Electronic requirements for redesign of Arduino PCR thermal cycler

[Andy Morgan]

Hey, so I'm currently an undergraduate genetics student and I'd like to do some diy biohacking to really get lots of hands-on experience while I'm studying. At the moment I'm just setting up a basic lab by building some lab equipment based off plans on the internet.

So, I've slightly redesigned the Arduino PCR thermal cycler (http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS) to make it a bit better, by replacing the two wiremound resistors (100watts) with a cartridge heater (300watts) (http://www.ebay.com.au/itm/Cartridge-Heater-3-8-Diameter-3-2-Length-220VAC-300W-/380898256650?pt=AU_B_I_Electrical_Test_Equipment&hash=item58af4e270a).

But the thing is: I have ZERO experience with electronics, and I don't know whether the cartridge heater will require too much power from the Arduino board or power supply, and all the explanations I've found on the internet seem to go WAY over my head.

Does anybody know whether the cartridge heater will work?

Any help would be greatly appreciated.

[John Griessen]

On 02/24/2015 10:49 PM, Andy Morgan wrote:
> But the thing is: I have ZERO experience with electronics, and I don't know whether the cartridge heater will require too much
> power from the Arduino board or power supply, and all the explanations I've found on the internet seem to go WAY over my head.
>
> Does anybody know whether the cartridge heater will work?

If you are asking if we will wade through an instructables video to figure it out -- no.

What you could do is some of the leg work needed to answer your question. This points out how
"just publishing data in some kind of format that actually was used to make something" is often
not enough for others to use efficiently. Was the control circuit made with open tools such
as KiCAD or gEDA_gschem and gEDA_PCB? If not, will you convert the schematic and bill of materials
into something email friendly like .svg or .gif image of the schematic and text list of the BOM?

Then maybe you will get helpful answers since the basic problem is easy for an electronics engineer
or electronics novice.

Here's a little sleuth work on what you sent already to maybe motivate you:

"ebay.com.au/itm/Cartridge-Heater-3-8-Diameter-3-2-Length-220VAC-300W"
From this we guess you are in Australia, where there are fewer parts sources than in USA, but some.

"3-8-Diameter" It is a rod with .375 in. diameter -- it could be bent in a U though....

"220VAC-300W" It is 300Watts when driven by 220VAC, which probably is not what your circuit puts out.
Does your circuit use a relay to switch power from the house mains to the heater, or more likely it
uses a transistor to switch 12VDC to a heater resistance...

Weatherman guess about your new part working: Cloudy with 70% chance of thunder storms imminent.

[Andy Morgan]

Yeah, fair enough.

I've attached the original circuit schematic in a .gif format, which is the only one I can find. And a rough BOM in a .txt file with as much relevant information as I could provide. The difference in the circuit schematic is that the two resistors would be replaced by the cartridge heater.

The mains power supply is 230V, 50Hz for New Zealand (you were close with Australia), and apparently the peak voltage would be 325V (230*sqrt(2)), though I'm not sure if that last bit of information actually helps.

Thanks for your help John (and I don't mean that sarcastically).

Andy.

[Simon Quellen Field]

Since the relay simply acts as a switch for the mains voltage, replacing two 100 watt 150 ohm resistors with a 600 watt resistor is a simple problem to solve.

300 watts / 220 volts is 1.36 amperes. The definition of a watt.

220 volts / 300 ohms is 0.73 amperes. Ohm's Law.

So now you need to check the rating on the solid state relay.

If it can handle the 1.36 amperes, then you need change nothing else.

If it can't, then replace it with one that can.

Since your bill of materials says it can handle 25 amperes, you are just fine simply replacing the old heating elements with the new one.

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[Andy Morgan]

Thanks very much Simon, that's a relief.

So, I'm guessing then that a 12VDC 500mA power supply (like the one they specified in the original: http://www.jaycar.co.nz/productView.asp?ID=MP3011&form=CAT2&SUBCATID=1000#12) will be fine then?

Thanks again,

Andy.

[John Griessen]

25A SSR-25 DA Solid State Relay Input: DC 3-32V Output: AC 24V-380V

from your BOM says the SSR can survive 25 Amperes rms.

So, your heater is 300 Watts at 230Vrms AC, which results in what current?

Power = V*I --> 300 = 230 * I --> I = 1.3 Amperes rms.

You're fine.

[John Griessen]

On 02/26/2015 02:43 AM, Andy Morgan wrote:
> So, I'm guessing then that a 12VDC 500mA power supply (like the one they specified in the original:
> http://www.jaycar.co.nz/productView.asp?ID=MP3011&form=CAT2&SUBCATID=1000#12) will be fine then?

For what?

If you drive your big heater with 12 V instead of 230V, proportionally less will happen.
Instead of 300W, you'll get (12/230 * 300Watts) = 16 Watts.

[Simon Quellen Field]

I presume the power supply is simply for the Arduino part of the project, which is unchanged from the original. In fact, the only thing that has changed is the heater. It's like swapping a 40 watt light bulb for a 100 watt light bulb. You don't have to change anything else.

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[Mac Cowell]

Also check out this design for a 2-tube arduino shield pcr thermocycler. Perhaps work on adding a lid? All FOSS. https://github.com/100ideas/PersonalPCRv1

This design was iterated and spun off into minipcr.com

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[Andy Morgan]

Yeah I saw the miniPCR design last night, pretty cool. Thanks for the link, its interesting to see the earlier designs of the miniPCR.

I'm gonna use a similar casing design to personalPCR. The PCR holder will be like the Coffee Cup PCR Thermocycler (http://www.instructables.com/id/Coffee-Cup-PCR-Thermocycler-costing-under-350/?ALLSTEPS) but with a heated lid (and a hell of a lot cheaper haha). And the electronics will be based off of the Arduino PCR Thermocycler design.

Hopefully, it should only cost about NZD$125 to build, and then I'll post something instructables for all to see.

The only thing I'm wondering is whether the heated lid needs to be particularly hotter than the other heated part? Or whether the same temperature will suffice.

[Andy Morgan]

Ah it all becomes clear, I was wondering why they listed a 12V power supply AND a regular power cable.

Thanks Simon.

[Josiah Zayner]

Keeping the lid at a constant temp of ~90C will generally suffice. Most PCR machines hold the lid at 90C - 105C.

I have tried doing the lid at same temperature as the tubes but received condensation. I think this might have been because of the different heat transfer rates? Maybe you can figure it out?

Looking on eBay these days you can buy most of the parts for the Arduino thermalcycler for much cheaper than the $85USD pricetag (inexpensive Arduino boards &c). Also, keep on eye out on eBay for thermal cyclers. Sometimes people don't know what the actual equipment is so they just list it as brand and product names so searching directly for brand names help. I have found some for under $100 that work great though this is from the US, so who knows what you might find?



