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Open Source Software Meets Do-It-Yourself Biology
destinyland writes "This article profiles a growing movement — DIY biology — that's made possible in part by open source tools. Using programs like BioPerl and BioPython, DIY biologists write their own code (computer and genetic), designing their own biological systems and altering the genome. A protein-folding simulator, Folding@home, is now the most powerful distributed computing cluster in the world, and as the movement evolves, cooperatives are also springing up where hobbyists pool resources and create 'hacker spaces' to reduce costs and share knowledge. 'As the shift to open source software continues, computational biology will become even more accessible, and even more powerful,' this article argues — while intellectual property and other bureaucracies continue to hobble traditional forms of research."
DIY Biology sounds pretty dangerous.
As long as the instructions it comes with are better than Ikea's...
...Folding@home, is now the most powerful distributed computing cluster in the world...
A Distributed Cluster? *Head Asplode*
Many of these biology experiments require very expensive machines, such as microarray machines, as mentioned by the article. I don't know if purchasing refurbished machines is a wise choice since we don't want data quality to be compromised. Also, don't forget about service plans when the machines break or producing inconsistent output. Not to mention various reagents, other chemicals, and supplies such as microarray chips that make the experiment yields high quality data. These easily reach hundreds of dollars a piece. Also, purchasing such chemicals will get you labeled as a terrorist.
Another issue is gathering the samples. If you're collecting yeast, that would be simple. Arabidopsis, other small plants, mice, or other small animals, you probably need quite some space. Humans? That won't be simple at all. You have to clear privacy issues, getting the research review board to sign papers, etc. Sample collection alone can cost you lots of money and time. You can always resort to publicly available data. But chances are that you won't be able to impress scientists much for going that route. Also, most of the important discoveries are already done on this data. Most likely, all you can do is to confirm existing results or to provide some tangential additional info.
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Error 500: Internal sig error
Do it yourself biology??
I prefer "do it with someone else" biology...
If I had a nickel for every time I had a nickel, I'd be richcursive!
Any progress since the last time this was on slashdot? No? Thought so.
Downloading computational biology software, that you have no idea how to use, makes you a molecular biologist, the same way that downloading finite element analysis software that you don't know how to use, makes you a mechanical engineer, downloading a SPICE simulator that you don't know how to use, makes you an electrical engineer, or downloading Pr0n that you can't re-enact makes you a sex expert. At least the Pr0n is easier to apply than a FEM or SPICE package, it being a "pictorial diagram", the disadvantage being that it requires a member of the appropriate sex (and species!) to re-enact.
"Science flies us to the moon. Religion flies us into buildings." - Victor Stenger
People have been experimenting with DIY biology for years. My first experiment is named "Venus", she is 9 years old now and is a sweet, lovable (if hyperactive) cheerleader. Overall, I'd say this experiment was a resounding success, although I am still waiting for others to replicate my results.
I've abandoned my search for truth; now I'm just looking for some useful delusions.
Awesome article. Our team has embraced the use of the R Stats package in our environmental assessment tool. We were sick of the COM object library to connect modern .NET tools to our tool so I decided to build a .NET wrapper for R. Still in early development but it works for us. We decided to release it under GPL for everyone to use. I think the title of article could read something like "Biologists take programming into their own hands" which is what I was forced to do during my MSc. and now once again in my position at U of S I find myself hanging out with the computer scientists a little bit too often.
A poll recently indicated 95%+ coders here. Something about computer science makes comments skew strangely. Look at an article on encryption, and you'll get quite a few accurate, thoughtful comments. Look at one on CPUs, or applied physics, and you got a lot of jokes and misunderstandings. Is there something peculiar about the field of computer science that makes a worldview tilted so much?
From the title I was looking forward to the news that I could DL the opensource software, get my PC hooked up to a robot arm and a webcam, and have it do my appendectomy.
sadly, i mostly encounter uncooperatives
this leads to do-it-by-yourself biology
intellectual property law is philosophically incoherent. it is your moral duty to ignore it or sabotage it
This concept of DIY biology is far, far older than science, itself. People have been manipulating livestock, crops, even our own genome, for a long time now. But the author of this article is right about new tools making the process that much more accessible and powerful.
