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?

Comments

Redundant?

[Ebon Praetor]

Didn't we see this article yesterday right here?

Re:Redundant?

[Heem]

nono. Not essentially. its the same article. word for word.
However, I'm glad it got posted again, for I missed the first posting of it, and I work for a biotech company. I don't know how the programmers in my company feel about this, but I tend to agree with Brenner in that it should be kept open-source. Of course, the size of my paycheck may depend on it costing an arm and a leg.

for dummies...

[vinnythenose]

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"?

Re:for dummies...

[cbare]

Well, we already have these:

http://www.oreilly.com/catalog/bioskills/
and
http://www.oreilly.com/catalog/begperlbio/

Scientific Method

[tbone1]

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?

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.

Re:Scientific Method

[Bikku]

Hear, hear.

Speed is of no interest wrt scientific objectives (although it may be of some value in engineering - the application of scientific knowledge for practical benefit). The biggest problem in trying to figure out how the world works, and get some reliable "knowledge", is that nature is extremely subtle and we humans are very good at fooling ourselves into believing our latest theories are actually true descriptions of nature. Hence the rigorous insistence on peer review as just one more mechanism to try to ensure researchers are not inadvertently deluding themselves.

I can't understand why anyone would think "It's the age-old debate". Seems crystal clear to me that the value of science as a method of generating knowledge lies in not making errors (and does not lie in making errors quickly).

Re-read The Feynman Lectures for a refresher on this?

Redundancy...

[metlin]

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.

Re:Redundancy...

[Anonymous Coward]

I think IP rights HELP the dissemination of knowledge.

As you mentioned, property rights (basically the right to exclude others from making using or selling your property) in knowledge does seem at first to be a problem. Everyone should be allowed to benefit, and widespread knowledge leads to more discoveries using that knowledge.

But unfortunately, today lots of "knowledge" comes at a high investment cost. To get many of the products we want, we have to let the maker get a little money out of the deal. So we grant them propety rights and tell them they can profit exclusively from this idea for a finite period of time, both to recoup investment they made (which beefitted us all but which the maker alone paid for) and to profit (to create incentive for the maker to make more useful things in the future).

In fact, granting IP rights allows inventors, etc. to publish their ideas when they often would be forced to keep them secret for fear of others appropriating their ideas. The vast majority of trade secrets are ideas that do not meet the threshold for patent protection. So the only way the maker can protect it is to keep it secret.

Re:Redundancy...

[caesar-auf-nihil]

Good research is best accomplished by having all access to all information, so that you don't have to re-invent the wheel or relearn the experiments.

So why do some companies reproduce research that 10 other groups/companies are doing?
1. To see if the work can actually be reproduced. Patents are notoriously unreliable for their reproduciblity in the chemical sector.
2. To learn more about the technology, to either improve it or use it for another project. By doing the experiments yourself, you get a lot of knowledge that is never written down on paper.
3. Having a completely different group of scientists working on a research project can lead to a completely different way of interpreting the results. Therefore, the conclusions and applications of the research are different. (Diversity of thought!)
4. The idiots forgot to do a literature search before starting their project. This unfortunately happens more often than it should.

It does look like at first glance that reproducing other previously done work is a waste of time. However, given the advantages of the first 3 points, it will continue to occur this way, and for the benefit of science, it probably should.

Software companies pockets

[Mac Nazgul]

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.

open source of university researchers' code!

[phranking]

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.

MMM Open Source BioTerrorism.. yummy!

[scorp1us]

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.

Re:MMM Open Source BioTerrorism.. yummy!

[hive42]

releasing genetic code into the public domin won't help bioterrorists, just knowing what the sequence of a piece of dna doesn't help a person know what it does or how that code can be used to alter other organisms pathogenic or otherwise the majority of academic genetics is already open source just look at http://www.embl.org, http://www.ensembl.org, http://www.ebi.ac.uk and this is software and dna sequences, computer code and the genetic code annot be equated we by no means understand teh gentic code well enough yet for that sort of thing to be possible and certainly is unlikely that we will in the near future

Peer or quickness?

[JJ]

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.

Advantages of open source scientific software.