Josiah

[Nathan McCorkle]

On Thu, Feb 26, 2015 at 6:48 AM, John Griessen <jo...@industromatic.com> wrote:

> On 02/26/2015 02:43 AM, Andy Morgan wrote:
>>
>> So, I'm guessing then that a 12VDC 500mA power supply (like the one they
>> specified in the original:
>>
>> http://www.jaycar.co.nz/productView.asp?ID=MP3011&form=CAT2&SUBCATID=1000#12)
>> will be fine then?
>
>
>
> For what?

Seems like it's the supply for the fan, switched by presumably a
MOSFET attached to pin-9 of the IC (arduino-software-pin 6) which is
labelled 'fan control pin' (this might be the net-name of the
circuit-net, depending on the CAD tool that was used by this
designer... where a net is a collection of pins that are all
'shorted'/connected together ).

[Andy Morgan]

Thanks for the heads up Josiah.

That's a bit annoying, I was hoping that I could have the lid at the same temperature as the tubes, allowing me to run the whole thing off of just the one simple circuit described in the original instructable.

Perhaps I'll look into using one peltier element for the base and another smaller one for the lid, although that might mean I'd have to hook up a whole other arduino board and solid state relay. Not to mention that all sounding a wee bit over my head. If I could hook them both up to the one arduino board that might be a little bit simpler though.

I came across this design (http://2013.igem.org/Team:Paris_Saclay/PS-PCR/detailed_description) that was build (and apparently for only 30 euros!) using peltier elements, but the electronic schematics look intense.

[Nathan McCorkle]

On Thu, Feb 26, 2015 at 11:33 PM, Andy Morgan <andrew....@gmail.com> wrote:
> I came across this design
> (http://2013.igem.org/Team:Paris_Saclay/PS-PCR/detailed_description) that
> was build (and apparently for only 30 euros!) using peltier elements, but
> the electronic schematics look intense.

That looks like a pretty nice design. Here is what I believe is
happening: The LM339N are op-amps which are going to 'buffer' the
arduino GPIO pin signal, and they are 'buffering' relative to opposite
polarity/voltage (see the - terminal of the triangles is connected to
either 76% or 24% VCC) to /prevent/ what is called 'shoot through' on
the two left-side MOSFETs (Q2 and Q4)... which is a condition where
both of the left or both of the right-side transistors were turned on
at the same time, allowing the top 12V Vcc to shoot-through the
transistors and straight to ground... just wasting power (and possibly
over-heating the transistors or stressing the power supply).

This would be a fun project to build a schematic and
printed-circuit-board for. I will have time in a few weeks I think.
But essentially it's an arduino on the left-side of the schematic
page:
http://2013.igem.org/wiki/images/b/b5/Pspcr_schema.png

and the peltier control stuff is on the right-side.


You could probably also just use a couple easydrivers:
http://www.ebay.com/itm/EasyDriver-Shield-stepping-Stepper-Motor-Driver-V44-A3967-For-Arduino-/400522271040

--
-Nathan

[Nathan McCorkle]

On Fri, Feb 27, 2015 at 12:20 AM, Nathan McCorkle <nmz...@gmail.com> wrote:
> This would be a fun project to build a schematic and
> printed-circuit-board for. I will have time in a few weeks I think.
> But essentially it's an arduino on the left-side of the schematic
> page:
> http://2013.igem.org/wiki/images/b/b5/Pspcr_schema.png
>
> and the peltier control stuff is on the right-side.
>
>
> You could probably also just use a couple easydrivers:
> http://www.ebay.com/itm/EasyDriver-Shield-stepping-Stepper-Motor-Driver-V44-A3967-For-Arduino-/400522271040

Whoops I meant this part:
http://www.ebay.com/itm/Stepper-Motor-Drive-Controller-Board-Module-L298N-Dual-H-Bridge-DC-For-Arduino-/170926726867?pt=LH_DefaultDomain_0&hash=item27cc06ded3

[Mac Cowell]

The reaction mixture will condense on the coldest part of the pcr tube, for instance, any surface not enclosed in the main heated block and exposed to ambient air.

One solution is to establish a temperature gradient from the top of the cap to the block by touching the cap with a second hot surface, preferably hotter than the main block such radiative and conductive heat transfer from the heated lid raises the temperature of all surfaces of the pcr tube exposed to air above the current temperature of the block. 

But you don't need s Peltier to do this. You just need a heat source you can keep at a constant temperature guaranteed to be hotter than any of the pcr temps.

It would be interesting to explore a hybrid design combining dynamic conductive heating in the tube block with constant radiative heating from a lamp or hot air flow positioned at just the right distance, instead of a heated lid in constant contact with the cap. Can the radiative heat source be set up to always add +20C to the exposed cap and 5-10 C to the reaction mixture? If so, perhaps such a design could lead to faster ramp times, by switching the radiator off during cooling.

Does the transparent plastic most pcr tubes are made from absorb IR?

Or maybe all that matters is if the reaction mixture absorbs the radiative energy. Not sure. Would pcr work in a transparent Quartz vessel in a freezer that was pulsed by a powerful IR source? Or would that be condensation city?

Cheers

Mac

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[Nathan McCorkle]

Grr... it is late and I didn't check the amperage/wattage of that...
and it seems like it would be too low. But essentially what you want
is a DC motor driver for an 'arduino' or that is 'arduino compatible'.
You would have to do some crafty ebay searching, and cross-reference
google, but I think something like this should exist pre-made.

The circuit the iGem project presents does seem like it would work
well... it looks like the response time of the LM339N is between 300ns
and 1.3 us... which is fine enough response for PWM control (where you
pulse the signal rapidly in short bursts... to approximate an analog
signal level from just a single supply voltage).


--
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[Mac Cowell]

Also, just want to point out that if you fill capillary glass tranfer pipettes (typically like $20 for 100, with volumes selectable from 0.5-50uL), they fit perfectly in the valleys of many sawtooth-style sinks (cheap). The surface to volume ratio is such that I don't think a heated lid is necessary.  Imaging from above is possible, potentially enabling qpcr-like applications.

They are just a bit of a pain to work with.

But the thermocycler is so simple in this case. Peltier, sawtooth heat sink with 5-10 ridges, mosfet for switching power, embedded thermocouple, microcontroller, and 5-10 glass capillaries, one per sample.

Cheers

Mac

[Andy Morgan]

Yeah I was thinking a second cartridge heater to use for a heated lid, as that would fit in well with my original design.

The only thing I'm not sure on is whether the one Arduino board could be used to control the temperature of two cartridge heaters simultaneously? And whether it could also be used to monitor the temperature of two thermosensors simultaneously?

I don't really want to get a second Arduino board and solid state relay etc., because like I said, I have ZERO experience with electronics.

