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Open Source And Genetics
UnanimousCoward writes "SFGate has an article about some researchers pushing for the open sourcing of genetic research software. Of course, the pros and cons are debated." It's the age-old debate; what follows the heart of the scientific method more? Peer review, or getting the information out as fast as possible?
Didn't we see this article yesterday right here?
If it gets open sourced can we expect to find a book on our bookshelves titled "Genetic Engineering for Dummies..." and "Learn Genetic Engineering in 21 days"?
--- I used to moderate, then I read the -1 articles and decided having to filter through them was not worth it.
This is just my opinion (YMMV, IANAS, etc), but I would argue for peer review, insofar as it relates to the ability to duplicate results and experiments. My thinking here is that the ability to duplicate results is at the heart of science. If others can't duplicate them, the results aren't accepted.
A grain of salt is provided for those who disagree.
The Independent: Reverend Spooner Arrested in Friar Tuck Incident - ISIHAC, Historical Headlines
Is essentially the same story
Shut up, be happy. The conveniences you demanded are now mandatory. -- Jello Biafra
Despite all the arguments favouring IP rights et al, I'd say that most of the research has to be open-sourced, so to speak.
There is no point in re-inventing the wheel. It becomes ridiculous when 10 different companies engage in enormous investments independently on 10 different projects, when they could have all done 10 different projects to begin with.
IP has it's own say, no doubt, but over doing it leads to commercialization of science, and defeats it's very purpose. Engaged in silly patent and copyright wars, we have no doubt postponed many a useful invention by at least a few decades, IMHO.
Science needs to be peer review. If science moves too fast then it will stumble and we will have another cold fusion debacle. That would be awfull.
Macs are used extensively in some areas of genetic research, to put some perspective on the open source involvement.
Why would I do any research?
How am I gonna make money? Grants? To what ends?
Open source is a better hobby than an occupation. Its easy to say "I want everything free to read", but someone has to pay for that research, and the government has a finite amount of grant money.
LSS is very much libre. Users of LSS packages are free to distribute copies without reference to the authors, make modifications and distribute the modified copies. They may even execute the software without charge, provided that they do it for a purpose for which the authors do not require payment, and the definition of LSS ensures that any LSS package can be executed for experimental purposes. However LSS is not always gratis. Some uses of the software will require payment.
The word "liberal" is derived from "libre". It denotes freedom of action. Hence "Liberal Source Software". The source is available, and you can do what you like with it.
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If someone researcher at a university is being funded privately, there is no problem with the research and software staying closed. If public tax money is used, I think a BSD style license should be used. I do think there is a valid point in not using GPL in these cases and using a BSD style license.
Right now with the boom in genetics this software is top-dollar in some cases. I doubt these emerging companies would be willing to part with their profit margins in the name of open source.
I would want access to certain nucleotide sequences. Just think of what one can do with a gene sequencer, a PCR kit, and the smallpox DNA sequence.
It's important to get informationout as quickly as possible, especially medical or scientific knowledge that can be quickly applied for our betterment. That said, peer review is incredibly important to ensure that the information being disseminated isn't MISinformation.
That's my brief 2 cents.
Be more clear in the writeup: the subject of the article is a petition to open-source any code that results from federal grant money from reseachers in a university setting. It is *not* about open sourcing all bioinformatic software, everywhere. In other words, code developed in a private setting, independant of university grant money - who cares? (at least in this case). Alternatively, grad students who strike it rich on code they wrote while on the government dole? Open source *their* work, since it was already paid for by the taxpayers. I don't see anything wrong with this particular distinction.
In our times people need to understand that information is always most usefull when free. Only when some piece of mind's work is released to anyone look at it this information can archieve it's full potential of changing society. Every single time that someone, somewhere, is hiding information this person is hurting everyone else in this world. Sure I don't talk about personal information and the kind of stuff that should not be know to others (because it would not be useful), but about scientific information... that's what make our world go forward, really.
The truly beauty of the free software and of the open source movement relies precisely in that kind of freedom.
This genetic software must be relealed as soon as possible. Not doing so is a way of harming society.
If someone patents your DNA sequence, and you are a surogate mother, do you have to pay royalties on the child? (Since you are giving birth for profit.)
