Openbiotech.com open source taq vector

[Sebastian S. Cocioba]

I don't know if anyone is aware of this company but they published an open source taq polymerase expression vector and sell it for 40 bucks along with instructions on how to isolate and purify. They also sell a very nice small 2kb plasmid with tons of restriction cut sites. Www.openbiotech.com just thought i would put this out there. Enjoy.

Sebastian S Cocioba
CEO & Founder
New York Botanics, LLC

Sent via Mobile E-Mail

[Mega]

Thanks for sharing!

Sounds great!!

[Sebastian S. Cocioba]

I really like their mission statement. Ill keep searching for awesome finds and post asap. We gotta keep the diy research alive! :)

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

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[Mac Cowell]

Wow!

231.313.9062 // @100ideas // sent from my rotary phone

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[Tom Randall]

The pdf they have of pOpenTag does contain the sequence of this plasmid, although in a very inconvenient format. I turned it into an annotated genbank file and put it up in case anybody wants it. (http://www.roningenetics.org/Sequencing.html) I also posted a slightly different, and to me, simpler, purification protocol for Taq I found a couple years ago based on the one they supply at the openbiotech website, it has fewer higher speed centrifugation steps (which I will use as the only way I have to get to 15000 rpm is in a microfuge), I have not tried either prep yet, I will try this one at some point. The comments in that protocol are those of the person who sent it to me, cant remember his name offhand.

Some of the descriptions of the plasmids on their website are not quite right. For pBR322 they say "pBR322 is a commonly used cloning vector. It contains a pUC origing, ampicillin resistance and supports blue-white screening." pBR322 is based on pMB1 (a ColE1 like plasmid), see Gene 2:95 for the original description of pBR322. It does not have a pUC origin and it does not offer blue/white selection. The need for a better way to select for inserts was a reason why the pUC plasmids with blue/white selection were developed in the first place. As to pUC19, a good reference is Gene 19: 259 (both of these older references are freely available) and its' origin and construction is more complex than having a "pUC" origin, it also involves sequence from some M13 phage vectors that had been developed for cloning and sequencing way back when. This is probably nitpicking, but those new to the field may get confused. If anybody from OpenBiotech is listening they might want to update the site a bit. They do deliver quickly. Hopefully Ill have some time in the future to make my own Taq now, this resource is very useful. If anybody at OpenBiotech wants some pBluesriptSSK+, another pUC like vector, I will be happy to send them some (and an annotated sequence file) if they want to offer that on their site. I think I have some pUC18 and either pUC8 or 9 stocked if they want either of those to offer also.
Tom

[Joseph Jackson]

The founders of Open Biotech will be speaking at the Open Science Summit coming up in a couple weeks.  They are a biotech startup here in the Bay Area and actually have some close ties to the origins of Biocurious from back in the garage days.  

[Mackenzie Cowell]

Hey Joe,

Since you know who the Open Biotech team is, would you mind inviting them to this conversation?  I'm sure we'd all love to hear more about their story and OpenBiotech.com.  Looking forward to it!

Mac

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[Avery louie]

I am impressed.  I will have to send some business their way.

[Bryan Bishop]

On Sat, Oct 6, 2012 at 2:35 PM, Mackenzie Cowell wrote:
> Since you know who the Open Biotech team is, would you mind inviting them to
> this conversation? I'm sure we'd all love to hear more about their story
> and OpenBiotech.com. Looking forward to it!

It's just John Schloendorn. I am glad it's someone we know already,
although now I have to worry about his frightening misunderstandings
about open source...

- Bryan
http://heybryan.org/
1 512 203 0507

[Joseph Jackson]

Thanks guys.  Seems like there is a lot of interest already!  Hopefully the amateur biology market will grow a lot in the coming years.

On Oct 7, 2012 2:54 PM, "Support Gateway" <sup...@openbiotech.com> wrote:

Hi, I'm Justin from Open Biotech.  Thanks for bringing me into the conversation Joe.  I've cc'd my direct email address and my cofounder John.  We're very happy to get any feedback and would be more than happy to offer any useful plasmids (may or may not experience some issues with licenses on some of them).  I'll look into making your suggested changes regarding pBR322.

John wants to chime in himself on some details.

Best

Justin

[Cathal Garvey]

What's he doing wrong in your eyes? The source code is available (and in
the absence of a "true standard" format, I wouldn't complain overmuch
about formatting). It's not patented, is it? Any license terms that
break freedomdefined.org?

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PGP Public Key: http://bit.ly/CathalGKey

[Bryan Bishop]

On Mon, Oct 8, 2012 at 3:29 AM, Cathal Garvey wrote:
>> It's just John Schloendorn. I am glad it's someone we know already,
>> although now I have to worry about his frightening misunderstandings
>> about open source...
>

> What's he doing wrong in your eyes? The source code is available (and in
> the absence of a "true standard" format, I wouldn't complain overmuch
> about formatting). It's not patented, is it? Any license terms that
> break freedomdefined.org?

Here are some of the frightening misunderstandings:

"Isn’t open source unprofitable? Open source principles did indeed
build a reputation of being unprofitable, largely due to the
experience in software development. Any given piece of software can
be copied indefinitely many times, for free, with zero skill required.
Why would I pay for a piece of software, when its creator encourages
me to legally copy it? Thus, it is at least a legitimate question how
to make money in open source software."

People have figured out how to make money in open source for a long,
long time. Open source is the money-making arm of free software,
that's the whole point of the re-branding and getting open source into
businesses. blah.