[Cathal Garvey]

Oh, nice idea! I wonder if even plastic capillaries at that scale are
conductive enough to work, I could see it being possible to make
"pinch-off" capillaries that you fill (by capillary action? :)) and
pinch, then lay on your micro-cycler made with a peltier, two heatsinks,
an LM35 temp sensor, and an Arduino micro or similar.

As usual with Peltiers, the big ask is current, so the complexity arises
from ensuring enough is delivered from a suitable power source through
the peltiers.

I wonder if a "constant heat flow" design couldn't be knocked together
with a heating element atop the fins on the reaction side, so heat is
conducted downwards through the fins to the tubes, and cooling is
achieved by ceasing to apply heat and letting the heatsink distribute
what remains. But, that's only marginally simpler than fixing up a
cooling fan to a simple heat-block anyway and just doing
coil-heating-air-cooling, which is possibly as efficient as these things
get until you start coming full-circle to convective PCR (pun welcomed
but not intended)..

On 27/02/15 08:35, Mac Cowell wrote:
> Also, just want to point out that if you fill capillary glass tranfer
> pipettes (typically like $20 for 100, with volumes selectable from
> 0.5-50uL), they fit perfectly in the valleys of many
> sawtooth-style sinks (cheap). The surface to volume ratio is such that I
> don't think a heated lid is necessary. Imaging from above is possible,
> potentially enabling qpcr-like applications.
>
> They are just a bit of a pain to work with.
>
> But the thermocycler is so simple in this case. Peltier, sawtooth heat
> sink with 5-10 ridges, mosfet for switching power, embedded
> thermocouple, microcontroller, and 5-10 glass capillaries, one per sample.
>
> Cheers
> Mac
>
> On Friday, February 27, 2015, Mac Cowell <m...@diybio.org

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[John Griessen]

On 02/27/2015 01:33 AM, Andy Morgan wrote:
> allowing me to run the whole thing off of just the one simple circuit described in the original instructable.
>
> Perhaps I'll look into using one peltier

Things can get complicated quickly. Think of how heat flows, and you'll see every time that
condensation is on things that lag the current air/sample-block temperature colder. When
air/sample-block is cooling down there is no problem. Peltier is complexity exxxtra. Lose it.

[John Griessen]

On 02/27/2015 02:29 AM, Mac Cowell wrote:
> It would be interesting to explore a hybrid design combining dynamic conductive heating in the tube block with constant radiative
> heating from a lamp or hot air flow positioned at just the right distance, instead of a heated lid in constant contact with the
> cap. Can the radiative heat source be set up to always add +20C to the exposed cap and 5-10 C to the reaction mixture?

Sure, and with a little fan to help cool. It will be tough to make them always add +20C passively, but it is
easy to use the micro and feedback loop to control it actively.

[John Griessen]

On 02/27/2015 02:35 AM, Mac Cowell wrote:
> But the thermocycler is so simple in this case. Peltier, sawtooth heat sink with 5-10 ridges, mosfet for switching power, embedded
> thermocouple, microcontroller, and 5-10 glass capillaries, one per sample

Would work fine with forced air heat and cool also. What is a good way to seal ends of capillaries so
they stay pure, yet are easy to unload? Maybe some high melting point wax, (above PCR temps)? Hot glue plastic?

[John Griessen]

On 02/27/2015 05:33 AM, Cathal Garvey wrote:
> h, nice idea! I wonder if even plastic capillaries at that scale are conductive enough to work, I could see it being possible to
> make "pinch-off" capillaries that you fill (by capillary action? :)) and pinch, then lay on your micro-cycler

+1

[Mac Cowell]

The capillary design is not as complicated as you make it sound, Cathal. I think evaporation is marginal in open 10 uL tubes, so they don't need to be closed, and if the peltier is ONLY connected to a heatsink, the thermal mass vs surface area ratio is actually really good even without more radiative or active cooling.

Perhaps the conductivity could be enhanced by heating plastic capillaries to 70 C in the sawtooth heatsink and placing temporary pressure on another inverted sawtooth heatsink from above, to force the tubes to confom into a triangular prism sharing more contact area with the bottom groove of the thermocycled heatsink.

Seriously, not many parts needed...

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[Andy Morgan]

I think that based on how much more complicated it would be to add an adequate heated lid (at a constant ~100degC), I'll probably go for a design that works by convection cooling as described in this paper (http://www.biotechniques.com/BiotechniquesJournal/2011/January/Rapid-DNA-amplification-in-a-capillary-tube-by-natural-convection-with-a-single-isothermal-heater/biotechniques-307538.html).

Since not having a heated lid would mean I'd be using paraffin wax/oil anyway, it wouldn't be that much of a change and the technique looks interesting.

I'll probably use the same design as in the original instructables article I linked to but change the depth of holes in the aluminum heating block.

Hopefully it will be easy to change the programming code to just keep the block heated to 95degC, and remove the fan.

[Nathan McCorkle]

On Mon, Mar 2, 2015 at 10:53 PM, Andy Morgan <andrew....@gmail.com> wrote:
> I think that based on how much more complicated it would be to add an
> adequate heated lid (at a constant ~100degC), I'll probably go for a design
> that works by convection cooling as described in this paper
> (http://www.biotechniques.com/BiotechniquesJournal/2011/January/Rapid-DNA-amplification-in-a-capillary-tube-by-natural-convection-with-a-single-isothermal-heater/biotechniques-307538.html).
>

There's also this type of method... but it has had setbacks:
http://www.scidev.net/global/innovation/news/venezuelan-diy-science-project-hits-stumbling-block.html
http://www.synthesis.cc/2009/10/the-lava-amp-is-alive.html

based on:
http://www.researchgate.net/profile/Nitin_Agrawal6/publication/6365283_A_pocket-sized_convective_PCR_thermocycler/links/0912f50646768af845000000.pdf

[Jonathan Cline]

Requirement #1:
 * Throw away the Arduino.


I am going to add to the FAQ: 
"Do not use Arduino for real projects.  It is like building an automobile out of Legos and then expecting to actually drive it."
 

Also, fyi to Nathan.  LM339 is a comparator not an opamp so it is not a good signal buffer.  Use an opamp.  See my article in Biocoder #6.


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################


On Wednesday, February 25, 2015 at 4:49:50 AM UTC-8, Andy Morgan wrote:

 

So, I've slightly redesigned the Arduino PCR thermal cycler (http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS) to make it a bit better, by replacing the two wiremound resistors (100watts) with a cartridge heater (300watts) (http://www.ebay.com.au/itm/Cartridge-Heater-3-8-Diameter-3-2-Length-220VAC-300W-/380898256650?pt=AU_B_I_Electrical_Test_Equipment&hash=item58af4e270a).