--- -- - -
Give me LIBERTY, or give me a check.
I don't think genetic code and source code should be treated the same. After all malicous sourcecode only hurts computers and inconvienices users. Genetic code effects us on a much more real level.
I can release code that has a bug in it and fix it pretty quicky. If it causes problems, it only causes problems. Meddling with life is not so trivial and the concequences can be fatal. It is for this reason that I am against open source genetics.
Slashdot's rate-of-post filter: Preventing you from posting too many great ideas at once.
That are given to offer an incentive to produce a product. I have no problem with Universities patenting research for funding. There's no way my paltry tuition can pay for the sonet ring around my campus, or the high end multiprocessing computers that seem to be in abundance (BYU). I do however take exception to the idea that the HUMAN genetic code can be licensed and sold. I don't see a problem with that researcher going on his own in his spare time and developing an alternate free source for his genetics program. However, if it is the work of many interested parties, (corporations, individual students and university admin, then it's just up to each person to do what they are able on their own. No one who is in open source makes software on company time and expects to give it away for free. In general, a researcher is employed by the university, on this specific case, however, he has them by the hoary beard, because they agreed to a contract that his work would be open, as solid as a contract if he would have had to patent all his work
http://cincyboys.blogspot.com/ Everything Cincinnati. Including the word 'Finnih'
"It's the age-old debate; what follows the heart of the scientific method more? Peer review, or getting the information out as fast as possible? "
Both peer review and getting the information out there are both important. Honesty in publication is most important. If your work has not been peer reviewed, then you should just say so.
There is also a danger in peer reviewed work being too easily accepted by people even though the work itself is shoddy.
Why not both? Quick publication with clear marks as unconfirmed or waiting to be replicated would do both. It also would provide a quick source of worthwhile experiments, repeating previous successs and confirming them.
So long and thanks for all the fish . . . !!!
I don't get the meaning. I know the faq says that this can happen, but sometimes I just wonder if d'man wants us to read and give more feedback, perhaps? What seems worse, is that then the moderators waste a bunch of points punishing people who complain.
Perhaps we are being "herded" towards a goal? While that's cool, I mean, you are d'man, after all, I wish you'd just say, "Hey, could y'all take another look at HERE and give some additional feedback? We need more profile data on some of you."
*O*H***W*E*L*L*
Software for research in genetics, biology, fluid dynamics, astronomy and any other subject that requires such colossal amounts of computations should, in my opinion, be open sourced. This way, several things can take place:
Well, you get the picture. All of this becomes incredibly expensive with closed source software. Of course, nobody said it has to be free software. Obtaining the source code could very well require an NDA, if that's what will float the developer's boat.
*O*H***W*E*L*L*
If public funds were used to finance the research, then it should be public information. The only exceptions should be driven by security concerns. If private monies are put into the mix, let us thank the donor for their donation.
We are the public and our tax dollars are used to generate this information. We own it.
Give it to us at the bare cost of distribution.
Unlike scientists who keep research secret until it is published in a peer-review journal, some software developers -- who get little credit when their code leads to a genetic breakthrough -- want to share their work as soon as it leaves their keyboards.
It's an old debate in the world of computing -- and a new culture clash in bioinformatics...
It seems like there is some confusion here. Sure there is some time-lag between the research and its publication, but peer-reviewed journals are in fact similar to bugzilla.
The problem being addressed by the petition isn't what is published in peer-reviewed journals, its what isn't being published. Making scientific techniques proprietary not only slows the advance of science, but takes technology which could benefit the public and allows a few people to benefit disproportionate to their contribution.
I once obtained RNA secondary prediction software from Washington University. Before we could obtain it, we had to sign waivers that we would not re-distribute it outside of our own research university. Once we got the software though, it came in source form. So AFAIK the source for academic software developed for life sciences is probably available upon request, you just can't redistribute it at will. As for publications, the alogrithms for predicting the RNA secondary structures were published, but not the code itself. Hope this is informative.
NO CARRIER
See
http://www.randomfactory.com/lfb/lfb.html
Look at it this way...It starts with patented genetic software, which leads to some sort of discovery that could cure some disease. Now the researcher that made the genetic discovery patents the actual base pair code (genetic code). Now they have the ability to charge what ever they want for the "treatment". That is a terrifying thought. This is a real Pandora's Box
"Unlike scientists who keep research secret until it is published in a peer-review journal, some software developers -- who get little credit when their code leads to a genetic breakthrough -- want to share their work as soon as it leaves their keyboards."
