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Open Source Biology Initiative
Nick dos Remedios writes "The Biological Innovation for Open Society (BIOS) initiative aims to make biological technology more readily available to biologists everywhere. The latest genetics and biology tools should be freely available to researchers over the internet, but instead access is typically restricted by commercial patents and prohibitive licensing fees. BIOS and its associated BioForge aims to overcome these restrictions to innovation by encouraging companies and public sector research organizations to contribute their research tools and technologies to the BioForge repository. In return, users of the technology are bound by an open source license to share all improvements with the original inventors and other license holders."
In my opinion, all research should be this way in fields that are directly related to the betterment of our health. Who would object?
You call it excessive, I call it ambitious.
Sadly, the most pressing problem isn't the availabilty of biological tools, but the fact that researchers are being allowed to gain patents on their genome sequences, even though such people as The Human Genome Organisation (HUGO) are against it. They've no problem with patented gene therapies, but patenting the genes themselves is just a horrible thing for cutting edge science.
Athletic Scholarships to universities make as much sense as academic scholarships to sports teams.
Even though DNA is 'open source', it's so hard to hack right now company's stand to make more money by hoarding ideas and insights.
I know I'm going to be modded up on this
Great, now the terrorists will be able to create genetically enhanced supermen to fight our all natural 100% human soldiers. We're doomed!!!
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...lots of those out there already; more on GForge here.
Splitting up the project load makes sense to me; that way one site - SourceForge - doesn't have to bear the full load. Also, it lets folks do custom things to make their site more useful - like Graal.
The Army reading list
CMOS = Canadian Meteorological and Oceanographic Society
ok, everyone share your porn, and we'll have nice nice database for scientific research
There are no atheists when recovering from tape backup.
I like this free kick we are on. I think everything should be free. No one should be allowed to make or invent anything that isn't open source, (at least that I want to use). I would ever have to spend money again. Of course I couldn't make any money either, seeing as how everything is free. The up side is that I wouldn't have to work anymore because I don't have to pay for anything. But then who is working to make my bread if everything is free?
Somethings have to be possessions of an individual, so that we can charge others to use them and make money ourselves. Jealousy or envy is not a reason to force someone to give something up. If you can make a saleble product from the tools you need, then buy the tools. OTherwise I would venture to guess that it is not worth doing to begin with. Gosh, I had to buy a computer to write code with, what a horrible thing that I had to pay for a tool that should be free!
Why select a name that has a specific meaning in your own sector?
This creates unnecessary confusion. A marketing faux pas that could have been easily avoided by simply choosing a lessor known acronym.
Based on upvotes, Ageism is the only "-ism" Slashdotters care about and think isn't SJW
Typically for academic institutions, you publish all of your techniques including changes that you made to the protocol to get your results. This, and the willingness to share and explain your approach, is called good science.
The problem comes when you try to open up approaches done by commercial companies. Many of these companies spent years putting together the kits that they sell. Only the restrictive licensing and patents allow them to fully recoup their losses.
Take Amaxa for example. They supply an electroporation kit that works wonders for expressing constructs in cells. Unfortunately each kit costs $300 for 25 transfections. My lab typically goes through 3 of these every 2.5 weeks. Now if Amaxa would just tell us what the composition of the buffers are, that is all that I need to put together my own electroporation system and save my lab at least 15k a year! As a downside, Amaxa would cease to exist. What would be the point of having a biotech company that develops new techniques? Selling support? Please.
... to make an "Open Sores" joke?
No?
I'll get me coat.
Most of the problems facing the "disenfranchised" of the world are not technical but political. Good on the BIOS project for their efforts, but I think peace and some common sense public health practices in the third world will go much further towards helping those people.
Here's hoping...
In some ways, it makes sense that dna sequencing hasn't been released to the public directly.
To analyze that amount of data and to create the sequence data, it requires insane amounts of cpu cycles and the companies doing the anaylzing, are paying lots of $$$ for the job they're doing without sure revenue.
The risk investment in researching is simply too big, to just hand out the results for free in this case.
There are no atheists when recovering from tape backup.