"We hope that these companies will adapt, ultimately acquire our open
source DNA sequences and begin competing on manufacturing the same
products. This will result in a business landscape where the key
competitive trait stops being how well you keep your secrets, and
starts being how efficiently you can make quality products. .....
Ultimately, we anticipate no less than an industry-wide collapse of
biological reagent pricing as a direct result of our open source
policies."

So the reasoning in that paragraph is: because people can share our
sequences, the other companies will collapse or be forced to adapt...
because...?

But still, I'm glad John is doing this.

[Cathal Garvey]

On the whole, those points are debatable, rather than outright false.
For example, I wouldn't doubt that going Open Source cuts profits,
although I'd confidently say that doing so extends the stable lifetime
of a company and tends to prevent boom-plateau-spiral patterns. And
that's leaving aside the ethical angle of simply making the world a more
excellent place. I guess my answers would be different, but not entirely
contradictory, either.

As to collapsing industries.. well, that happened in open source, and
it's still happening. Linux itself is still a minority operating system
(although the stats from Humble Bundle show it creeping up on MacOSX at
least, and both of them creeping on Windows), but relatives/derivatives
of Linux first came to entirely dominate the embedded market, then got
ripped off for MacOSX, and most recently became the de-facto for mobile
operating systems (iOS, Android).

Open Source does kill proprietary, for certain values of "open" and
"proprietary". And certain elements of an entirely closed ecosystem
simply can't survive the advent of openness; if you have the option of
two plasmids, and all else being equal one lets you sell derivatives and
the other doesn't, are you really going to bother buying the latter?

On 08/10/12 15:37, Bryan Bishop wrote:
> On Mon, Oct 8, 2012 at 3:29 AM, Cathal Garvey wrote:
>>> It's just John Schloendorn. I am glad it's someone we know already,
>>> although now I have to worry about his frightening misunderstandings
>>> about open source...
>>
>> What's he doing wrong in your eyes? The source code is available (and in
>> the absence of a "true standard" format, I wouldn't complain overmuch
>> about formatting). It's not patented, is it? Any license terms that
>> break freedomdefined.org?
>
> Here are some of the frightening misunderstandings:
>

> "Isn�t open source unprofitable? Open source principles did indeed

[Nathan McCorkle]

Hi Justin and John,
It would be really awesome if you could stock a strain of
Kluyveromyces either lactis or marxianus, along with the pKLAC2 or
similar plasmid. You can find the sequence on NCBI, but I don't know
if NEB has licensing on it since they use it in their Protein
Expression Kit:
http://www.neb.com/nebecomm/products/producte1000.asp

If you even just carried the plasmid, I'd be fine, as there is a good
amount of literature isolating natural strains from yogurt and similar
milk products.

Thanks,
-Nathan

Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Cathal Garvey]

Hey OpenBiotech guys: great stuff, thanks! Will have to order a shot of
plasmid from you guys for the E.coli end of my work. :)

The more Open Source wetware we can find, provide, share or sell, the
faster this field will grow. Thanks for choosing open!

[Josiah Zayner]

Am I missing something but aren't all vectors open source?

Also, $40 for pUC19? that is ludicrous. Even companies give that away for free.

[Jeswin]

On Tue, Oct 9, 2012 at 10:35 AM, Josiah Zayner <josiah...@gmail.com> wrote:
>
> Am I missing something but aren't all vectors open source?
>
> Also, $40 for pUC19? that is ludicrous. Even companies give that away for
> free.
>

Nothing in life is free. I don't understand why you think a physical
item is free. The word "free" is over-used nowadays. I created HBV
plasmids in my lab. We sell it for a price. Work was done to produce
it. We created mutations into the stock plasmid and verified the
plasmid by qPCR and by sequencing it.

Start-ups, like the OpenBiotech and the company I work at, need a
revenue stream. We can't afford to give stuff away. The big guys can
probably give away samples.

Why are you complaining? Just get your pUC19 and other stuff from the
people who give it away.

[Josiah Zayner]

I never said it should be for free. Of course it costs money to ship and produce. But I thought Open Science was about helping people to do science not charge them 10x or more what it costs to produce.

I don't need pUC19. In fact people can acquire it from:
http://www.the-odin.com/ocondb/listings.php

for $4.

My original question was never answered though. Are not all plasmids open source? The sequence and maps for almost every single one are available?

[John Patton]

No not all plasmids are open source.  Many times different sequences within these different plasmids are patented.

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[Cathal Garvey]

In the sense that the "source" is visible, yes. According to the
generally accepted definition of "Open Source" as meaning "ready and
legal to modify and redistribute under reasonable terms", no.

There's also the code clarity factor. Javascript could be said to be
"open source" if all you want is to see the source code, but most
javascript is highly obfuscated by minimisation to reduce bandwidth
costs. That wouldn't be considered open source unless there's a link to
the source (the GNU foundation actually offered a standard for linking
to licenses and sources in this case).

Similarly, if your plasmid source is just a string of ACGT without
useful, standard annotation, it's not really open source, either, even
if the license is friendly.

I think, given recent discussions on the meaning of open, it may be
useful to coin and use the term "Free Wetware" to describe biomaterials
in the same way that "Free Software" is used to describe software. Free
Wetware is open source (useful, highly annotated format), copyleft
(ensures forward freedom), and free-as-in-libre (guaranteed freedoms for
the end user to modify, hack and redistribute or sell).