Yeah, people who make hammers do usually not get credits of building the house.
If it is a revolutionary new software tool with a lot of brilliant thinking behind it, we will get credits, papers in scientific journals, etc.
Don't give me that.
It must be teamwork that leads to a scientific breaktrough. This includes coders, biologists, and many other disciplines.
I truly believe that scientific software is one the disciplines where open source really won't work.
A coder in bioinformatics software and human genetics.
Unlike scientists who keep research secret until it is published in a peer-review journal, some software developers -- who get little credit when their code leads to a genetic breakthrough -- want to share their work as soon as it leaves their keyboards.
If coders do decent scientific work, they will get the credits they deserve. If not, not.
Furtermore, scientific software is not the same as a the latest xml parser. It can not be coded by just anyone. You have to understand what it is supposed to do. That's why they call it science.
There is serious money involved (think pharma's and biotechs). That is why there is not going to be lots of open source in bioinformatics software. The stuff that is there, is written in Perl by biologist (people who do not necessarily have formal training or talent for coding).
A scientific coder.
What should be open source and free beer free is the specialized software used by many researchers for processing DNA and Protein sequence information. For instance, take the very nice software package Vector NTI. Does many things researchers want. Also costs $5000. Instead of NIH (government science funding agency) money being spent many times (once per funded lab), what they should do is earmark some money to get programmers to write for free usage software like Vector NTI. It would cut down on the redundant purchase of software by many government-funded laboratories. Don't even get me started on how much research money is being spent on Windows, Word, Excel, PowerPoint, and Adobe Acrobat...
I work in genetics, and particularly with the computing aspect of it. My lab has a tight budget, and open source analysis software would be a tremendous help to us.
Of course, we have some OSS tools already, namely EMBOSS and others, but the big hitters in the bio-computing field (VectorNTI, MacVector, DNAstar, etc) run in the $5000-10000 range per license. Right now, they are much more usable than their open sourced cousins. I'd love to see genetics software continue to be developed open source. We could give less taxpayer money to software corporations.
"It's the age-old debate; what follows the heart of the scientific method more? Peer review, or getting the information out as fast as possible?"
The scientific method is both peer review and the fast, free flow of information. Further, both are so intertwined that it is impossible to separate the two or say one is more important than the other. Without the free flow of information, one cannot cannot give a proper peer review of the work. Without good peer review, the information you get is garbage, thus clouding the review and making the knowledge suspect.
The work should be made open source after good review, not before. That way, you build upon that previous work such that the next scientific advancement is upon solid ground.
-When going for broke, go for Ithaca!
Geeting info ASAP for review is the only REAL peer review. What journals call ``peer review'' is just editorial censorship of any real advance in science; any revolutionary science is deemed ``not suitable for publication''. Or sent to refeeres chosen by the *editor*. Any paper that does not conform to the prevailing views is NEVER published in major journal---want to check? Only more-of-the-same.
So, as a scientist myself, I vote for fast release: let ME (a real peer) do the review. Editorial censorship? Thank you very much, but no, I stopped needing paternalism after my early teens.
Gustavo A. Concheiro Perez
bioinformatics.org
They host a large number of these open-source bio software. Really worth a look if you're interested in the topic.
Being that by the end of the week I'll actually be working for a biotech software company, I sure hope that the scientific community doesn't force mandatory Open Source. Now while the agrument can be made that keeping the software restricted is hindering the biotechnology industry, compared to the evils of gene patenting, software has a very small role in the big picture.
Now even though I would love to find my own gene and would probably patent it and start a company like everyone else, I do believe that patents on genes that occur naturally is wrong. Its akin to patenting Heart Failure, and then forcing everyone to pay you dues whenever they try to see if someones heart is at risk to failing, or when they try to revive the heart. Now whats even worse is that the patents of genes are used to create a monopoly where only the patent holder and those who have enough cash are allowed to try to fix the gene. Its like the hypothetical heart failure patent holder suing Abicor for creating an artifical heart.
