Re: OpenPCR

[fiaraz]

I was looking into it and spoke to the madlab group in Manchester who informed me that it was ok but not as good as the lamp based PCR machine.  which i am now looking to construct but time is such a rare commodity.

On Thursday, January 31, 2013 1:00:02 AM UTC, G Lyons wrote:

Hello all-

I was wondering what peoples' experiences have been with the OpenPCR thermal cycler. Is it simple to construct and is it just as effective as the regular ones?

Thanks!

[Dakota Hamill]

I havn't heard of any amateurs or DIY'ers who created a fully functioning light-bulb PCR.  Russel Durret had one and I re-created the circuit from it, but he never to my knowledge tested ramp times or ever completed a successful PCR.  I havn't either.  I have a "professional" build light-cycler I got off ebay, the Idaho Technology RapidCycler, and although it is a bit faster than the peltier machines I've tested it against, so far the peltiers seem to beat it out on amplification quality / concentration (only done 2 amplifications...not a great sample size).  Though, this could be because I am not providing ample enough program times to account for the poorer heat transfer between plastic/air vs plastic/aluminum.

Dealing without heated lids kind of sucks because pipetting mineral oil is annoying, and the OpenPCR offers that I believe.  You could get an older peltier based machine and hope it worked off ebay (sometimes it is cheap enough to take the gamble), but for newer PCR machines with heated lids that really work, you may even find the price comparable to OpenPCR.

From observing OpenPCR over the past few years, but never actually using one, I'd say they did a nice job filling the complete void that existed for a relatively easy to assemble plug-n-go machine.  Are there areas where one could improve upon it? Sure; price, ramp time, sample #, size.  But you could argue anything and everything in existence could be improved upon, and that's how progress is made.


 

[Josiah Zayner]

http://www.ebay.com/itm/MJ-Research-Programmable-Thermal-Controller-Model-PTC-100-PTC100-Used-Condition-/221168862233?pt=LH_DefaultDomain_0&hash=item337eb10419

Can do 60 samples compared to OpenPCRs 16

OpenPCR costs: $599 not including shipping

This costs: $316 and includes shipping and guaranteed to work or full refund.

Troll eBay for MJ research thermal controllers I found mine for $45 and $35 shipping and it works fine.

Search for "thermal controllers" even though the units are typically called thermal cyclers because people list them as Thermal controllers and no one bids on them.

If you don't believe me check this really nice one that went for <$130 two weeks ago:
http://www.ebay.com/itm/MJ-RESEARCH-PTC-100-PROGRAMMABLE-THERMAL-CONTROLLER-/251212740568?pt=LH_DefaultDomain_0&hash=item3a7d7237d8

If OpenPCR gave back to the community I might be more inclined to tell you to support them but look at their website. No PCR protocols or tutorials. No links to tell you were to buy reagents. Most comments on their forum are not even answered. Seriously, don't support people who are just out to make money off of DiyBio folks.

[Cathal Garvey]

Dude, that's unnecessarily hostile. The guys behind OpenPCR are pillars
of the community, and they designed the fecking thing from scratch: what
do you expect them to "give back"? This wasn't a community project in
the first place, it was their project, which they open sourced completely.

If you don't like the support, that's one thing. But these guys aren't
out to "make money off the DIYbio community", they were out to fill a
void and offer a more reasonably priced (first hand) thermal cycler that
had open-source code and controls.

On 31/01/13 23:32, Josiah Zayner wrote:
> http://www.ebay.com/itm/MJ-Research-Programmable-Thermal-Controller-Model-PTC-100-PTC100-Used-Condition-/221168862233?pt=LH_DefaultDomain_0&hash=item337eb10419
>
> Can do 60 samples compared to OpenPCRs 16
>
> OpenPCR costs: $599 not including shipping
>
> This costs: $316 and includes shipping and guaranteed to work or full
> refund.
>
> Troll eBay for MJ research thermal controllers I found mine for $45 and
> $35 shipping and it works fine.
>
> Search for "thermal controllers" even though the units are typically
> called thermal cyclers because people list them as Thermal controllers
> and no one bids on them.
>
> If you don't believe me check this really nice one that went for <$130
> two weeks ago:
> http://www.ebay.com/itm/MJ-RESEARCH-PTC-100-PROGRAMMABLE-THERMAL-CONTROLLER-/251212740568?pt=LH_DefaultDomain_0&hash=item3a7d7237d

> <http://www.ebay.com/itm/MJ-RESEARCH-PTC-100-PROGRAMMABLE-THERMAL-CONTROLLER-/251212740568?pt=LH_DefaultDomain_0&hash=item3a7d7237d8>8

>
> If OpenPCR gave back to the community I might be more inclined to tell
> you to support them but look at their website. No PCR protocols or
> tutorials. No links to tell you were to buy reagents. Most comments on
> their forum are not even answered. Seriously, don't support people who
> are just out to make money off of DiyBio folks.
>
>
> On Wednesday, January 30, 2013 7:00:02 PM UTC-6, G Lyons wrote:
>
> Hello all-
>
> I was wondering what peoples' experiences have been with the OpenPCR
> thermal cycler. Is it simple to construct and is it just as
> effective as the regular ones?
>
> Thanks!
>

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>

[Josiah Zayner]

How was that hostile?
I did not personally attack them at all. I pointed out empirical things.

