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Startup Offers Pre-Built Biological Parts
TechReviewAl writes "A new startup called Ginkgo BioWorks hopes to make synthetic-biology simpler than ever by assembling biological parts, such as strings of specific genes, for industry and academic scientists. While companies already exist to synthesize pieces of DNA, Ginkgo assembles synthesized pieces of DNA to create functional genetic pathways. (Assembling specific genes into long pieces of DNA is much cheaper than synthesizing that long piece from scratch.) Company cofounder Tom Knight, also a research scientist at MIT, says: 'I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"
5' 5", 110lbs, female, further details can be found in attached magazine. Do you give volume discounts?
The key innovation of the BioBrick assembly standard is that a biological engineer can assemble any two BioBrick parts, and the resulting composite object is itself a BioBrick part that can be combined with any other BioBrick parts.
Sounds great in theory. In reality, you'll always be missing one of those stupid little yellow bricks and they won't sell them individually.
Apparently they've streamlined a technique whereby the biological mishmash of understanding is standardized into 'code-like' organization. So instead everyone looking up how to make their own gene of their liking, knowing everything about the whole process from the DNA, to the organism to output, you instead just plug in what you want.
In biology there are known 'promoters' (that say "Start"), terminators ("END"), with the gene in the middle, and a number of other little addons and 'features'. Currently in the lab I have to paste these together on my own, from different sources, using different techniques on each. I have to bring each piece into my local standard before I can put them all together. Because it is MUCH easier to change a few bases, or add/delete, than it is to synthesize de novo entire strands of DNA, there exists a need to have modular, standardized 'code' that can easily be swapped from one project to another. These guys make that easy, I guess. When your goal is not just to change/alter a gene, but to set up a few altered/new/engineered genes (or even an entire pathway) at once, this could save a lot of headache.
Do the founders wear bras on their heads?
Oh, and by the way, if there are any ambitious young coders who want to revolutionize bioengineering, all you have to do is write some decent software which can objectively navigate the complicated but exceedingly logical rules of basic cloning. Someone who could write a program with a nice GUI where you just dragged around genes along a plasmid backbone, told it what organism you're to be working in, and have it spit out the plasmid one should use, the oligos & primers needed to be ordered, along with the enzymes to be used could enable a lot of time to be saved in the lab and make a lot of synthetic biology MUCH more accessible. It's a simple kind of code. Great fun for the programming mind. But the current software is god-awful, and exceedingly limited.
First, I agree completely. I can't tell you how much time a program like that would save.
.ab1 files from sequenced clones and quickly align and compare them to the theoretical construct, and then indicate what needed to be done differently. For example, "your inserts are forming concatemers: adjust their concentration relative to the vector during the ligation step, or treat them with CAP (alkaline phosphatase)." or "this particular sequence has internal cut sites: use this restriction endonuclease instead."
I'd just like to add in a quick feature request. It would be very nice if it could take the
The software that I'm using now does allow you to figure out situations like the above, but all it does is alignments; Analyzing the reasons why something didn't work out takes guesswork, and the comparisons prettymuch have to be done manually. For the concatomers example, I'd have to back to my original insert sequence, make a text document of the DNA sequence, import multiple copies into the program, reverse a couple of them (sense/anti-sense), and then manually align the second and third copies. It's very time consuming when it really shouldn't be.
"Operating systems suck: you're better off using only the BIOS" --trainsaw.com
+1. It blows my mind how terrible the software is. Bioedit has some powerful tools in it, but finding out whether or not it has a tool you haven't used before, and then figuring out how to use it often takes hours. But it's really the little things that it does to you when you are worn down from trying to make it do new things that really goes above and beyond, to that realm of "Oh my god, whoever made this was an evil genius."
For instance if you tell it to line the similar parts of two sequences it asks you if you want to save the statistics. Then while you're annoyed with that, it resizes the window to almost fullscreen. You go to close it, and it closes the window behind it, usually the page for the genomic sequence.
I would generalize it to any young coder should consider bio-related software. For instance imaging software for microscopy is also terrible in my experience. Imaris is useful for pulling together multiple microscope images over time to make a 3d movie. Importing multiple files to stitch together, the version we have invariably puts what should be the last frame as the second frame. I'm told the more current version fixes that, but as far as I can tell the solution is that the new version doesn't even attempt to put the movies together.
Wow. Retarded reply gets modded up to the highest post.. I'd be surprised, but hey, it's a non-IT article on Slashdot.
How would you feel if I told you that teenagers have been using biobricks to do some of this "pipe dream" stuff for about 10 years now. That there's an annual international competition to showcase what they come up with and that has been running since 2003? That biobricks are a standard part of genetic engineering of microbes for industrial use? That basically everything you said was so horrendously outdated and ignorant that you sound like someone talking about the impossibility of heavier than air flight in 1913.
I know things have been bad around here for a long time and we've all come to just accept it, but would it be too much to ask that the moderation system undergo a little bit of review? I'm gunna ask the Taco.
How we know is more important than what we know.