Also, I'm with Jeswin; if you don't like paying a company for a product
that another one is offering for free, don't buy it. But I'd balk at
being entirely mercenary here; I sometimes buy expensive chocolate bars
from a local company rather than cheaper chocolate from a multinational,
because of the side-benefits of supporting local economy and encouraging
development. Likewise, given the option to buy puc19 from a dedicated
open source company or getting a sample from a commercial company whose
other products I have no interest in.. Not only is the former supporting
a development project I approve of, the latter is actually very slightly
dishonest if I don't actually plan to be a customer (not that I have any
guilt!).

Put another way, nobody's forcing you to buy DNA at any price, so
there's no need to condemn them for offering it at a price of their
choosing (unless they patent it and forbid you from getting it
elsewhere/making it yourself; then I invite you to bitch away! :)).

On 09/10/12 15:53, Josiah Zayner wrote:
> I never said it should be for free. Of course it costs money to ship and
> produce. But I thought Open Science was about helping people to do science
> not charge them 10x or more what it costs to produce.
>
> I don't need pUC19. In fact people can acquire it from:
> http://www.the-odin.com/ocondb/listings.php
>
> for $4.
>
> My original question was never answered though. Are not all plasmids open
> source? The sequence and maps for almost every single one are available?
>
>
> On Tuesday, October 9, 2012 9:47:45 AM UTC-5, phillyj wrote:
>>

>> On Tue, Oct 9, 2012 at 10:35 AM, Josiah Zayner <josiah...@gmail.com<javascript:>>

>> wrote:
>>>
>>> Am I missing something but aren't all vectors open source?
>>>
>>> Also, $40 for pUC19? that is ludicrous. Even companies give that away
>> for
>>> free.
>>>
>>
>> Nothing in life is free. I don't understand why you think a physical
>> item is free. The word "free" is over-used nowadays. I created HBV
>> plasmids in my lab. We sell it for a price. Work was done to produce
>> it. We created mutations into the stock plasmid and verified the
>> plasmid by qPCR and by sequencing it.
>>
>> Start-ups, like the OpenBiotech and the company I work at, need a
>> revenue stream. We can't afford to give stuff away. The big guys can
>> probably give away samples.
>>
>> Why are you complaining? Just get your pUC19 and other stuff from the
>> people who give it away.
>>
>

[Andreas Sturm]

http://www.neb.com/nebecomm/products/producte1000.asp

I love that kind of stuff :) 

Antibiotic free selection in yeast, protein of interest is excreted in medium. 

The only bad thing about this: The price, it's horrible!!!!!! 

[Josiah Zayner]

It is just my opinion that providing something cheap adds more for the community. If people want to make money they should go for it. But also, if they want to make money I should be able to suggest that they are overcharging.

I support open science and free science. Most people who do these things are not independently wealthy and so have a small budget. If Open Science is going to be significant in my opinion, tools need to be placed in the hands of people easily and cheaply.

I have nothing against OpenBiotech.com they are trying to make money but I question how much they are trying to further Open Science.

The whole Hacking culture was started because people demanding free access or cheap access to things. In fact in The Conscience of a Hacker aka Hacker's Manifesto it says "We make use of a service already existing without paying for what could be dirt-cheap if it wasn't run by profiteering gluttons"

I am not calling OpenBiotech.com profiteering gluttons at all or maybe I am. But I can provide these same plasmids to people for the cost of shipping or slightly greater.

What is the point of Open Science? To advance science? To make money?

If it is to advance Open/Free Science then support things like the Open Construct Database I am trying to build where people can obtain plasmids and strains for 10x times less than OpenBiotech.com charges. A friend just shipped me a Taq plasmid with a 6xHis tag so it can be purified using metal chromatography suuupper easy. If people want it they can just ask. It will be on the Open Construct database as soon as I receive it with protocols for purifying the Taq. You can even use the crude bacterial cell lysate for a quick and dirty PCR.

If the point of Open Science is to make money then support whomever you wish.

But seriously I have not been on this list long but $500 PCR machines and $40 plasmids all under the banner of Open Science when I can acquire a $70 functional PCR machine on eBay and a plasmid for the cost of shipping. Is this really Open Science? Sounds like Profit Science to me.

</End Rant>

[Reason]

> -----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On
> Behalf Of Josiah Zayner
> Sent: Tuesday, October 09, 2012 11:34 AM
> To: diy...@googlegroups.com
> Subject: Re: [DIYbio] Re: Openbiotech.com open source taq vector
>
> I have nothing against OpenBiotech.com they are trying to make money
> but I question how much they are trying to further Open Science.
>

[snip]

>
> I am not calling OpenBiotech.com profiteering gluttons at all or maybe
> I am. But I can provide these same plasmids to people for the cost of
> shipping or slightly greater.
>
> What is the point of Open Science? To advance science? To make money?

It is exceedingly hard to further a cause without developing ways to make
money in doing so. Charity - such as offering services at cost - is
inherently limited, as does not scale well. Philanthropy is helpful in early
stages when there is little incentive for businesses to be established, and
where the level of philanthropy that can be mustered can make an impact
given the size of the market, but is increasingly less so thereafter. There
must be businesses as soon as possible in order to attract and help support
an ecosystem of investment and interest, and in order for growth to take
place at all: you can only grow provision of a service easily if there is
profit in providing that service. Opposition to this process of
commercialization of a space is opposition to growth and progress, no matter
how well intentioned.

Reason

[Nathan McCorkle]

On Oct 9, 2012 12:34 PM, "Josiah Zayner" <josiah...@gmail.com> wrote:
>

> I am not calling OpenBiotech.com profiteering gluttons at all or maybe I am. But I can provide these same plasmids to people for the cost of shipping or slightly greater.
>

Are you working purely out of your home lab? If not, are you sure you're not just passing some invisible cost up the chain to your employer/school?