You believe they filled a gap and maybe they did. I believe there was no need for a $600 openpcr machine. I know we have had this discussion to death in other threads.

I know you live in Ireland and having stuff that heavy shipped from eBay and go through customs can be a bitch. However, I think your case is more of an exception case rather than rule.

From this list and online it appears that a large majority of DIYBioers are Americans. In that case it is hard to tell them to support a product that doesn't support the community when eBay is such a great and cheap resource.

I have no reason or need to argue with you. You seem like a decent guy at heart from what I see online.

--

[Jeswin]

On Fri, Feb 1, 2013 at 10:36 AM, Josiah Zayner <josiah...@gmail.com> wrote:
>
> You believe they filled a gap and maybe they did. I believe there was no
> need for a $600 openpcr machine. I know we have had this discussion to death
> in other threads.
>

There is a need for cheap brand new PCR machine. eBay products are
sketchy. What sort of contamination could be on it? How long could it
last? Shipping is expensive and things could get damaged in the
process.

>
> From this list and online it appears that a large majority of DIYBioers are
> Americans. In that case it is hard to tell them to support a product that
> doesn't support the community when eBay is such a great and cheap resource.
>

The number of people on or where they are the list mean absolutely
nothing. I found that early on. What appears is not always what's
going on. There's no need to think USA is the only place where
innovation can take place. I think it might be a bit easier though.

There are people in Syria doing DIYbio, in the middle of a civil war!

[Cathal Garvey]

> Seriously, don't support people who are just out to make money off of
> DiyBio folks

This was what I was responding to. I understand that you don't see the
value in OpenPCR as a project, and that's fine; just a difference of
opinion. But I don't think that statement was a fair thing to say about
Tito & Josh offhand.

On 01/02/13 15:36, Josiah Zayner wrote:
> How was that hostile?
> I did not personally attack them at all. I pointed out empirical things.
>
> You believe they filled a gap and maybe they did. I believe there was no
> need for a $600 openpcr machine. I know we have had this discussion to
> death in other threads.
>
> I know you live in Ireland and having stuff that heavy shipped from eBay
> and go through customs can be a bitch. However, I think your case is
> more of an exception case rather than rule.
>
> From this list and online it appears that a large majority of DIYBioers
> are Americans. In that case it is hard to tell them to support a product
> that doesn't support the community when eBay is such a great and cheap
> resource.
>
> I have no reason or need to argue with you. You seem like a decent guy
> at heart from what I see online.
>
> On Jan 31, 2013 5:32 PM, "Josiah Zayner" <josiah...@gmail.com

> <mailto:josiah...@gmail.com>> wrote:
>
> http://www.ebay.com/itm/MJ-Research-Programmable-Thermal-Controller-Model-PTC-100-PTC100-Used-Condition-/221168862233?pt=LH_DefaultDomain_0&hash=item337eb10419
>
> Can do 60 samples compared to OpenPCRs 16
>
> OpenPCR costs: $599 not including shipping
>
> This costs: $316 and includes shipping and guaranteed to work or
> full refund.
>
> Troll eBay for MJ research thermal controllers I found mine for $45
> and $35 shipping and it works fine.
>
> Search for "thermal controllers" even though the units are typically
> called thermal cyclers because people list them as Thermal
> controllers and no one bids on them.
>
> If you don't believe me check this really nice one that went for
> <$130 two weeks ago:
> http://www.ebay.com/itm/MJ-RESEARCH-PTC-100-PROGRAMMABLE-THERMAL-CONTROLLER-/251212740568?pt=LH_DefaultDomain_0&hash=item3a7d7237d

> <http://www.ebay.com/itm/MJ-RESEARCH-PTC-100-PROGRAMMABLE-THERMAL-CONTROLLER-/251212740568?pt=LH_DefaultDomain_0&hash=item3a7d7237d8>8

>
> If OpenPCR gave back to the community I might be more inclined to
> tell you to support them but look at their website. No PCR protocols
> or tutorials. No links to tell you were to buy reagents. Most
> comments on their forum are not even answered. Seriously, don't
> support people who are just out to make money off of DiyBio folks.
>
>
> On Wednesday, January 30, 2013 7:00:02 PM UTC-6, G Lyons wrote:
>
> Hello all-
>
> I was wondering what peoples' experiences have been with the
> OpenPCR thermal cycler. Is it simple to construct and is it just
> as effective as the regular ones?
>
> Thanks!
>
> --
> -- You received this message because you are subscribed to the
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> Learn more at www.diybio.org <http://www.diybio.org>

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> <mailto:diy...@googlegroups.com>.

[John Griessen]

On 02/01/2013 09:46 AM, Jeswin wrote:
> There is a need for cheap brand new PCR machine. eBay products are
> sketchy. What sort of contamination could be on it? How long could it
> last?

Sure, a big benefit of openness is repair and upgrade possibilities.