Doesn't this mostly just duplicate the efforts of bioinformatics.org?
"The Bioinformatics Organization, Inc. (Bioinformatics.Org) was founded to facilitate world-wide communications and collaborations between practicing and neophyte bioinformatic scientists and technicians. The Organization provides these individuals, as well as the public at large, free and open access to methods and materials for and from scientific research, software development, and education. We advocate and promote freedom and openness in the field as well as provide a forum for activities which facilitate the development of such resources."
This is just another example of someone trying to carve out a niche in the "hot" area of bioinformatics - the same way as this profusion of Live-CD's for Bioinformatics. It seems to me it's all quite divisive. Bioinformatics models itself on the OSS movement for the most part, but its inherent bindings with industry means there seems to be a lot of people trying to make names for themselves with "projects" even if it means duplicating the effort of someone else.
(Yes I am a bioinformatician)..
I don't read your sig, why do you read mine?
If there is no financial incentive, who will pay for the research? Government funding has faded over the years leaving private industry to pay for much of the basic research upon which commercial enterprises are built. People need to understand, drugs are not expensive because the pharmaceutical industry is taking huge profits (unethical, I know) but they're expensive because research is *enormeously* expensive, combined with the fact that most drugs fail clinical trials. The money has to come from somewhere.
Open source biology, eh? Sound nice, but please, let's have someone to regulate and watch over these actions. The potential to improve the quality of life through biological engenieering is as big as the potential to end it.
This is a really nice idea. The problem is that all this research costs money and a lot of it is being done by publicly owned companies. A publicly owned company has an obligation to its stockholders to make profit and generally to maximize that profit.
That's not just someone's idea, but that's actually the law.
So, this research costs money and it's being done by companies that are obligated to make a profit off of this research they've paid for. So, they sell the results of that research for insanely large amounts of money.
Now, we say, "that's just insanely priced," but in economic terms, that's "what the market will bear," which in layman's terms means that enough people are willing to pay that "insane price" that it's worth it to keep it at that price.
This all follows very standard formulas that apply to most industries, not just drug companies. So, we sit around and talk about the evil of the drug companies, but the fact is, they're just doing their job as the law specifies.
I have no problem with us changing the law, but it's kind of like changing the rules of the game after the game has started. All the players hurt by the new rules cry foul, for obvious reasons.
Uhhhh, _very_ few people know what BIOS means. Sure, we know what it means on /., it could also be argued that a significant percentage of people on the internet know, but that data is heavily biased.
For instance, when I worked for an ISP, I had a hard time telling people (lots of everyday life friends, peers and fellows) what ISP meant.
Cross-sector acronyms not only exist, they are very common. We (IT sector) can't even keep acronyms for a single thing (UML comes to mind), much less settle on what they mean (Sorry, brainfart, but there are hundreds out there).
I doubt naming it BIOS will have any kind of impact whatsoever.
It's even very likely that the IT sector has tons of acryonyms that already exist in the medical world.
And if the space shuttle's replacement will be using free software? No, seriously folks. How do we expect to progress as humanity unless every aspect of our large scientific projects become open and shared? Space exploration is going to stagnate unless they start using open technologies.
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There's also a branch of creative commons formed to work on this.
Science Commons
They're more focused on 1. supporting open access to scientific literature, especially taxpayer-funded literature and 2. building licenses and modular contracts that allow companies and universities to waive some IP rights when it makes sense (such as, if we know we aren't going to make money on a gene patent and you could use it to cure tuberculosis, good on ya, but if you want to use it to make a viagra competitor, we get a piece...so to speak).
The cost of sequencing and data analysis is actually quite low, and all publically funded (NSF/NIH) data should be made available to the public.
The best way to make sure that this data remains open source is to increase funding to national granting agencies like the National Science Foundation and the NIH.
"Asleep at the switch? I wasn't asleep, I was drunk!" -- Homer
I can see this taking off after some 'critical mass' is achieved. A big problem will be IP agreements that working researchers have with their employers. Some are so restrictive that 'the company' holds IP ownership on discovery totally unrelated to the employees 'paid for' expertise.