[Josiah Zayner]

I use all my own equipment and supplies.

[Josiah Zayner]

Cost of materials:
LB broth: $40 for ~25 liters worth of culture
Ampicillin: $10 for ~120 liters of culture
Miniprep columns: $55 for 50 preps but columns can be easily regenerated and used indefinitely

Amount of culture needed for a miniprep that could be sent to 5 people 10mL...

That works out to probably $1 per person for an aliquot of plasmid.

[Jeswin]

On Tue, Oct 9, 2012 at 1:29 PM, Josiah Zayner <josiah...@gmail.com> wrote:
> I use all my own equipment and supplies.
>

So you're one of those lucky few DIYbiologists with a real personal
lab. That's really great.

Is cross-contamination an issue with plasmids (used as expression
vectors, cloning). We see cross-contamination in highly specific
detection assays using qPCR. Not sure if this is a problem in the
other uses of plasmids.

If cross-contamination is a possible issue, would the DIY producer
verify the plasmid?

[Nathan McCorkle]

On Tue, Oct 9, 2012 at 1:38 PM, Jeswin <phill...@gmail.com> wrote:
> On Tue, Oct 9, 2012 at 1:29 PM, Josiah Zayner <josiah...@gmail.com> wrote:
>> I use all my own equipment and supplies.
>>
> So you're one of those lucky few DIYbiologists with a real personal
> lab. That's really great.
>
> Is cross-contamination an issue with plasmids (used as expression
> vectors, cloning). We see cross-contamination in highly specific
> detection assays using qPCR. Not sure if this is a problem in the
> other uses of plasmids.

Where is your sample coming from, mini/maxi-prep? Depending on how
small the contam signal is, I wonder if that's just mispriming of the
primers.

[Jeswin]

On Tue, Oct 9, 2012 at 2:10 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
>
> Where is your sample coming from, mini/maxi-prep? Depending on how
> small the contam signal is, I wonder if that's just mispriming of the
> primers.
>

oh, our contamination issue was solved a long time ago. We used to
purify our plasmids in the same lab as the qPCR. The contamination was
random and solved after moving all PCR work to an air-flow hood.

I was asking about contamination issues from DIY folks who would like
to provide plasmids.

[Josiah Zayner]

Never done qPCR on a miniprep. I don't see how there could easily be plasmid cross contamination though. That is what antibiotic selection is for I thought.

[Cathal Garvey]

Have you any children or dependents? How much rent do you pay? After all
other expenses, what standard of living do you expect? Have you a wife
or other partner who (quite reasonably) expects that you contribute to
the costs of living and the costs of enjoying that life?

It's easy to cry foul when someone tries to make a living when you have
a very low-cost lifestyle, which is normal for students and postgrads.
But, life gets expensive very quickly, and that's got nothing to do with
being profligate. Kids are expensive, and trying to skimp on them does
them an injustice. Living space is expensive, and cutting short on that
means less sleep due to noisy children, means less happiness and
productivity, means less money earned already. And, enjoying life (which
is critical, not an optional extra) costs money. I wouldn't ask anyone
to sacrifice their joy so I can have cheap pUC19.

Leaving aside *all* of the above, what are your development costs? Are
you paying for the man-hours and prototyping costs of designing and
ordering the plasmid that you're producing so cheaply? No, you're taking
someone else's work and undercutting them because you feel you deserve
$5 plasmids, even if it's only a one-time expense.

I spent three solid months alone designing my plasmid, without pay. I
spent �1000 ordering the thing, and another unpaid month waiting for it.
Now I'm spending month after month testing the thing so I can release it
with a working instruction manual. Because I'm releasing open source and
patent free, I can safely expect that sales will suffer a rapid falloff
due to saturation of the community, and I'll have to make another
product just to keep making a living.

So please, tell me I should expect to make a comfortable living selling
my plasmid for $5 and netting in the range of perhaps (maybe?) 500
sales, giving me $2500. I'd love to know how that'll cover not only my
unpaid past work, but even my present costs of childcare, food, rent,
and happiness.

On 09/10/12 18:29, Josiah Zayner wrote:
> I use all my own equipment and supplies.
>
> On Tuesday, October 9, 2012 12:19:33 PM UTC-5, Nathan McCorkle wrote:
>>
>>

>> On Oct 9, 2012 12:34 PM, "Josiah Zayner" <josiah...@gmail.com<javascript:>>

>> wrote:
>>>
>>
>>> I am not calling OpenBiotech.com profiteering gluttons at all or maybe I
>> am. But I can provide these same plasmids to people for the cost of
>> shipping or slightly greater.
>>>
>>
>> Are you working purely out of your home lab? If not, are you sure you're
>> not just passing some invisible cost up the chain to your employer/school?
>>
>

[Josiah Zayner]

You have these things to pay for, sure, but how can you place that on other people such that it is their responsibility to take care of you? 

No, I don't have many expenses that is the lifestyle I live. Should I be hated for it?

I am not undercutting anyone. Just as they provide a service for what they think it should cost so do I. 

Everyone wants to be paid for their work and that's great. Then do work that is worth being paid for. 

In the Open Source Community I spent years and ten of thousands of lines of code developing a piece of software, IP Sorcery. At one time it was in the top 500 most downloaded software on Sourceforge. Never asked a cent for it and never received a cent for it. People sell training courses to use this software, someone wrote a chapter in a book about how to use the software and never even told me. It has been put in Linux Distributions and used to discover security bugs. Some college courses use it. It is free as in Knowledge. I would like to think it is that way because it was free. But maybe I am wrong, maybe people would have paid me what it's worth for using it. I didn't and don't ever want money for it though. 