The build-out of world trade over the last century has wrought some damaging changes to the world ecology. Invasive species, pernicious plant diseases, and the like are spreading world-wide. Government efforts in this realm have been sporadic and often do more harm than good. The ability of smaller, private organizations to conduct sophisticated science on a smaller budget will be a boon to the restoration of endangered species, for example.
But, I tagged this article with the whatcouldpossiblygowrong tag. Danger ahead.
Best regards.
"As the shift to open source software continues..."
Stop the shit, I'm going blind from it, stop it!
Oh... shiFt... Nevermind, continue, continue, good job...
Vijay Pande is a Stanford professor and funded primarily by the same agencies that fund most of the biomedical research in this country - most importantly, the NIH. (Disclaimer: they fund my work too.) He has full-time scientists (i.e. people who spent most of their 20s in school) and computer engineers writing code and assistance from hardware vendors (ATI/AMD and NVIDIA, at least). FAH is a great example of how to leverage distributed computing resources and volunteer effort, and it's an excellent technical solution to what is potentially a very expensive problem, but the intellectual effort is *not* distributed. I don't mean any of this as a criticism (I wish I had five petaflops at my disposal too), but this is not an example of "hobbyists" performing research free of bureaucracy. (In fact, the umbrella project for much of Pande's work now has a relatively large bureaucracy at Stanford, which surely wasn't suffering from a lack of bureaucracy to begin with.)
The article makes some vague statements that IP limits traditional biotech research. In fact, empirical studies do not back up such claims. John Walsh, Charlene Cho, Wesley Cohen, View from the Bench: Patents and Material Transfers , 309 Science 2002-2003 (2005). Some highlights:
"Thus, of 381 academic scientists, even including the 10% who claimed to be doing drug development or related downstream work, none were stopped by the existence of third-party patents, and even modifications or delays were rare, each affecting around 1% of our sample."
"In addition, 22 of the 23 respondents to our question about costs reported that there was no fee for the patented technology, and the 23rd respondent said the fee was in the range of $1 to $100."
19% of the respondents reported that other scientists had not complied with material transfer requests (i.e. requests for data or samples), but analysis found that "The patent status of the requested material had no significant effect on noncompliance."
An additional, more focused case study of a highly-commercialized area of research with a lot of patent activity found that "only 3% of respondents reported stopping a project in the past 2 years because of a patent."
I tell you what's sorely needed: an open-source biology that should be to Monsanto what Linux is to Microsoft.
AC
that's exactly what she says
is that you francesca?
intellectual property law is philosophically incoherent. it is your moral duty to ignore it or sabotage it
"many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist's budget." That must be a (bad) joke. Forget the open-source/custom-made software and discount price hardware acquired on eBay, biology is first and foremost about wet lab. And not only it costs *a lot* but one needs licenses to purchase certain products. I have worked in biomedical research for almost ten years and I know that if you're in academia then you can purchase, say, enzymes and genetic vectors at their catalog price; but if you're industry then you get hit with 5-6 digit licensing fees. The only way to do at home what they claim to be doing is by using stuff from their academic research labs. Besides the risks involved (those cell line are actually cancer cells and engineered bacteria are mutant germs, not to mention the radioactively labeled nucleic acid probes that might end up in the toilet) the logistics are a nightmare. Storing liquid nitrogen in your basement? Discarding ethidium-bromide and acrylamide gels? Biological experiments are different from software development, they need follow up and supervision through the end, which may take 2-4 days. Drosophilla flys can't be frozen like bacteria. How do you discard biohazardous materials and mutagen/teratogen substances at home? There are many reasons why DIY biology is a very bad idea; it's a disaster waiting to happen.
Those geeky scientists really only want one thing: Cat Girls!
Girls with cat ears, and a tail. Just like in the manga!