But the thing is: I have ZERO experience with electronics, and I don't know whether the cartridge heater will require too much power from the Arduino board or power supply, and all the explanations I've found on the internet seem to go WAY over my head.

Does anybody know whether the cartridge heater will work?

Any help would be greatly appreciated.

[Cathal Garvey]

Arduino is fine and highly productive for beginners compared to PIC
whatevers. There's a reason Arduino is a household name and
PIC-number-number-number-number is not.

I've built functioning thermal cyclers on Arduinos without issue, and
with easily reasonable code (although I was using a pre-written
finite-state-machine library, the availability of which is just more
reason to use a widely used platform like Arduino).

On 24/03/15 02:38, Jonathan Cline wrote:
> Requirement #1:
> * Throw away the Arduino.
>
>
> I am going to add to the FAQ:
> "Do not use Arduino for real projects. It is like building an
> automobile out of Legos and then expecting to actually drive it."
>
>
> Also, fyi to Nathan. LM339 is a comparator not an opamp so it is not a
> good signal buffer. Use an opamp. See my article in Biocoder #6.
>
>
> ## Jonathan Cline
> ## jcl...@ieee.org
> ## Mobile: +1-805-617-0223
> ########################
>
>
> On Wednesday, February 25, 2015 at 4:49:50 AM UTC-8, Andy Morgan wrote:
>
>
>
> So, I've slightly redesigned the Arduino PCR thermal cycler
> (http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS

> <http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS>)

> to make it a bit better, by replacing the two wiremound resistors
> (100watts) with a cartridge heater (300watts)
> (http://www.ebay.com.au/itm/Cartridge-Heater-3-8-Diameter-3-2-Length-220VAC-300W-/380898256650?pt=AU_B_I_Electrical_Test_Equipment&hash=item58af4e270a

> <http://www.ebay.com.au/itm/Cartridge-Heater-3-8-Diameter-3-2-Length-220VAC-300W-/380898256650?pt=AU_B_I_Electrical_Test_Equipment&hash=item58af4e270a>).

>
>
> But the thing is: I have ZERO experience with electronics, and I
> don't know whether the cartridge heater will require too much power
> from the Arduino board or power supply, and all the explanations
> I've found on the internet seem to go WAY over my head.
>
> Does anybody know whether the cartridge heater will work?
>
> Any help would be greatly appreciated.
>

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[Jonathan Cline]

It is several x more expensive as a building block, similar to the Lego
analogy -- and always needs to add more pieces. It is not for real
("college undergrad level") projects. The household name comes from
the marketing push and the plethora of required 3rd party pieces --
which makes money for those other companies (including the kit
suppliers, like Ada), who also do more marketing, and so on. The
lameness of Arduino needing shields which boost business for kit
suppliers and make it a well-known product placement in catalogs is no
justification for using it in an engineering design. "There's a reason
xx is a household name" could apply to many xx's which are similarly
worse choices. Unfortunately the projects built with Arduino are also
falsely labelled "diy low cost" when in fact they are not at all low
cost in comparison and others are also led astray. When a lot of script
kiddies talk volumes about a technology, it does not mean the technology
is beneficial. A lot of the talk is simply confusion or from lack of
education. Technology which works does not get as much verbiage in
comparison precisely because it "just works" once the initial learning
curve is overcome.

The software application which allows cutting & pasting the code you
mention into your projects likely works on any number of better hardware
kits since it is in a high level language.

So I repeat my recommendation and have improved it slightly --

Requirement #1:
* Sell the Arduino on ebay.

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

[Cathal Garvey]

That's all well and good, but putting together a thermal cycler with an
Arduino requires no shields, less and more reasonable code, and no
additional equipment (programmers, etcetera) over and above the Arduino
and USB. It requires an AC solid state relay, LM35 sensor, a heat gun
and a computer cooling fan.

Telling people to use PICs because they'll save €5 on the cost of the
chip, even if it wastes days of their time because the community is
smaller and more techie and purist, is a bit useless. People want to get
stuff done, and people are rarely without the €5 needed to grab an
arduino, copy/paste some ubiquitous code, and get stuff done.

[Brian Degger]

Agree with both of you. 

If you are hard core electrical engineer, you might use something else, there is no need for a requirement 1.

 

But on the other hand, I would have to say where would 3d printing be without arduino?   

Remember Arduino is just a breakout board for atmel mega(and arm and many more including texas instrument chips if you want) + an programing environment/ide.

Who was it built for? Electrical engineers? Nup, it was for people like cathal and me, who want to tinker, and to enable designers to make hardware prototypes and readymades.

If you get further down the line, its likely you design your own pcb board with what you want, keep the chip, and away you go.

Brian   

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----------------------------------------

[Avery louie]

I am just going to leave this video here.  It is of a pneumatic, person-sized, lego car.

https://www.youtube.com/watch?v=_ObE4_nMCjE

Nothing wrong with an arduino really.  Actually the lego comparison is pretty apt- they are expensive, slow, but compatible with a lot of things and a great way to get into engineering.  There are plenty of alternatives, but none of them seem to be as popular (k'nex, I am looking at you).  And eventually you want to build something like a building or a space ship and they are not a viable option (imagine if your floor was made of legos- ow).

The LM339 is a comparator- however if we are being picky, it should be fine for buffering logic level signals to drive high/low side switches as described in the circuit, particularly to modulate the power to the peltiers devices (as suggested).

--A

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[Cathal Garvey]

Mm, and the price of a bare ATMEGA with the Arduino bootloader burned on
often floats around ~€1, so if one desperately wants to develop
something that can be minimalised and commercialised later PIC style,
the scope is all there. I think the overhead of the bootloader is in a
small startup time penalty and code size overhead but otherwise minimal,
and it comes with Serial as a core service which can be very valuable.

I know people who've developed stuff in raw C for PIC chips just for the
small performance boon and to say they'd done it, but even they hadn't
much conviction that the extra effort had won them much at the end.

> ## jcl...@ieee.org <mailto:jcl...@ieee.org>
> ## Mobile: +1-805-617-0223 <tel:%2B1-805-617-0223>

> ########################
>
> On 3/24/15 1:17 AM, Cathal Garvey wrote:
>
> Arduino is fine and highly productive for beginners compared
> to PIC
> whatevers. There's a reason Arduino is a household name and

> PIC-number-number-number-__number is not.