It's not about Me, it is about We.

I have also invested alot of time and resources in Open Science. Maybe not as much as you. 

I think my time and money is a gift to the community. You think your time and money deserve to be paid for by the community. 

 
You are a smart person Cathal. I see your posts and you are an asset to this Group. However, I think there are other ways to make money besides overcharging people for things that should be dirt cheap. Otherwise you are no better than these corporations you choose to not support. 

A $50 plasmid, open source or closed source, is not going to change the way people do Open Science. It is just going to make you money. A $5 plasmid probably won't greatly effect Open Science but at least it is trying to.

Again:

Is a $500 PCR machine going to change Open Science when you can buy them functional on eBay for less than $100.

Is a $38 dremel fuge attachment going to change open science when one can buy old Micro-Centrifuges on eBay for less than $50.

Is a $50 plasmid going to change open science when it is standard procedure in academia/Non-for-Profit to send someone a plasmid for the cost of shipping? 

Open Software has Linux.

Open Hardware has MakerBot and Arduino, Rasberry Pi.

Open Science has a $500 PCR machine.....

Arduino, Linux, MakerBot all have blown up their respective fields not just because they were open but because they were cheap or free. You think Arduino would have changed hobby electronics if the people who designed it and wrote libraries for it charged $70 or $100 for it? 

How can I even write libraries or software to donate for an Open PCR machine when I cannot even afford it? 

Do as you wish that is your ability and your freedom as a citizen scientist. I just think there are things that can be done better and I am trying to do them better. I am not trying to undercut anyone or put anyone out of business. I don't care if people list their plasmid in the Open Construct database for $50. Do I think it is overpriced? Yes? But whatever works, works. If people pay $50 then charge them $50. I want more than money though. I want people to have cheap access to science to watch all the cool and amazing things people come up with even if I don't make any money. 

There are alot of smart people out there and all they need are the resources.

[Cathal Garvey]

You're comparing apples to oranges. I'll agree with you when it's as
cheap and easy to hack life as it is for software, so that I can even
consider an alternative method of making a living.

Meanwhile, I'm kind of sorry for your attitude to life; you must have so
much bitterness when someone charges you a margin for coffee; why didn't
they give it away for free and just hope for tips? Profiteering pigs.

[Jeswin]

The difference between what Josiah does and what Cathal does is that
Cathal (and the Open TAQ vector folks) built their vectors. That is an
expensive process and nothing compared to cloning/maxiprep. The main
point Cathal makes is, if you undercut folks like him, who are
charging a modest fee for their product, then you risk putting their
R&D on the chopping block. I doubt that Cathal or Openbiotech are
getting huge profit margins for their work.

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[Cathal Garvey]

Pretty much exactly my point, thanks Jeswin. I'd have zero problems with
Josiah designing, testing and releasing his own plasmid for $5 if he
likes and can afford to do so; that's awesome work, great community
spirit and a boon to the community. But I cannot afford to do the same
thing, so I resent being treated as a greedy capitalist because I charge
what I *have to charge* in order to continue doing this at all. And,
although it won't change my fundamentally vulnerable business model at
all, I resent seeing someone take my hard work, *deliberately*
undercutting me ASAP, and accusing me of overcharging, all for the price
of a sample.

Free Wetware must reserve the right to resell, and I believe in that.
And I won't take any efforts to prevent reselling. But it would
essentially just insult me to see someone doing it just to prove a
misguided point or to make their own quick buck explicitly at my expense.

I imagine the Arduino guys get bothered seeing other companies copy
their entire product line without improvement and undercut them.
Fortunately for them, their customers aren't freetards, and are willing
to pay for a great, ethical company, knowing that their money goes to
better R&D. If everyone bought SEEDuinos because they were half the
price, Arduino would be out of business long ago, and we'd be back to
square one on OSHW. Because they don't, Arduino remains in business, and
fully open.

[Josiah Zayner]

I don't want this to become a flame war.

I am not reselling anyone else's plasmids. None of the plasmids I have are from OpenBiotech.com

I am not deliberately undercutting anyone I am selling/giving people these plasmids at what I determined was fair.

I don't understand the whole design, test and release thing?

Say I order a gene in a vector from IDT for $300 or less (http://www.idtdna.com/pages/products/genes/custom-gene-synthesis). It takes two weeks at _MOST_ unless the sequence you sent them has repeating sequences or something. If you order primers and clone a gene yourself from genomic DNA we are talking $20-$30

If you cut it out with restriction enzymes and insert it into pUC19 so it will _Open_. Enzymes are ~$40/10,000 units. You probably use two Enzymes so you invested $80. (http://www.clontech.com/takara/US/Products/Molecular_Biology/Restriction_Enzymes/Restriction_Enzyme_Overview?utm_source=google-adwords&utm_medium=cpc-takara&utm_campaign=RestrictionEnzymes-campaign)

Mini prep and Sequence it. $5-$10. (LB on eBay is super cheap. Mini prep kits from Zymogen are $50 for 50. Sequencing for $2.99 http://www.epochlifescience.com/Service/Sequencing.aspx)

Test that protein expression works if that is the point of the gene. (IPTG cheap, LB cheap, I hope you chose a 6xHis tag, $79 for 25mL for rechargable NTA resin that can be used for years on hundreds or even thousands of protein preps http://www.mclab.com/Ni-NTA-Agarose.html?gclid=CO6Q36-q-bICFYZaMgodAWwA6A)

Total cost for one plasmid charging the most money ~$500 if you charge for complete kits and gene synthesis. Approximate time 1 month depending on how long gene synthesis takes.