Now I'm the grandest Tiger in the Jungle!
The only times patents are used are when an actual product is produced. This can be a kit, a drug, a novel assay, whatever. The point is, that it was developed. This development (in science, at least) takes lots of time and money, and that is why patents exist. Something has to safeguard your time and money, otherwise there isn't a point to developing things in the first place.
You have to realize that while many people use software on a day to day basis, the people who use biochem kits and such are almost all able to make them themselves with little effort and knowledge of the composition. It's not the same as patenting an operator. Open sourcing kit composition is a way to destroy your company unless said kit is really complex (most aren't).
you pie in the sky everything should be free, but never contribute anything but demands people need to understand one simple thing.
someone has to pay for all this research and work, and to pay for something they have to make something in return.
I know that is not how it works in your mothers basement, but that is how it works for those on the outside!
This may get more resistance from the schools than the private sectors. All universities make you sign away EVERY possible disovery you make, as a student or professor, and they are more inflexible about this than many companies. Mike Eisen told me that he imbeds GPL code into his code so that it cannot be exclusively owned by UC. Universities have realized the cash cow biotech really is. Look at university of Madison wisconsin. They still make money on "vitamin D milk".
Merely discovering things that exist in nature in any other field is not patentable.
If I am inspired by some strange cave formation and design a new method of supporting buildings around it, perhaps I can patent it the particular method of supporting buildings. But I can't just patent the cave formation after discovering it and sue anyone who then applies any principles contained therein to anything.
10 PRINT CHR$(205.5+RND(1)); : GOTO 10
The thing you have to understand out the medical field is that (unlike software patents) royalties (and expected royalties) from medical patents have funded a huge amount of research that simply would not have been done otherwise. Furthermore, the costs to bring a new medicine to market are very high due to FDA regulations, and no company or research institute would have the means to do so if they were not given some sort of monopoly to sell the drug on the market.
I would agree that any research funded by public sources should be public, if if any of it isn't than that should be dealt with. Also, concidering how much profit the drug companies are making, I would agree that we could decrease the length of medical patents at the with out a significant negative impact on the rate of progress. If we approved them for 10 years extended by 5 years at the time of FDA approval, that would give a company time to get their through drug tested and brought to market, with at least 5 years with a monopoly on it's sale. However if a company did not pursue creating an actual product from their idea, they would loose the patent sooner, and even if they did the patent would expire 5 years sooner than it will today.
But after those tweaks you are basically left with a choice - make these privately developed drugs available to the people who can afford them now, and to everyone else once the patent expires - or don't have them at all for decades until the public sector gets around to it. Especially concidering how political the public sector funding can be, I for one am happy that we have a healthly, vibrant private medical sector - that works in addition to, and above and beyond what the public sector can do on it's own.
IANAPL (Patent Lawyer), but I believe that the patent office has not been granting patents purely for gene sequences anymore (I won't speak of the initial rush to patent all sequences, ESTs, SNPs, etc.)
IMO, two of the best examples of a useful patent, and a valid granting of a patent, stem for Taq and GFP.
-> Taq: this protein allows people to amplify the smallest amounts of DNA into very useful quantities. The processes of using Taq both in genome sequencing, "DNA fingerprints", and making things like the GFP Bunny make it a contender for "molecule of the year". From my understanding, the patents granted dealt with:
1) isolation of Taq from natural sources
2) use of Taq to amplify DNA
3) isolution of Taq from non-natural sources (using other organisms)
-> GFP: this protein allows people to easy visualize events as they occur in an organism without having to resort to difficult, variable procedures. The patents granted dealt with:
1) the use of GFP for visualization of various events
2) the use of GFP as a biological marker (identify transgenic organisms)
As someone mentioned previously, you can't patent an arch that you see in nature, but you can patent a device that utilizes the arch's principles to support a structure. I feel that these gene patents are *not* simply patenting a sequence (contrary to the media reports), but patenting the use of the sequence.
And if someone modifies some of those letters and creates a better protein, then it's time for a new patent!