>
> I've built functioning thermal cyclers on Arduinos without
> issue, and
> with easily reasonable code (although I was using a pre-written
> finite-state-machine library, the availability of which is
> just more
> reason to use a widely used platform like Arduino).
>
> On 24/03/15 02:38, Jonathan Cline wrote:
>
> Requirement #1:
> * Throw away the Arduino.
>
>
> I am going to add to the FAQ:
> "Do not use Arduino for real projects. It is like
> building an
> automobile out of Legos and then expecting to actually
> drive it."
>
>
> Also, fyi to Nathan. LM339 is a comparator not an opamp
> so it is not a
> good signal buffer. Use an opamp. See my article in
> Biocoder #6.
>
>
> ## Jonathan Cline

> ## jcl...@ieee.org <mailto:jcl...@ieee.org>
> ## Mobile: +1-805-617-0223 <tel:%2B1-805-617-0223>

> ########################
>
>
> On Wednesday, February 25, 2015 at 4:49:50 AM UTC-8,
> Andy Morgan wrote:
>
>
>
> So, I've slightly redesigned the Arduino PCR
> thermal cycler

> (http://www.instructables.com/__id/Arduino-PCR-thermal-cycler-__for-under-85/?ALLSTEPS
> <http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS>
>
> <http://www.instructables.com/__id/Arduino-PCR-thermal-cycler-__for-under-85/?ALLSTEPS

> <http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS>>)
>
> to make it a bit better, by replacing the two
> wiremound resistors
> (100watts) with a cartridge heater (300watts)

> (http://www.ebay.com.au/itm/__Cartridge-Heater-3-8-Diameter-__3-2-Length-220VAC-300W-/__380898256650?pt=AU_B_I___Electrical_Test_Equipment&__hash=item58af4e270a
> <http://www.ebay.com.au/itm/Cartridge-Heater-3-8-Diameter-3-2-Length-220VAC-300W-/380898256650?pt=AU_B_I_Electrical_Test_Equipment&hash=item58af4e270a>
>
> <http://www.ebay.com.au/itm/__Cartridge-Heater-3-8-Diameter-__3-2-Length-220VAC-300W-/__380898256650?pt=AU_B_I___Electrical_Test_Equipment&__hash=item58af4e270a

> <http://www.ebay.com.au/itm/Cartridge-Heater-3-8-Diameter-3-2-Length-220VAC-300W-/380898256650?pt=AU_B_I_Electrical_Test_Equipment&hash=item58af4e270a>>).
>
>
>
> But the thing is: I have ZERO experience with
> electronics, and I
> don't know whether the cartridge heater will
> require too much power
> from the Arduino board or power supply, and all the
> explanations
> I've found on the internet seem to go WAY over my head.
>
> Does anybody know whether the cartridge heater will
> work?
>
> Any help would be greatly appreciated.
>
>
>
> --
> Scientific Director, IndieBio Irish Programme
> Got a biology-inspired business idea that $50,000 -
> & 3 months in a well equipped lab could accelerate?
> Apply for the Summer programme in Ireland:

> http://indie.bio/apply-to-__ireland <http://indie.bio/apply-to-ireland>
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[Jonathan Cline]

It was built for high school students.

## Jonathan Cline
## jcl...@ieee.org
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[Brian Degger]

Nope, that came later.

It was designed for/by/with Interaction Design Institute Ivrea students/faculty and designers. 

Pic was taught to school students in the good old days before Arduino(and still is in many places).  

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[Jonathan Cline]

Hmmmmmmmm

"wastes days of their time " .. starting out with the equivalent of
Legos might create a fast model prototype but then wastes more time when
moving from prototype to a more stable build. Requires rebuilding from
scratch. Think longer term. Most likely any kit board is a tool which
will be reused in a new project later which then runs into the typical
obstacles and has to be replaced with a better kit, creating an upgrade
cycle which wastes time. Start out with a solid kit first.

"the community is smaller " .. in fact the Arduino community is a drop
in the bucket, though a vocal and photo-polished one, compared to the
larger design communities using more professional building blocks. Note
"professional design" does not mean complex it only means a little bit
of homework is necessary and maybe less glossy photo's.

"less and more reasonable code" .. the code is in a high level language
so it is likely the same. "copy/paste some ubiquitous code" .. If it
is ubiquitous then there is nothing specific tying it to Arduino anyway.

It is not necessary to defend your use of Arduino in past projects.
Arduino is simply not a good recommendation in 2015 for new designs or
redesigns. If you're building an automobile today you don't need to use
an engine with a hand crank. When you designed the DremelFuge you
considered the design options and settled on an industrialized component
with suitable motor, a Dremel. You might have evaluated shiny plastic
objects from Toys R Us like a kiddie toy blender but you smartly passed
on these as underpowered. Just a little bit of homework up front gives
the design significant legs.

I didn't suggest anything about PIC in this thread either so there is no
need to compare. If you would really like, you can review past opinion
from the 90s on PIClist regarding why college students or more advanced
younger dudes should not start or continue projects with the Basic Stamp
(PIC based) - for same reasons as above: more expensive, typically
under-powered so rapidly outgrown, technology likely later to cause
frustration, though great for high school students and younger, and also
not recommended as the basis for solid designs (i.e.: things which
aspire to be more than toys).

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

[Nathan McCorkle]

On Tue, Mar 24, 2015 at 10:29 AM, Jonathan Cline <jcl...@ieee.org> wrote:
> Hmmmmmmmm
>
> "wastes days of their time " .. starting out with the equivalent of Legos
> might create a fast model prototype but then wastes more time when moving
> from prototype to a more stable build. Requires rebuilding from scratch.

Meh, fail-fast and agile are the current mottos in
engineering/software-development. Refactoring is not seen as a major
impediment. Obviously an engine ECU or ABS system needs more stringent
design guidelines. A smart programmer knows when to hack something
together quickly, and when to optimize.

> Think longer term. Most likely any kit board is a tool which will be reused
> in a new project later which then runs into the typical obstacles and has to

Really? I don't think many people really think much about reusing an
arduino... unless their project failed, most people are of the mindset
"if it ain't broke, don't fix it". In fact, most of what I hear these
days is how people are getting more and more lax because arduinos are
cheaper and cheaper, and using a slightly larger project enclosure box
is no problem for them.

> be replaced with a better kit, creating an upgrade cycle which wastes time.
> Start out with a solid kit first.

Arduino is pretty solid, unless you're complaining that an embedded
system uses object-oriented code (which some embedded designers avoid
like the plague)

>
> "the community is smaller " .. in fact the Arduino community is a drop in
> the bucket, though a vocal and photo-polished one, compared to the larger
> design communities using more professional building blocks.

Maybe it's a drop in the EE bucket, but in the hobbyist/easy-to-use
space it's pretty much king. Not many non-EEs can stand to install
gigabytes of some development environment, wade through
multi-hundred-page specification documents to setup some control
registers... just to get their chip to boot. Programming it might be
similar at some point, but plug-n-play has been a slogan for what, 20
years... it's a desired trait. Even I have had ideas/projects stall
because datasheets for MCUs are so dense, community support is so
poor, example code incomplete, etc... and I've been studying this
space for many years as a determined non-EE hobbyist.

> Note
> "professional design" does not mean complex it only means a little bit of
> homework is necessary and maybe less glossy photo's.