If you are charging on a per plasmid basis and you are using primers it costs on the order or $50 or less. Approximate time 2 weeks.

Am I missing something?

[kingjacob]

First, everyone has living expenses and in order for open science to scale, people have to make a living at it. Just look at the open source community as an example. What percentage of commits are done by employees of software companies? 

Second, Not sure what youre getting at by your list of examples. Linux has only been able to grow to where it is because of enterprise support (see investors in OSDL[2]). Makerbot is 2x more expensive than the open source project(reprap) it's based on. $500 for a brand new pcr is a good price if you actually use it. You can spend that much in reagents a month doing active research. 

Also $50 for cathals plasmid is probably too cheap a price for what it is. NEB is currently selling pUC19 a plasmid they didn't spend a dime developing for $63/50ug[1]. 

1:http://www.neb.com/nebecomm/products/productN3041.asp

2:http://en.wikipedia.org/wiki/Open_Source_Development_Labs

--

Cheers,
Jacob Shiach

editor: Citizen Science Quarterly

pi: Brightwork CoResearch

t: @jacobshiach

[John Griessen]

On 10/11/2012 11:06 AM, Josiah Zayner wrote:
> If you are charging on a per plasmid basis and you are using primers it costs on the order or $50 or less. Approximate time 2 weeks.
>
> Am I missing something?

Sounds like you're still not counting the testing time, or choosing to
develop something that is useful and weeding out mistakes and the useless,
or the fixed costs of operating, and as was already said, profit.

So do you not like the idea of assessing how many early adopters there are in
the "market" and spreading out your costs over the sales you expect?
With people setting up to clone and resell any open documented kits, the
initial price would have to be higher since after a month sales would go to
the cheap cloner for many buyers. If you setup as clones'r'us, you might be driving
open wetware prices higher for novel, pieces that are part of a movement.
If you setup as clones'r'us, you might slow progress in this odd open product realm,
not speed it up.

[Jeswin]

On Thu, Oct 11, 2012 at 12:06 PM, Josiah Zayner <josiah...@gmail.com> wrote:
> I don't want this to become a flame war.
>

We can keep it civil. Written below is what I think is a clarification
of Josiah's idea and everyone else's ideas of development and pricing:

I think what Josiah is saying is that he found a plasmid he found one
company (openbiotech) was charging too much relative to other
companies (i.e. free or low-cost). In my opinion, openbiotech probably
sells it because all shoppers try to get their shopping done in as few
locations as possible. They are providing it as a convenience. The
bigger companies may not ship outside commercial addresses so Josiah
thinks to sell a cheaper plasmid (pUC19) to DIYbio'ers.

The problem arose when he said if it is OpenSource plasmid, then it
should be possible to copy the plasmid and sell cheaply since the
final product is easy to duplicate. If only older plasmids that are
commonly used are copied, I doubt there is little resistance (barring
any legal issues). Now, if Cathal releases his plasmid sequence
(development cost = thousands of dollars) and sell plasmids (verified,
quality-assured) through his business, he is hoping to get back
development costs and run his business creating more items for
DIYbio'ers. If someone chooses to clone Cathal's plasmid and undercut
him, he is unable to continue R&D if he takes a loss in income due to
this.

At some point in the life cycle of a plasmid (or other Intellectual
property), it is better for the consumer that the IP holder reduce
his/her dependency on the product. This promotes progress and keeps
inventors from resting on their laurels.

If my account of the main points of the discussion are incorrect,
please correct me.

> https://groups.google.com/d/msg/diybio/-/OzaZgIJfxk4J.

[Cathal Garvey]

That's more or less the shape of my outlook, yes. And I'm entirely on
board with inventors having to continue inventing. The minute you stop,
you should stop calling yourself an "inventor": now you're just a
"seller". The only issue is with products that can be copied more or
less instantly by cloner resellers, because it can potentially eliminate
that initial market advantage that is so essential to an innovative company.

For the most part, this initial market advantage works pretty well when
the community of customers is on-board with the project, and as long as
customer-producer relations remain pretty good. It's only when an
attitude carries over from the copyfight wars that everything should be
free-as-in-beer and artists will magically get money somewhere that
trouble arises.

To address that misconception, artists do, in fact, need money to live.
Copyright is no longer the answer, even if it were enforceable. But it's
unfair to demand that they give away music for free; many fans will
happily pay to help produce more great music. It's unfair to ask that
they all be performers; not all great musicians are great performers.

Likewise here, it's unfair to demand that a person who invents something
release it for free-as-in-beer and look for magic money elsewhere.
That's the only contention that I hold in this debate; whether or not
someone can compete on price for an older vector like pUC18/19 is
inconsequential; the market is saturated with pUC, and nobody depends on
it to continue innovating. Eventually, the same may be true of one of my
designs, but I sincerely hope that by then I'll have recouped my costs
and made enough additional money to live comfortably on while I make the
next thing people might like.

Josiah: If I misunderstood you to be saying that you planned to open
Clones'R'Us and copy novel OpenBiotech designs at an undercut price,
then I'm sorry for having done so. Selling cheap pUC is unlikely to hurt
anyone. Attacking p2kb or other novel designs, is.