[Nathan McCorkle]

On Thu, Jan 31, 2013 at 3:32 PM, Josiah Zayner <josiah...@gmail.com> wrote:
> Seriously, don't support people who are just out to make
> money off of DiyBio folks.

That's definitely what the eBay sellers are in it for, so why are you
supporting their marketplace? openPCR will survive if it can compete,
the ebay links enable potential consumers to be informed of the
market, but c'mon the openPCR guys started this as a DIY project like
all the rest we talk about in this group.


--
-Nathan

[Thomas Landrain]

I think you could be surprised by the proportion of non-American on this list. Just check again the map of local groups on diybio.org

[Josiah Zayner]

You are buying a product from the eBay sellers, not directly supporting them, you are just paying the person who is charging the least.

If someone is willing to pay 5x what they could pay there usually is a reason. i.e. why someone would buy an OpenPCR machine rather than a PCR machine off of eBay. If someone buys an OpenPCR machine they are either trying to support OpenPCR, having a need, like needing something shipped outside the US, or just not trusting eBay.

I am not arguing that there are not people from outside the US in DIYBio or on this list.

Cathal, I have no idea what Josh and Tito are about, this is true.

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[Bryan Bishop]

On Fri, Feb 1, 2013 at 5:23 AM, Cathal Garvey
<cathal...@cathalgarvey.me> wrote:
> of the community, and they designed the fecking thing from scratch: what
> do you expect them to "give back"? This wasn't a community project in
> the first place, it was their project, which they open sourced completely.

Actually, it was somewhat (but not entirely) derived from community design:

https://groups.google.com/forum/?fromgroups=#!topic/diybio/8oMYA5LxbN0%5B176-200-false%5D
https://groups.google.com/forum/?fromgroups=#!msg/diybio/8oMYA5LxbN0/_FP4MJk9YygJ

and some other threads that I can't remember IDs for.

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

[Sebastian S. Cocioba]

Personally, if openpcr can obtain the developmental velocity of makerbot's thing-o-matic et al, I see that future models will be mind blowing. For now it still is the cheapest, brand new, thermacycler and probably the only that has such an open community for troubleshooting. Try asking tech support on a used MasterCycler from eppendorf and see what you get :P. i called them to ask for a repair quote and they charge 800 just for diagnostics. If you really sit down and crunch the numbers you'll see that its a worth-while investment. As for making a buck, I don't see how selling your creation as a kit is such a bad thing. You could make it yourself from plans and no ones discourages you to not. Its just more difficult than if one were to have it as a kit. We pay for the convenience and to compensate the individual for their work. Complaining about the price, I too am guilty of that, seems to be silly once you factor everything...or even most things.

Sebastian S Cocioba

CEO & Founder

New York Botanics, LLC

Sent via Mobile E-Mail 

On Feb 1, 2013, at 1:50 PM, roksprok_ <zac.cu...@gmail.com> wrote:

Regarding reactants/tutorials, openbiotech.com has MasterMix to use. It looks like they even sell the kit itself.  

http://www.openbiotech.com/category_s/1818.htm

There are many protocols for PCR online, and if you have problems feel free to post to the group and someone can help you out.  One advantage of the OpenPCR machine is that you know people on the diybio group have them and can help troubleshoot.  Its a lot harder to troubleshoot a random ebay device that wasn't designed for easy repair.  

On the subject of costs, I'd argue that reactants and plasmids are expensive enough that the x00 dollars you might save on a new device will be outweighed by a few faulty reactions.  

To view this discussion on the web visit https://groups.google.com/d/msg/diybio/-/1MW9iJK0OhcJ.

[Josh Perfetto]

I really appreciate all the support this community has given to OpenPCR. Today OpenPCR is a tidy kit that you buy, put together, and it just works, but it certainly took a lot of effort to get to that point.

I think people sometimes get too hung up on price. There is no PCR machine cost barrier for anyone who wants to experiment and do PCR at home. It can be done with three pots on the stove. This is adequate for basic experimentation and is the way I first did PCR. When people are ready to move up to bigger projects which involve more runs, samples, and controls, there are a lot more costs for reagents, primers, and gel runs, so the absolute cost of the machine has to be put into some perspective.

The goal of the OpenPCR project was to provide an open source, hackable, easy to use, extremely accurate PCR machine at low cost, and build some community around it. It also provided a heated lid, which was important to me as I had observed many novice users get failed reactions due to contamination/improper technique when using mineral oil.

I think sometimes the benefits of open source/interfaces/community are not obvious because ultimately a PCR thermocycler is a simple machine and there is not much you can hack it to do other than change temperature. However as open source quantitative machines become commonplace this distinction will grow.

-Josh

[Cathal Garvey]

I have yet to see any other PCR machine out there not built out of a
bulb or coffee-can that you can write your own software for.. but I was
able to do that for OpenPCR relatively easily when I decided I didn't
like the Adobe Air software provided:
https://github.com/cathalgarvey/openpycr

..of course, this was *after* a prolonged email thread between me, Tito
and Josh, in which they rebuilt the software repeatedly just so I could
use it on the deprecated version of Air Adobe were offering on Ubuntu.
That's customer service I would be stunned to see anywhere else in
biotech without an expensive maintenance contract.