I'm sure there are lots of pros that would say arduinos are OVERKILL
and that a few well-connected discrete hardware ICs would do the job
better, faster, cheaper, lower power, and be hardier.

>
> "less and more reasonable code" .. the code is in a high level language so
> it is likely the same. "copy/paste some ubiquitous code" .. If it is
> ubiquitous then there is nothing specific tying it to Arduino anyway.

Hiding ugly code and things that beginners/scientists don't need to
know is part of the success though. Engineers I work with can't even
handle verbose debug messages in our software's output... these are
highly trained people who are working as EEs, but still have trouble
parsing a few lines of error messages/tracebacks. This is why Apple is
the most profitable company, because their stuff is clean and
intuitive.

>
> It is not necessary to defend your use of Arduino in past projects. Arduino
> is simply not a good recommendation in 2015 for new designs or redesigns.

Again, this is a pretty bad comment. Use what is appropriate for the
job, arduinos are more than overpowered for most applications people
use them for. There are about 5000 analog engineers in the world, and
millions of digital. Arduino is also not just the hardware, it's the
IDE and community and libraries. People have ported different/better
hardware to arduino-land (teensy, MSP430 via Energia, probably others
I don't know of).

> If you're building an automobile today you don't need to use an engine with
> a hand crank. When you designed the DremelFuge you considered the design
> options and settled on an industrialized component with suitable motor, a
> Dremel. You might have evaluated shiny plastic objects from Toys R Us like
> a kiddie toy blender but you smartly passed on these as underpowered. Just
> a little bit of homework up front gives the design significant legs.

Again, no one needs an 8MHz computer to blink christmas lights or even
control thermocycling. If anyone used something faster, it might be
just as open to scrutiny.

>
> I didn't suggest anything about PIC in this thread either so there is no
> need to compare. If you would really like, you can review past opinion from
> the 90s on PIClist regarding why college students or more advanced younger
> dudes should not start or continue projects with the Basic Stamp (PIC based)
> - for same reasons as above: more expensive

I don't see how anyone can really talk about price unless you live in
some country with really bad or expensive postal service... in which
case any integrated circuitry will be about equally hard to come by.
Price isn't a valid point in my opinion outside shipping, because you
can get fully-assembled arduinos for about $3, or $5 if you want it a
few weeks sooner. Seriously, drinks at Starbucks cost more than these
computers.

[Jonathan Cline]

I think the snip below is the clarification which leads to agreement.
When I say Arduino, I mean AVR hardware based kits. I'm not talking
about the software, which, since it is compatible with better hardware,
then the obvious choice is to pick the better hardware. Why use Lego
when you can easily switch to using real nuts & bolts. The software
used for Arduino is java based on Processing out of MIT which is still
good for it's purposes.

Regarding cost, the points mentioned pro/con have been simultaneously on
both sides of the fence so watch out. Typically pro-Arduino peeps will
argue for the kits because they don't require purchase of a programmer
then later will also argue that higher individual cost of boards are
okay because price is not a concern (the programmer is a single tool,
one time minimal cost) . Since this circular argument doesn't make
sense it probably just goes back to the pro-Arduino peeps preferring the
choice because of the glossy pictures and the perception of community
(much larger and helpful communities to help with real designs exist,
simply go find them). The best design choice is to buy a $20 chip
programmer as a 1-time purchase, and buy some cheap chips and cheap
copper boards and solder 'em up (this is scalable, longer term, more
educational) . This was also the recommendation on numerous chip
discussion lists for anyone serious about building anything more
interesting than simple blinking led's (it's not just my opinion).
But even this point is less necessary today anyway with the new hardware
choices as you've said, especially with built-in USB downloading across
the board. The choices steering toward using Arduino hardware are simply
even less valid today.


Biology analogy: we can also pipette using straws, and recommend that
everyone do this (esp years ago when pipettes were expensive), but why
recommend this today? Buy a real pipette, the real tool.

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

[Cathal Garvey]

> Biology analogy: we can also pipette using straws, and recommend that
> everyone do this (esp years ago when pipettes were expensive), but
> why recommend this today? Buy a real pipette, the real tool.

To borrow that analogy, if straws were as accurate and easier to use for
99% of use cases than micropippettes, you can be damned sure we'd
recommend straws over micropippettes. The fact that straws are,
actually, terrible is the reason we recommend serious people buy
(cheaper, off-brand) micropippettes.

And, for 99% of the stuff a person on this list is likely to want to do
that can be done with a microcontroller at all, arduino is just fine, so
why recommend something with a steeper (read: distracting) learning
curve and longer development times? Because it'll scale better someday?
Because the difference of €5 means you're more likely to get a product
out this year than next, or the year after that, so "scaling" begins to
sound more like "timewasting".

Don't penny-pinch early and don't over-optimise early. If an arduino can
help you ship a thing today instead of tomorrow, always go Arduino. If
you need something bare-metal with ultra-low cost and no code overhead
(i.e. the overhead is put on you in dev-hours instead of being
built-in), sure; get something else.

[Jonathan Cline]

On 3/24/15 12:50 PM, Cathal Garvey wrote:
> > Biology analogy: we can also pipette using straws, and recommend that
> > everyone do this (esp years ago when pipettes were expensive), but
> > why recommend this today? Buy a real pipette, the real tool.
>
> To borrow that analogy, if straws were as accurate and easier to use
> for 99% of use cases than micropippettes, you can be damned sure we'd
> recommend straws over micropippettes. The fact that straws are,
> actually, terrible is the reason we recommend serious people buy
> (cheaper, off-brand) micropippettes.

This is exactly the point I implied, yes. Now fill in the blank, "The
fact that [Arduino's] are, actually, terrible is the reason we recommend
serious people buy (cheaper, off-brand) [what they determine they need
after doing a little homework]"

I'm not sure where this perception of "steep learning curve" comes from
(unless it is another symptom of the new social-media-ADHD-generation
"if I can't google the answer in 10 seconds then forget it"). Doing a
couple days of homework first and a few more days of up front design
time is not a steep learning curve. Learning to solder is not a steep
learning curve and is also a valuable life skill (not "distraction").
Using a real programming IDE as opposed to a
pointy-clicky-for-humanity-majors is not a steep learning curve. Anyone
on this list is aiming for harder science than the equivalent of mixing
vinegar and baking soda in a balloon. Now if you didn't personally
know where to look (newbie design communities alive & thriving), that is
a different and perhaps difficult past occurrence for you which made for
a steeper curve than necessary, though it is not valid as a
recommendation for newcomers today. Also to mention that these skills
learned will boost employment opportunities and perhaps salary which
adds up significantly over a long term. It is not like recommending
some obscure art of basket weaving, this is really, really valuable
stuff, even literally $$$.