By the way, I shared your optimism on design costs and turnaround times
in biotech when I started out, too. While it may be sometimes true of
simple products, you'd be surprised just how messy biology really is!

[Cathal Garvey]

I'm kinda assuming that the returns will be like the "mobile app" or
"mp3" sales figures; make it somewhat cheaper, and you get enough
additional customers to make up the difference. Win-win: more people
with biohacker-centric DNA to play with, and more money to do more hacking.

[Josiah Zayner]

I agree with this sentiment. Win-win if it works.

[Josh Perfetto]

On Thu, Oct 11, 2012 at 8:09 AM, Josiah Zayner <josiah...@gmail.com> wrote:

A $50 plasmid, open source or closed source, is not going to change the way people do Open Science. It is just going to make you money. A $5 plasmid probably won't greatly effect Open Science but at least it is trying to.

Hi Josiah,

If you're looking for something to do, there is this great openly available registry of biological parts (partsregistry.org) but it is hard to get the DNA parts because they only provide them to iGEM teams. If you wanted to clone them all and offer them for $5 each I think it would have a huge impact on open science.

-Josh

[John Griessen]

On 10/11/2012 01:44 PM, Cathal Garvey wrote:
> many fans will
> happily pay to help produce more great music.

Even a remix:

http://www.reverbnation.com/c/fr5/artist_549874?eid=A549874_14901141_24013473&fsc=9d018b892a3

Elizabeth needs rent money too.

On 10/11/2012 01:44 PM, Cathal Garvey wrote:
> whether or not
> someone can compete on price for an older vector like pUC18/19 is
> inconsequential; the market is saturated with pUC, and nobody depends on
> it to continue innovating. Eventually, the same may be true of one of my
> designs, but I sincerely hope that by then I'll have recouped my costs
> and made enough additional money to live comfortably on while I make the
> next thing people might like.

Yay Cathal!

[Josiah Zayner]

No actual scientists I know actually use BioBricks because it is not anymore useful than anything else. You still have to do restriction digests and ligations like normal cloning. Interesting idea for high schoolers and undergrads to help them become interested in science though.

Sure, having genes in plasmids would be useful for people and I could clone them all myself but that is ridiculous. Especially when they are already out there.
If you want something look up the paper and write the lab and ask, have your local Open Science Space acquire a FedEx # and you seem even more legit because you are willing to pay for shipping. Yeah sometimes it will be a hassle, I am sure, but that is what an Open Construct Database should be for.

If I had years of pointless time to waste replicating what other people have already done just so I can call it open and make a few bucks, yeah, sure, I would do what you suggest. But seriously?

What do I think would benefit Open Science?

Free and/or Cheap access to a lab and equipment 24/7.
Proper teaching and mentoring so people don't waste their time on something such as DNA barcoding.

Easy to say right?
But I am spending my time and efforts and money trying to do these things. Developing ways to make a sustainable free/cheap Open Science Lab near a great institution of higher learning that has people with/acquiring Ph.D.s who attend.

Maybe it won't work. Maybe I will fail and become destitute from giving everything away for free or cheap but there is so much more to my life than money so I am not concerned.

I mean really, what do people really think would benefit open science? I think that should be a new thread.

[Josh Perfetto]

It need not be limited to biobricks but open constructs of any kind. I don't think it's quite as easy to get plasmids as you say. One problem is a lot of the labs will want you to sign an MTA before they will provide the plasmids, which place restrictions on what you can do with them. Thus they are no longer free.

-Josh

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[Max Hodak]

Just wanted to jump in here really quickly.  My startup built the open source taq vector for Open Biotech.  We spent a bunch of time figuring out the IP situation to ensure that the product would actually be unencumbered: this is really nontrivial to do given how patent oriented the life science industry is.  (Case in point: Open Biotech originally asked that we use a specific "IP-free" expression vector, which turned out to not be IP free at all, and resulted in brief lawsuit threats.)

Josiah, you're welcome to hate on Open Biotech and others for selling this vector for more than $5.  But given how basically the entire industry is stacked against you today, it seems silly to demonize the people who are trying to help.  If it's not worth $40 to you, don't buy it.  But I just want to point out that the hard part here in many ways wasn't the actual biology, but building something that could be legally distributed.

[Cathal Garvey]

Hey Max,
Kudos for your work toward open biotech, and sorry to hear about your
troubles with the vector situation! If you don't mind sharing what
supposedly IP-free vector that was, it might help others from falling
into the same trap?

I have to concur that the IP situation is one of the biggest challenges,
not actual implementation. Even an open-source GFP kit would necessarily
have to be wild-type GFP, with dreadfully bad characteristics compared
to modern mutant forms, simply because it's apparently out of patent by
now. And that's a real shame, that we have to dance around 15-20 year
old patents just to approach what should be entirely routine.