Who would win this election: Andrew Weiner vs Andrew Weiner's weiner.
"Sir, the new beetle you were working on? It crashed. Shall I reboot it?"
Please do not read this sig. Thank you.
The wife and I have been doing DIY biology for years and we have 3 kids and 3 grandkids to show for it.
Intellectual property [law] hobbles research? Actually, intellectual property laws promote research, by giving inventors a means of supporting their work in a competitive marketplace that is independent of government funding. Without IP laws-and without respect for them-the government would wield even more power than now (already too much) and efficiency would suffer even more.
Biology has not traditionally been computationally intensive, but that has changed in the last 20 years. Computer modelling of ecology, disease epidemiology, and cellular processes has been tremendously helpful. With the age of the genome merging into the age of the proteome the trend is only going to grow. Biology is or will shortly be as computationally intensive as physics. Witness the explosion of Bioinformatics departments in Universities in the last 10 years. The main trouble is that most of the problems in biology (finding patterns in nucleotide sequences for example) are not interesting problems for computer scientists. The computational techniques, for the most part have been worked out and are just a matter of number crunching. The trick now is to employ them on the mountain of data generated by the biologists. It doesn't surpise me that biologists are learning to do their own coding, or at least learning enough of the lingo to go talk to the local programmers.
.. and create THC-producing dandelions or clover! Seriously.
http://en.wikipedia.org/wiki/The_White_Plague
Scared me way more than any "grey goo" idea.
Don't forget R/Bioconductor! Not only is R free/free, but there are thousands of available Bioconductor packages ready for out-of-the-box use. Also consider Cytoscape and or EGAN for graph visualization of established and experimental bio-knowledge. http://www.bioconductor.org/ http://www.cytoscape.org/ http://akt.ucsf.edu/EGAN/ (full disclosure - I work on EGAN)
a few more favorite things: http://genome.ucsc.edu/ http://www.biomart.org/ http://www.taverna.org.uk/
more data warehouses: http://www.ncbi.nlm.nih.gov/pubmed http://www.ncbi.nlm.nih.gov/pubmed/
Don't you guys remember the underwater city of Rapture? It became easy and accessible to splice one's own gene sequence and all hell broke loose down there. What did you think those splicers were doing? Heroine? Mark my words, this will start with harmless science projects but soon the populous will be killing little girls for ADAM and shooting lighting at each other out of their hands. Hell's come the surface!
Motorcycles, Robots, Space Gossip and More!
coming to a upper respiratory near you.
The Kruger Dunning explains most post on
B: Honey, I've got my DIYbio kit and I'm headed to the basement! Don't bother me for a while I'm busy making a baby!
A: Don't you need me for that?
B: not anymore. not... any... more...
Well, one element down: elaborate, specialized equipment... if this works, in a few years, you'll just order it from your garage http://www.cubespawn.com
Um, cloning genes into plasmids and propagating them in E.coli so that you can manipulate (mutate) the sequence invariably requires some kind of antibiotic selection. Letting people muck around in their garages with plasmids conferring antibiotics resistance in bugs that have the potential to become resident in your intestines and persist indefinitely in the environment is a horrendously bad idea.
It's why all labs that do this stuff routinely are required to adhere to physical containment guidelines.
Pretty fucking scary indeed.
I finished my PhD in phylogenetics in 2008 and have been a professional bioinformatican since then.
This story doesn't really suprise me, I'm amazed anyone bothered to write it.
Yes, we all use bioperl and GPL java libraries, which are free - but that's only because we're all such shit coders (and tbh working on low-complexity, high-specificity tasks - grep, anyone?) that making a proprietary package good enough that everyone else would need to pay for it isn't gonna happen any time soon. But I can't think of any amateurs that I've ever met, or even heard of, that are actually working in this field.
At the end of the day, like loads of other people have already pointed out, we all rely on sequencing which definitely *isn't* cheap or free. At. All.
Sorry.
Joe Parker
Oxford University / Kitson Consulting, Ltd.