Take a second to look at your perspective, reflect on the analogy of
engineers going into a biology context and saying: "Look, this is
Biology, but it is also called a Part. We'll call it a biobrick. But
this is a re-usable Part. It is characterized. We summarize these
characteristics on a Data Sheet." Then the engineers facepalming
themselves when the biologists respond: "Yea but I don't want to get
distracted by reading a data sheet. It is too much of a steep learning
curve. I'm just going to continue doing these custom cut & paste jobs."


You can continue to try to offer convincing points for why Arduino is a
good design choice in today's world of course...

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

[John Griessen]

On 03/24/2015 02:50 PM, Cathal Garvey wrote:
> And, for 99% of the stuff a person on this list is likely to want to do that can be done with a microcontroller at all, arduino is
> just fine, so why recommend something

I guess that's it. The learning curve time 99% of diybio list folk will put up with is about bio not about electronics
or coding embedded systems or mechanical designs.

Maybe running programs on an embedded-in-the-lab-gear linux, or embedded-in-the-lab-gear python interpreter-compiler though...

[Cathal Garvey]

Well, if your lab gear runs Linux then your options are drastically more
open; even a barebones/gutted Linux like Android can run Lua, for
example (my phone does, not that I use it for anything)!

[Jonathan Cline]

The fundamental point is to design by reducing components and complexity until the desired effect still remains and surpasses expectations, which can then perhaps be called beauty.   http://en.wikipedia.org/wiki/Hacker_ethic   Bundling the fruity language up into a convenient term, "cost", is one way to put it, as a billing metaphor, or maybe as a phrase, using master level craftsmanship.

Lab gear running linux with big display and a web server is 90's.  2015 is for the internet of things: simplified wireless sensing and controlling with a native smartphone/tablet app as the master.  Lab gear redesigned today should not have buttons or jacks or a display panel at all.  Maybe it should not even have a power cord.   It should be either entirely software-free and bounded, or a wireless invisible agent.

To bring this back to the thermal cycler here is a recent PLoS One paper which is well written in terms of technical detail:

Development of a Real-Time Microchip PCR System for Portable Plant Disease Diagnosis

   Koo C, Malapi-Wight M, Kim HS, Cifci OS, Vaughn-Diaz VL, et al. (2013) Development of a Real-Time Microchip PCR System for Portable Plant Disease Diagnosis. PLoS ONE 8(12): e82704. doi:10.1371/journal.pone.0082704    Published: December 12, 2013  Received: June 7, 2013; Accepted: October 26, 2013 


The authors chose the following hardware in their implementation.  I found the article just now before coming to the description of their design choices, so I didn't purposely single anything out here.  Why might they have chosen the specific development environment and hardware components that they chose?  


-Begin quote-

Real-time PCR can directly quantify the amplicon during the DNA amplification without the need for post processing, thus more suitable for field operations, however still takes time and require large instruments that are costly and not portable.  ...  Here we present a stand-alone real-time microchip PCR system composed of a PCR reaction chamber microchip with integrated thin-film heater, a compact fluorescence detector to detect amplified DNA, a microcontroller to control the entire thermocycling operation with data acquisition capability, and a battery. The entire system is 25×16×8 cm³ in size and 843 g in weight. The disposable microchip [aka microfluidic chip] requires only 8-µl sample volume and a single PCR run consumes 110 mAh of power.

...
Compact fluorescence detector. The optical setup used in the real-time microchip PCR system is based on the detection of fluorescence dyes that intercalate with DNA, where fluorescent intensity is proportional to the amount of amplified DNA in the reaction chamber of the PCR microchip. The dye is excited with light emitted from an LED, and the emission light passing through series of filters and lenses to eliminate excitation light is detected through a photomultiplier tube (PMT) (Figure 1C). SYBR Green dye (QIAGEN, Valencia, CA, USA) was used as a fluorescence dye, which absorbs blue light (497 nm) and emits green light (520 nm). As a light source to excite the SYBR Green, a blue LED (470 nm, NSPB310B, Nichia, Tokushima, Japan) was used. The excitation filter (ET470/40x, Chroma Technologies, Brattleboro, VT, USA) was placed after the blue LED to further narrow down the spectrum, and a dichroic mirror (495DCLP, Chroma Technologies) was used to reflect the excitation light vertically to the PCR microchip placed on top of the optical housing. An aspheric lens (352330-A, Thorlabs, Inc., Newton, NJ, USA) was placed between the dichroic mirror and the PCR microchip to focus the excitation light onto the reaction chamber. The emission filter (ET535/50 m, Chroma Technologies) was placed before the PMT to transmit only the emitted light from the PCR sample. As a fluorescence detector, a compact PMT (H10721, 5×2×2 cm³, Hamamatsu, Hamamatsu City, Japan) was utilized because of its superior sensitivity compared to photodiodes even though the size and cost is higher. Since the amplicon detection is based on fluorescent intensity, drift in baseline readout of the PMT could result in inaccurate measurement of amplicon fluorescent intensity. Therefore, the PMT was warmed up for 1 hr by applying a working voltage of 5 V before any real-time PCR runs so that the degree of this drift becomes negligible.

...

Microcontroller for PCR thermocycle control and data acquisition. In order to create a smaller and truly portable real-time PCR system, a compact battery-operated microcontroller unit (MCU) board was developed to control the thermocycling of the microchip as well as data acquisition and data display. The developed board is composed of an MCU and a custom-built printed circuit board (PCB) for the MCU. An 8-bit CMOS flash model microcontroller (PIC16F877, Microchip Technology Inc., Austin, TX, USA) was selected as the MCU and was programmed using the CCS-C language on the MPLAB IDE software suite (Microchip Technology Inc.) to regulate all operations of the system (thermocycling control, LED excitation light control, data acquisition from the PMT, and data display). Figure S1 shows the PCB schematic.

For thermocycling control, a proportional-integral-derivative (PID) control scheme was used, which measures the difference between current and target temperatures, and then change the current temperature to minimize this difference. To read the temperature of the reaction chamber, a fine-tip thermocouple (K-type, OMEGA, Stamford, CT, USA) was attached on the glass slide of the microchip (1 mm apart from the reaction chamber) using thermal grease (Thermalcote, Aavid Thermalloy, Concord, NH, USA) to form a tight thermal contact. Temperature reading from the thermocouple was converted and amplified to 5 mV/°C by an analog to digital (A/D) converter (AD8495, Analog Devices, Norwood, MA, USA), and this value was transmitted to an analog port of the MCU. This temperature information was then used to process the PID control for adjusting the pulse-width modulation (PWM) duty cycle of the current flow. By controlling a PSMNR5-40PS transistor (NXP semiconductor, Eindhoven, Netherlands), which was used as a switch, the MCU could control the current flow from a voltage source (15 V) to the heater. The PWM control signal from the MCU was sent to the gate of the transistor to switch the current flow. For faster cooling of the PCR microchip during thermocycling to minimize the total run time, a cooling fan (GB1206PHV1-AY, Digi-Key, Thief River Falls, MN, USA) was attached on top of the fluorescence detector housing as illustrated in Figure 1A and connected to the voltage source (15 V) and another PSMNR5-40PS transistor to let the MCU control turn on and off the cooling fan.