Again, thanks for doing so! I'll be buying some stuff from OpenBiotech
for my own lab, no question. :)

On 13/10/12 06:51, Max Hodak wrote:
> Just wanted to jump in here really quickly. My startup built the open
> source taq vector for Open Biotech. We spent a bunch of time figuring out
> the IP situation to ensure that the product would actually be unencumbered:
> this is really nontrivial to do given how patent oriented the life science
> industry is. (Case in point: Open Biotech originally asked that we use a
> specific "IP-free" expression vector, which turned out to not be IP free at
> all, and resulted in brief lawsuit threats.)
>
> Josiah, you're welcome to hate on Open Biotech and others for selling this
> vector for more than $5. But given how basically the entire industry is
> stacked against you today, it seems silly to demonize the people who are
> trying to help. If it's not worth $40 to you, don't buy it. But I just
> want to point out that the hard part here in many ways wasn't the actual
> biology, but building something that could be legally distributed.
>
> On Friday, October 12, 2012 1:32:10 PM UTC-7, Josh Perfetto wrote:
>>
>> It need not be limited to biobricks but open constructs of any kind. I
>> don't think it's quite as easy to get plasmids as you say. One problem is a
>> lot of the labs will want you to sign an MTA before they will provide the
>> plasmids, which place restrictions on what you can do with them. Thus they
>> are no longer free.
>>
>> -Josh
>>
>>

>> On Fri, Oct 12, 2012 at 8:02 AM, Josiah Zayner <josiah...@gmail.com<javascript:>

>>> To post to this group, send email to diy...@googlegroups.com<javascript:>
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>>>
>>>
>>>
>>
>>
>

[Max Hodak]

I'd rather not name them directly, but I'll point out that the company in question has trademarked the phrase "IP-Free".  The whole thing is kind of ridiculous.

So, if you're looking at a supposedly free expression vector and notice a (tm) sitting there next to the statement of freedom, double check those license agreements.

[kingjacob]

Allow me to name them then cause that's beyond ridiculous. The company is DNA 2.0 and Here's the trademark.

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Jacob Shiach

[Bryan Bishop]

What precisely is wrong with trademarks?

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[kingjacob]

Nothings wrong with trademarks. It's just funny and a tad ironic that they'd have ip on the phrase ip-free.

I was curious and emailed them to ask what they meant by IP-Free, this was their response.

"Thank you for your inquiry. IP-Free means that you do not need a license to use the vector. In other words we do not retain the rights of this vector and you're free to use for your benefit."

That's good to know, if you buy their vector you can use it.

Cheers,
Jacob Shiach

editor: Citizen Science Quarterly

[John Griessen]

On 10/13/2012 04:23 PM, kingjacob wrote:
> "Thank you for your inquiry. IP-Free means that you do not need a license to use the vector. In other words we do not retain the
> rights of this vector and you're free to use for your benefit."
>
> That's good to know, if you buy their vector you can use it.

IOW: It's "free-as-in-freedom" if you buy it.

or paraphrased,
"Free, IF you pay..."
"Shoowa, youse can Uuuuse it howev'ah youw want -- If ya pay me..."
"Free, as long as you pay up."
"freepay"

Har!

So, now we're all clear on the tactics and realities of the legal minefield of biotech, right?

[Max Hodak]

They were taking it to mean that it was free for *your* purposes as an end-user, which couldn't include anything construable as competing with them (including simply distributing the resulting assembly, which could lead to people not ordering synthesis for the same thing later).

[Cathal Garvey]

Face. Palm.

[Nathan McCorkle]

On Thu, Oct 11, 2012 at 12:06 PM, Josiah Zayner <josiah...@gmail.com> wrote:

I think you're missing a lot in regards to human effort, the time
bioHackers/bioScientists spend building a working plasmid can be
immense. Sure it might be as simple as googling a protein, terminator,
promoter, localization sequence... but realistically you still have to
spend hours and hours screwing around with pipettes and ice baths and
aliquoting enzymes so your whole batch isn't in the heat of the lab
degrading.

When synthesis gets cheaper, sure you can start talking about
significantly cheaper cloned plasmids, but until then if a
bioHacker/bioScientist is planning on their hard work paying off I
plan on respecting their efforts. Sure money isn't everything but you
can't eat plasmids for dinner, you've got to pay someone to work a
photosynthesis field if you're not a subsistence farmer, unless the
local farmer wants to barter food for plasmids.

Personally I've been waiting to do any real copy/paste bioHacking or
directed evolution until DNA synthesis gets cheaper... which has lead
me to research how to synthesize my own DNA. The synthesizer will all
be open-source, the parts will cost between $5k-$15k. I owe ~$60k for
University which allowed me easy access to professors and many
laboratories, library access, online journal access, interlibrary loan
access, lab supplies, relevant courses. If I'm to open up DNA
synthesis, I'd like to at least pay off school. I think this is
reasonable since current generation DNA synthesizers cost at least 3
times what I owe for schooling. I'd rather not be ripped off by
cloners, or even the big corporations for that matter. Getting ripped
off won't stop me, but it will certainly 'leave a bad taste in my
mouth' and spike my stress hormone levels.

--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Cathal Garvey]

Hear hear! Can't wait to watch the talk, but delighted to see you guys
doing a great job and with the right attitude and aim. Long live open! :)

On 25/10/12 23:40, OpenBiotech wrote:
> Hi,
>
> I'm Justin from Open Biotechnology. Awesome finding such a lively
> discussion about us. Everything we've developed and are developing is open
> source. I gave a short talk at the open science summit over the weekend
> where I explained the motivation behind the company and what we are hoping
> to help accomplish.
>
> The video of that is up on youtube for those that are interested
> http://www.youtube.com/watch?v=zCQmDUURe3I
>
> also for anyone in the DIY bio community that develops something they think
> might be useful we would be more than happy to offer it for them if they
> don't want to go through all the trouble.
>
> The floor needs to be dropped out of the molecular tool and reagent
> industry as the crazy use restrictions often present and obscene costs get
> in all of our way in developing useful stuff. Ultimately my first love is
> in making regenerative medicine happen.
>
> -Justin
>
> http://www.openbiotech.com

[Mega]

Will there be an OpenPfu Polymerase Plasmid? :D

Does anyone know if / where you can get one? 

[Koeng]

Synthesize it and give it out to us :D