but I haven't seen much evidence that the biology community has moved beyond the "Jurassic Park" model where you can pick up a piece of DNA and turn it into an organism. In fact, the biology community hasn't even learned the lesson of Jurassic Park where gene splicing produced chaotic results. Cross-species splicing is still a common technique, no? I c

  • Bah, this software won't last long. (Score:4, Funny)

    by Caspian (99221) on Saturday February 18 2006, @05:18PM (#14751720)
    The market will be overtaken by Microsoft Visual DNA++ in around five years.

  • Nice for basics (Score:4, Interesting)

    by nucal (561664) on Saturday February 18 2006, @05:18PM (#14751724)
    Seems like a decent suite of web based apps for basic stuff.

    Although it is mainly protein oriented, there are several molecular tools available at ExPASy [expasy.org] that I use a lot.

    Also, VectorNTI [invitrogen.com] is now free if you join their user group. It's a really powerful suite for plasmid design and molecular analysis.

  • Think of the possibilities! (Score:3, Funny)

    by ndansmith (582590) on Saturday February 18 2006, @05:32PM (#14751790)
    Welcome to Gentoo DNAx!
    god@adam ~ $ su - root
    Password:
    adam ~ # emerge flying invisible glowinthedark
    Calculating dependencies |

  • What is the story here? (Score:4, Insightful)

    by Anonymous Coward on Saturday February 18 2006, @05:49PM (#14751883)
    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).
    • Not only is the innovation of the software insignificant, but the implementation is certainly lacking. It doesn't even do +1, +2, +3, -1, -2, -3 analysis for finding open reading frames.

      This is non-news. And what's especially funny is that most of the commenters here on Slashdot have no idea what this software does, and they shoot their uneducated, ignorant opinions into the whole issue.

      • And what's especially funny is that most of the commenters here on Slashdot have no idea what this software does, and they shoot their uneducated, ignorant opinions into the whole issue.

        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 hypoth

    • For the purposes of having the same scientifically ignorant yapping about patents and creationism, this is a good a pretext as anything else, I suppose.

      But, yeah -- GCG and other have been making software with this functionality since the early 1980's, and probably before that. I'm astonished that Drew Endy didn't simply burst out laughing when New Scientist asked him about it.

  • 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 po
  • 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/ [bioinformatics.org]. 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.

  • What comes to mind is (Score:3, Funny)

    by Tablizer (95088) on Saturday February 18 2006, @06:39PM (#14752111) Homepage Journal
    Frankenstein built via wiki-style callaboration. A troll adds two dicks, somebody removes one, but the troll adds it back again...
  • This is ok in it's limited way, but since it doesn't let you predict tertiary structure you can't use it to build anything cool, like a life form.

  • As far as I can tell from the description this application implements this piece of Haskell code:

    code [] = []
    code ("Phe":s) = "UUU":code s
    code ("Leu":s) = "UUA":code s
          . . .
    code ("Gly":s) = "GGU":code s

    I've left out about 20 lines because I don't want to give it away when I could advertise in on /. and sell it for $20,000 a pop.
    • I've left out about 20 lines because I don't want to give it away when I could advertise in on /. and sell it for $20,000 a pop.

      Whew - my secret is safe.

      No idea why this is news. I did something like this back in late 80's...
  • We all went about our business knowing the world was going to end some day but not really sure how or when. All the fear, the paranoia about nukes, religous zealots and in the end it was some grad student dicking around making protein sequences online. He designed a super virus, just to see if he could do it, not really intending to actually manufacture it. Then there was a mix up at the lab....
  • Of course the technology to sequence genes and deduce their protein counterparts has been around for a while. But as we know proteins are three-dimensional structures, with intricate folds and chemically active sites (think enzymes) that will partake in only specific reactions and ONLY in certain ways. They also operate in highly regulated environments. Heat the protein beyond a certain tolerance level, or substitute an innocent-looking peptide somewhere in the chain, and you end up with a malfunctioning
  • I have the software, its great. Alt-P will actually apply for a patent on the genes you 'discover'.
  • ...by BUILDING them! But it would save time if the site had templates based on famous models...
  • There have been significant roadblocks in the formation of genes. The first one, and most importantly, is that even if we could predict (and we currently cannot) what our desired protein or RNA would do, there is no guarantee that it would fold correctly. We could take elements of existing genes (motifs/domains) and fuse them together to interact with our proteins of interest, but when this has been tried in the past, the protein folds up on itself into a big gob of oil.

    The second issue is that we are sti

    • Re:Trivial... (Score:4, Insightful)

      by Daniel Dvorkin (106857) * on Saturday February 18 2006, @06:45PM (#14752137) Homepage Journal
      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.

      On to the bigger question ... I think the real thing that bothers me is, why is the biology field so devoid of computer people?!

      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.

      • 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.

        That's funny...where I work (the broad institute) we have a LARGE number of scientists who are incredibly good at both math and statistics. You need those tools to play the game, if you're into identifying m

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