So to recap, forcing companies to make their software open source, not very important. Preventing companies from patenting naturally occuring genes, much more important.
Right?
Seriously, with the amounts of money to be made in tomorrow's genetics industry at stake, corporations are going to protect the research they fund and will do their own debugging, thank you very much.
What's in a Sig?
There is really no argument here, the article is confused. The software is a TOOL for the research. The results of the research can be peer reviewed, the software can be open source. In fact the latter would even aid the former. There is no clash here. Researchers AND developers can be totally happy.
As backup to what I say, I am involved in creating some software for analysis of microarrays. I would be quite happy for this software to be open source. Indeed it would allow more researchers to then use the software to get results to go in their peer-reviewed papers.
The whole point of what is called "the Scientific Method" (check out any 1st year university-level science textbook for what this means) is that any research has to be peer-reviewed and results have to be reproducible. In this sense, the scientific community has been "open-sourcing" their work for centuries. Keeping work secret invalidates it as serious research. Open-sourcing the tools with which the research is carried out only makes sense.
There was an interesting discussion on this topic last year over on bionet.software, with contributions from several authors of significant bioinformatics software (search for 'open source' in the bionet.software group at groups.google.com).There's also a good interview with Ewan Birney (of BioPerl and EnsEMBL fame) about open source bioinformatics here:
http://conferences.oreilly.com/biocon/
Like some of the other contributors to this thread, the argument I find most convincing is that peer-reviewed scientific publications usually (and for very good reasons) require full disclosure of methods - why should software be exempt from this? Similarly valid criticisms were made about _Science_'s decision to publish the Celera human genome paper with only conditional access to the primary data. Biotech companies are of course free to conceal both their data and methodology, but the scientists involved should not then expect the right to contribute to the peer-reviewed literature.
There are also sound economic reasons for an open source approach to significant scientific software: it's ironic that software developed with public funding has in some cases been commercialized by the host institution of the programmers, leading to a situation where other laboratories that receive grants from the same funding body end up paying substantial license fees! (some funding agreements are now savvy enough to include a clause preventing this). In fields like molecular biology, there's also the risk that initially reasonable license fees can rocket when the software proves to be useful. This is pretty much what happened in the case of GCG, a set of sequence manipulation utilities originally developed by a university department, but later acquired by a large biotech company. The increasingly restrictive and expensive license was one of the factors that led to the creation of EMBOSS:
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
a GPL/LGPL'd alternative that in many respects now surpasses GCG, and runs on a wider range of Unix-like platforms (including Linux, Cygwin and MacOS X).
I recently gave a presentation for the Central Valley Bioinformatics Users Group (www.cvbig.org) titled "Clustering BLAST with Linux, Perl, PHP, and Postgres". Some of the slides are available here. I say some, because I just started the process of open sourcing my work. Management at Sagres Discovery (my employer) has been very receptive to releasing my code. And why not? My involvement in the open source community (and CVBIG in particular) taps the company into large reservoir of skills and experience (not to mention potential employees). Besides, open sourcing the tools does not mean open sourcing discoveries. Bioinformatics will continue to benefit from the open source movement. Fortunately, many in academia and industry recognize its value.
First entomology, then virology, and finally bioinformatics systems. Bugs follow me wherever I go.
I received the following email message from the CFO of a company called LabBook, about my Bull Shit Markup Language (BSML) web page.
Appearently, they would prefer that people searching for "BSML" did not turn up my web page. I wonder if they've tried to get the Boston School for Modern Languages to change their name, too?
Now isn't the whole point of properly using XML and namespaces to disambiguate coincidental name clashes like this? If LabBook thinks there's a problem with more than one language named BSML, then they obviously have no understanding of XML, and aren't qualified to be using it to define any kind of a standard.
Maybe LabBook should put some meta-tags on their web pages to decrease their relevence when people are searching for "Bull Shit" or "Modern Language".
-Don
========
From: "Gene Van Slyke" <gene.vanslyke@labbook.com>
To: <don@toad.com>; <dhopkins@maxis.com>
Sent: Monday, November 12, 2001 10:36 AM
Subject: BSML Trademark
Don,
While reviewing the internet for uses of BSML, we noted your use of BSML on http://catalog.com/hopkins/text/bsml.html.
