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Old 05-18-2011, 06:47 AM   #1
GW_OK
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Default Trade Secrets in Science

I've been pondering this post for a while now, and the latest censoring of info (in the Ionosphere thread in the iontorrent forum) has brought me here to ask why sequencing companies are so damn secretive about stuff. I'm not singling out any one company over another, since they all have their little bits of info they won't share.

Should only authorized users know how long you incubate the end-repair reaction? Is it really that imperative that only your customers (and sometimes not even then) know what the sequence of your adapters are?

It's not like this is top secret stuff anyway. When I wanted to know what was in all of the GA2x reagents I went and found the illumina patents and then proceeded to tell the reps when they stopped by what was in each one, after they told me it was proprietary knowledge.

Are they worried about the competition? Isn't most of the main tech patented and licensed anyway? Do they want a lock on reagents as a revenue generator? How much does something like the NEBnext kits hurt the bottom line? Here's a tip, just refuse to support libraries or runs thereof created with non-company stuff.

Isn't one of the most basic tenants of science communication within the community? Do we not have, in every article, a methods section delineating how every process presented was preformed?

Sigh, I don't know. Maybe it's just the coffee talking. Feel free to agree or disagree, but I'm a little annoyed with it.
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Old 05-18-2011, 06:57 AM   #2
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It's all about the perceived risk to the bottom line, a bit like how printer manufacturers do everything in their power to stop you using third-party ink cartridges or topping up your toner.

I think it's time sequencing companies embraced the fact that scientists are born tinkerers and used that to their advantage. Access to as much information as possible may mean we can develop protocols that enable new types of sequencing experiments to be done. The resulting paper is going to be free marketing for that instrument. Also, having all the info indexable by Google is going to encourage users without machines to try and plan out their own experiments and maybe buy an instrument in future.

A good example would be the single-strand transcriptomics protocol developed at the Sanger.

Last edited by nickloman; 05-18-2011 at 06:59 AM.
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Old 05-18-2011, 07:54 AM   #3
tonybolger
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Quote:
Originally Posted by GW_OK View Post
I've been pondering this post for a while now, and the latest censoring of info (in the Ionosphere thread in the iontorrent forum) has brought me here to ask why sequencing companies are so damn secretive about stuff.
It's a good question, especially since the information is out there anyway - perhaps they just like the warm fuzzy feeling of fake secrecy, when in reality, they are just making things awkward for their customers for no good reason.
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Old 05-18-2011, 09:22 AM   #4
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well, not just the reagents and adapter sequences .. their software is even more fuzzy. one cannot get comprehensive information on the assumptions in their algorithm, intermediate files for data extraction .. and a very superficial but huge documentation manual!
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Old 05-18-2011, 10:25 AM   #5
GW_OK
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Quote:
Originally Posted by tonybolger View Post
It's a good question, especially since the information is out there anyway - perhaps they just like the warm fuzzy feeling of fake secrecy, when in reality, they are just making things awkward for their customers for no good reason.
I know, right? I think anybody could, with time and money, figure out just about everything "proprietary". Who are they really keeping the secrets from? And nickloman's comment on scientists being tinkerers is dead on. Let us play with your stuff, sequencing companies. Let us make it better.
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Old 05-18-2011, 11:17 AM   #6
krobison
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I have a degree of sympathy for very small players who are keeping true trade secrets, since many things in the field are not patentable and therefore if you fully publish certain details any of the big players could duplicate your product & wipe you out.

I can also understand a company wanting to minimize the risk of a customer inadvertently accessing outdated information. But, the surest way to do that is to make it hard to get to the official source!

That said, behavior such as Ion's is unspeakably stupid. It is horrendously short-sighted to equate your user base with your current ownership. Future owners will want to look under the hood. Furthermore, for sequencing the various steps are discrete and may be distributed across organizations due to collaborations or other factors.

As an example I have described recently at BioIT, my organization does not own a sequencer. As a result, we have accessed almost every platform through outsource vendors. In some cases we have simply handed raw nucleic acids to the vendor, whereas in another case we constructed libraries, applied SureSelect and sent them only the final library preps.

As Tony said, most of this "security through obscurity" is an illusion. Do you really want to behave like the music industry, which fought an expensive and counter-productive battle against unauthorized distribution, particularly when spreading the information costs you nothing?
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Old 05-18-2011, 11:34 AM   #7
epistatic
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As a strong proponent of reproducible research, I think that (within reason) published work should have the ability to be verified by other scientists. The ability to reproduce research should not hinge on the hidden aspects of unseen analysis algorithms, changing kit components, etc. Companies should be as open as they can to promote true science.

Generally information is hidden for a reason. Often the information infringes on non-licensed IP or in the case of new products, conflicts with the marketing message.
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Old 05-18-2011, 12:13 PM   #8
wraithnot
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As a fellow scientist and tinkerer, I completely agree with you. However, I once heard a biotech CEO address a similar point from a completely different angle. He basically said that if they gave out too much information then other researchers would use the information to beat his company to the punch by making key improvements, patent those improvements, and force his company to pay to license the patents.