[rice_burners_suck]

*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:

• While some folks are using the software, others can optimize it for increased speed. One of the things that bothers me when I read about some great new supercomputer is wondering how many of those bajillion cycles per second goes to waste because of nonoptimal computation loops. A small change here will make a large difference in the amount of time it take to achieve results.
• The software can by analysed and broken up into distributed programs which can be run on millions of computers worldwide, a la SETI@home.
• Distributed programs can be analysed and combined into one monolithic program that runs on a supercomputer.
• Scientists (or programmers) can add features to these programs, making them perform multiple similar purposes. Or, scientists can pick out a specific computation that they need done on huge amounts of data, and save countless hours, days, or even months that would have been spent computing unnecessary data.

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*

Re:Advantages of open source scientific software.

[Erich]

Some things don't work so well hugely distributed. Your example, fluid dynamics, for instance.

Most fluid dynamics simulations (at least the ones that I helped do) involve lots of I/O. Distributed.net-type-things don't work for anything requiring huge amounts of I/O. They might work in a beowulf-type setting (our fluid dynamics stuff split up across nodes fairly well) but there is a really large amount of traffic, which won't work when people are on the end of a 56k modem. For distributed.net, there is very little traffic compared to the amount of computation. Similar for seti@home.

Most things that require large amounts of computation, though, also require large amounts of bandwith to go through large amounts of data.

Re:Advantages of open source scientific software.

[rice_burners_suck]

One: I don't write VB vandalism. That's right. VB isn't code. It's vandalism. I don't write that trash.

Two: I code in C. I use efficient algorithms. And when the time comes, I optimize the hell out of the 2% of the code that needs it, resulting in enormous performance gains.

Three: I am 4 1337 h4x0r!!!!!!11111111111 j00 suck!!!!11111111111

Re:Macs and Genetics

[well_jung]

Yeah, but we use Open Source software extensively. We use Linux quite a bit (though not as much as Solaris), Perl for damn near everything, and Apache for our web servers.

We use Mac's too. For image processing. And one particular Gene-specific application. But that totals maybe 10 machines. We have more Linux desktops. And more Penguins (4) in the data center than Apples(0).

We own what we bought

[jamesmartinluther]

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.

But science is open-source

[DaoudaW]

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.

Re:But science is open-source

[caesar-auf-nihil]

"The problem being addressed by the petition isn't what is published in peer-reviewed journals, its what isn't being published."

There are several reasons for scientific research being published. Sometimes its because it is tied up in IP issues. Other times its because the work did not pass peer review and the original researchers decided not to press the issue. Or, the original researchers decided not to do additional research to answer the reviewer's comments. Finally, it may be because the experiments did not work. The sheer amount of information that is not made public because the experiment was a failure is staggering. To try and go through all that though, may or may not be of benefit.

All that being said, I do agree that making scientific techniques proprietary does slow the advance of science. However, there are cases where you don't want the technique to become common knowledge. The Manhattan Project is a perfect example of this.

a real life case

[myc]

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.

The software that is used, not the data

[atheist666]

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...

Re:The software that is used, not the data

[Phillip2]

"what they should do is earmark some money to get
programmers to write for free usage software like Vector NTI. "

The same argument of course applies to pretty much all software, not just bioinformatics software.

Actually I think that there is a more convincing argument here. I would argue that the process which is used to generate data is in fact a material part of that data. Without access to the software that operates on the primary data to produce the final result, it is not possible to replicate that result independantly. If bioinformatics wants to be taken seriously as a science, then it needs to able to address the issue of repeatability. Code is part of the methodology, methodology is part of the result. If code is not freely available, then the result is not either.

Phil

Open source it all!

[atomicgirl]

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.

Science is a process of both!

[caesar-auf-nihil]

"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.

Here's another site that follows this stuff

[rchatterjee]

bioinformatics.org

They host a large number of these open-source bio software. Really worth a look if you're interested in the topic.

The importance of full disclosure

[RDW]

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).

Open BSML, instead of protecting the trademark!

[SimHacker]

As long as we're repeating ourselves today:

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.

Re:Open BSML, instead of protecting the trademark!

[SimHacker]

Protect their good name??! "BSML" is NOT a good name!!!

Hello! Earth to LabBook! BSML is a HORRIBLE name, if you want anyone to take you seriously! Any company that would actually name a serious commercial product "BSML" is totally nuts!

It's silly for them to go after someone who has been using the name BSML for years with its most obvious meaning: Bull Shit Markup Language!

They should use XML namespaces to prevent any problems of name clashes, not legal threats of trademark disparagement.

-Don

Scientists and Open Source

[os2fan]

This is slightly off topic, [in that I deal with Open Source Science, rather than the opening of source of a scientific project] but relevant.

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.