While we find your use humorous, we have registed the BSML name with the United States Patent and Trademark Office and would appreciate you removing the reference to BSML from your website.
Thanks for your cooperation,
Gene Van Slyke
CFO LabBook
========
Here's the page I published years ago at http://catalog.com/hopkins/text/bsml.html:
========
BSML: Bull Shit Markup Language
Bull Shit Markup Language is designed to meet the needs of commerce, advertising, and blatant self promotion on the World Wide Web.
New BSML Markup Tags
CRONKITE Extension
This tag marks authoritative text that the reader should believe without question.
SALE Extension
This tag marks advertisements for products that are on sale. The browser will do everything it can to bring this to the attention of the user.
COLORMAP Extension
This tag allows the html writer complete control over the user's colormap. It supports writing RGB values into the system colormap, plus all the usual crowd pleasers like rotating, flashing, fading and degaussing, as well as changing screen depth and resolution.
BLINK Extension
The blinking text tag has been extended to apply to client side image maps, so image regions as well as individual pixels can now be blinked arbitrarily.
The RAINBOW parameter allow you to specify a sequence of up to 48 colors or image texture maps to apply to the blinking text in sequence.
The FREQ and PHASE parameters allow you to precisely control the frequence and phase of blinking text. Browsers using Apple's QuickBlink technology or MicroSoft's TrueFlicker can support up to 65536 independently blinking items per page.
Java applets can be downloaded into the individual blinkers, to blink text and graphics in arbitrarily programmable patterns.
See the Las Vegas and Times Square home pages for some excellent examples.
Take a look and feel free: http://www.PieMenu.com
Science and Open Source are different animals.
Just because Scientists appear to be independent agents, it does not mean that Science in itself is not cohesive.
Open Source was to some extent initiated by published listings, including source code for the early Unixen. When this was closed, the attempt was to develop "free" copies of the utilities, and then, the ultimate operating system.
The Open Source is now just moving into more advanced applications, replicating the larger commercial things in scope.
In some extent, Web Browsers were the first really open-source application that was a class leader. Netscape made a browser that rolled in the email client and ftp client, but Mosaic was there first.
But what we need is some sort of open-source idea development.
Science, especially as practiced in the West, is more based on a "religion" that has won its place through arguement, rather than cooperation.
In essence, an idea that moves into a spot becomes entrenched, and more difficult to move. So a new idea needs to arrive as more powerful to displace it through arguement.
For this reason, Scientists tend to be more cautions of letting ideas gain a foothold.
In the book "The Cathedral and the Bazaar", Eric S Raymond contrasts the world of acedemia and open source, the former competative and the latter cooperative.
Acedemia places fully developed ideas in competition, and your status in acedemia depends on your publications. The Open Source community is more open to the development of someone else's idea, and overlooks the flaws in the supplied implementation.
So whereas Scientists rejected, say, Velikovsky's ideas as crazy [because the presented package as a whole does not work], the open source people accepted Linus' alpha kernel as an idea to be extended into Linux.
We could have an open source Science that looks into alternate views. An Enthusist's science, not guided by acedemia, so to speak. But we disparage the opportunities as cranks, and build no alternate to acedemia.
de Bono offered Six Hats of thinking, as an alternate. Maybe we should look at this.
OS/2 - because choice is a terrible thing to waste.
I don't think you can get a patent on a naturally occurring thing. Genes are naturally occurring, so you can't "own" a particular gene sequence. I think the patents in this area are for methods of isolating/modifying/etc. the genes that are already there. If I come up with an innovative way to identify or isolate or modify a particular gene, then I can patent my method. I can patent the new gene created by my innovative method. But I can't find a gene then say, "I found it, I want to patent it and own every occurrence of this gene in nature." That is not possible with our current patent laws. I think this system is ok for now. Without allowing people to obtain patents on the results of bio-research, would you spend millions (billions?) of dollars doing the research? (Answer: Note, not if you are smart.) Neither would the companies currently doing this research. We need to provide some incentive to them, let them recoup their investment costs and even allow profit (gasp!). Patent law is the best friend of innovation and dissemination of scientific information. It provides motive to create. It allows monumental investment in something that, once disclosed, can be used by anyone (since it is only an idea).