The implication was that most modern patents are based on fairly predictable progress rather than completely unexpected breakthroughs. And the game is to figure things out more quickly than anyone else and get the key patents. So the situation is probably not going to change unless the bar is raised for how "non-obvious" something has to be in order to be patented.

Another aspect is that universities are getting far more interested in patents and the money they can bring in. A great deal of research sponsored by government grants is patented these days so it's not just private companies that are involved. I have some first hand experience in this- I was an inventor on a patent application in graduate school and I got a cut of the proceeds when it was licensed!

Quote:
Originally Posted by GW_OK View Post
I know, right? I think anybody could, with time and money, figure out just about everything "proprietary". Who are they really keeping the secrets from? And nickloman's comment on scientists being tinkerers is dead on. Let us play with your stuff, sequencing companies. Let us make it better.
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Old 05-18-2011, 02:08 PM   #9
Joann
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Patents and patent applications are a very good source of wet lab technical data that may indeed not appear elsewhere in published form. Furthermore, the use exclusivity stemming from a granted patent expires approximately 20 years out from the filing date and biotech patents themselves often reference standard lab methods, including older patents. Published patent applications provide a current view of the patent pipeline.

In the Nature Protocols article, "Patent searches as a complement to literature searches in the life sciences--a 'how-to' tutorial, by Frank Seeber
doi: 10.1038/nprot.2007.355 use of published patent data to obtain "proprietary" information is also described.

It may be useful, especially in academic discussion, to reference a sequencing methodology through patent literature citations. That way, everybody is on the same page. This also enables patented vs non-patented technologies to be differentiated. (Scirus is one source where patent citations can be downloaded to a bibliographic format along with regular academic journal publications.) For an unpatented novel sequencing method, you have one year from date of your academic article publication to file for a patent on the work! And only the inventor(s) can file.
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Old 05-18-2011, 05:42 PM   #10
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Having been on both sides of this argument, I can say there is a no way to please everyone.

I like to tinker as much as anyone, but there is danger in knowing too much. You will break IP's without knowing if you dig too deep. There are plenty of people that don't care about IP, but they probably haven't invented anything.

Adapter sequences seems like frivolous information, but who is the first person you call when your Clusters have low intensity? I bet it's not the oligo factory.

And how many people would tell the truth if you tinkered with your machine? I imagine the first thing people blame is the machine. This has always been a nightmare for support teams.

There is a healthy medium for sharing information. A well moderated forum is a decent start. Yes, moderated.
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Old 05-18-2011, 11:19 PM   #11
tonybolger
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Quote:
Originally Posted by SeqAA View Post
I like to tinker as much as anyone, but there is danger in knowing too much. You will break IP's without knowing if you dig too deep.
How so? Accidentally build a sequencing machine or part thereof?

And there's also the likely violation of the 'non-obvious' requirement for patents if you can just accidentally do it as an individual 'power user'.

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Originally Posted by SeqAA View Post
There are plenty of people that don't care about IP, but they probably haven't invented anything.
Yum, straw.

Quote:
Originally Posted by SeqAA View Post
Adapter sequences seems like frivolous information
And how exactly do you distribute a tool for cleaning up the adapters from the sequence data (legally i mean), given their non-distribution policy?

I've asked, and no dice. It's not like i'm trying to sell my own library prep kits. Yet the sequences are available (in the wrong format) from a dozen different sources online.
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Old 05-19-2011, 06:28 AM   #12
GW_OK
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Quote:
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but there is danger in knowing too much. You will break IP's without knowing if you dig too deep.
I'm sorry but that's a horrible thing to say to a scientist.
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Old 05-19-2011, 07:12 AM   #13
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Agreed, I've just seen it happen before. Biased opinion

The adapter sequences was just an example. I also agree there is little point in hiding them, and I have cloned them just to get the sequence before. I was playing devil's advocate on this one. You could say the same thing for buffers as well. You can usually derive the contents of system buffers, but who is responsible when a run doesn't work with homebrew?

Last edited by SeqAA; 05-19-2011 at 07:17 AM.
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Old 05-19-2011, 07:55 AM   #14
GW_OK
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Whoever makes the reagents is the one who should be on the hook if they don't work properly. And that speaks to the honesty of the researcher, I think. The companies can also request lot numbers and such to verify.
I understand your advocacy of the devil, but if the company says outright that non-authorized reagents won't be supported, what's the harm in at least telling us what they are? And if they are patented, let us know that, too. I don't think anybody' going to be making a buck off something if it's already patented. Plus, if you're working on something that is going to head into IP territory, you can at least know where the boundaries are...
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Old 05-19-2011, 09:07 AM   #15
SeqAA
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Quote:
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Whoever makes the reagents is the one who should be on the hook if they don't work properly. And that speaks to the honesty of the researcher, I think. The companies can also request lot numbers and such to verify.
I understand your advocacy of the devil, but if the company says outright that non-authorized reagents won't be supported, what's the harm in at least telling us what they are? And if they are patented, let us know that, too. I don't think anybody' going to be making a buck off something if it's already patented. Plus, if you're working on something that is going to head into IP territory, you can at least know where the boundaries are...
See, this just sounds too reasonable
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