...

The overall real-time microchip PCR system requires 5 V for the microcontroller, A/D converter, PMT, op-amp, and LCD display, and 15 V for the heater and cooling fan. For the LED and the gain-control of the PMT, 3.2 V and 0.6 V are used, respectively. To make the system portable, a 2200 mAH 15 V Li-ion battery (Tenergy, Fremond, CA, USA) in conjunction with a 5 V voltage regulator (LM7805, Fairchild Semiconductor, San Jose, CA, USA) provides all voltages and power to the system. A voltage divider using two resistors was used to provide 3.2 V and 0.6 V from the 5V regulator. All circuit components are placed on a PCB designed using an electronic design automation (EDA) software tool (open source program, www.kicad-pcb.org) and fabricated by a PCB manufacturer (Advanced Circuits, Aurora, CO, USA).

-End quote-

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

On 3/24/15 1:54 PM, Cathal Garvey wrote:

[Simon Quellen Field]

I respect you, and your engineering talents.

But are you really are recommending that the electronics novice design his own PC board using a CAD system, ship it off to a PC board manufacturer, and solder in all the parts of the power supply and microprocessor and clock system, and program the chip on a separate programmer board?

My recommendation would be to use a $2.54 Arduino Nano clone. It already has the 3 volt regulated power supply, so you don't need one of the voltage divider circuits (and its regulated to boot). I'd swap the other voltage divider for a diode (getting a regulated half volt supply).

You get USB for free. Your battery can be a 6 volt Lithium Ion instead of 15 volts, which will make it last a lot longer (ten of those volts were wasted as heat in the 5 volt regulator).

Now, when you find out you have made a mistake, you don't need to re-engineer the PC board and send it out for manufacture again. You can debug it over USB, in the device, instead of needing a programming board and swapping out the chip every time. It is easily field-programmable, via a download over the web.

And the result is a much smaller board, unless you want the electronics novice to try to build a surface mount device with parts on both sides, like the Arduino Nano clone.

You made the analogy of building things out of Legos. The analogy I would use is: Why try to re-invent a new engine for each project when an engine designed and built by experts can be had for less than $3? Your parts count alone is several times that, and the time it would take to design and build it is measured in weeks for an expert, and years for the electronics novice.

The design you reference is not part of the Internet of Things. It has no network connection. Adding that to an Arduino Nano is a matter of simply connecting the USB port to an Internet connected machine, such as a $35 Raspberry Pi. Since the project doesn't really need real-time monitoring or control, the Raspberry Pi alone could be used. It will still cost less.

The device you reference also does not talk to your smartphone. But the Arduino Nano interfaces easily to a $2 Bluetooth module.

I have on my desk here an Intel Edison. It is basically a PC on a postage stamp for about $60. In addition to the PC, it has an Arduino Compatible separate processor on the same postage stamp, for doing real-time measurement and control. That would be a real Internet of Things platform to start with -- it has built-in Wi-Fi and Bluetooth, and runs Linux today, and will be running Windows 10 in a few months. I would not recommend that an electronics novice try to build one himself.

Re-inventing the wheel for each project is not the definition of beauty.

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[John Griessen]

On 03/25/2015 07:13 PM, Simon Quellen Field wrote:
> Intel Edison. It is basically a PC on a postage stamp for about $60. In addition to the PC, it has an Arduino Compatible separate
> processor on the same postage stamp, for doing real-time measurement and control.

The black-swift is priced at $25, postage stamp size also, and has plenty of IO wires to connect another MCU.

I think we'll see more and more multi MCU systems.

[Cathal (Phone)]

I've got two Black Swifts on order, they look great!

--
Sent from my Android device with K-9 Mail. Please excuse my brevity.

[Mateusz Zalega]

On 03/24/2015 03:38 AM, Jonathan Cline wrote:
> Requirement #1:
> * Throw away the Arduino.
>
>
> I am going to add to the FAQ:
> "Do not use Arduino for real projects. It is like building an
> automobile out of Legos and then expecting to actually drive it."

I don't want to actually disprove the point, but:
https://www.youtube.com/watch?v=_ObE4_nMCjE

msgctl

[Jonathan Cline]

The trap you guys are falling into is called "jumping to implementation before design".  The suggestion to throw away the existing board elicited immediate reactive responses to pick a new one.   Be proactive on the design instead.  Do not propose implementation solutions before deciding what the device is even going to do, for simple example, what LED's it is using to show heating/cooling cycles.  Jumping immediately to "OK let's pick a board!  Let's pick a chip!"   (and "Let's use arduino!") is a classic type mistake.  Compare designs of peers.  Look at the strengths and goals of the designs.  I already mentioned that there is not a "one size fits all" with embedded boards so attempting to find one is not likely to reach a conclusion.   [Note Simon I would suggest if you're giving away boards to random people, maybe try handing out Teensy 3.x's or Teensy LC's instead of the nano's.]

There will almost always be a custom board in an embedded project.  Including a thermocycler.  It does not have to be made in CAD or etched by a fab.  It does not have to be complex.  The power relays are mounted to something and wired to something, that something is a board.  The temp probe is going to be wired to something.  The user LED's are wired to something.  Don't make a rat's nest of jumper wires.   These should be neat and connected on their own board.  It could be a pre-drilled copper bus board.  It could be a custom etched board with traces drawn with a ruler and a sharpie permanent marker.  These are possibilities.  In discussing design (which is what I have been attempting to start here) compare the competing designs and list the likely possibilities.  If you go with a kit board vs components, then immediately what comes to mind is: does this board have a prototyping area to add components to it, or what components is that board missing that will need to be put on a second board anyway.   No, the arduino boards do not have prototyping areas.  What I didn't blatantly say, and I guess I should have, and will now, is:  start out with the idea of creating the custom board so the form factor will fit in the space you want with the mounting options you want, and ideally everything will be on one PCB.   [Note: The small Arduino boards do not have mounting holes.  The only way to mount them is to use it's header pins.] 

I don't know where this "electronic novices can't do these complex things" perspective comes from.  Is it any different than crufty liberal arts school teachers saying, "Ohh, watch out for calculus, you don't want to try that, it's tooooo hard for you!!"   I was a novice once.  I took a piece of 1/8" thick waste acrylic out to a workshop and drilled 0.1" holes in it for an IC and components to fit into because I couldn't afford to purchase an FR4 copper clad board, then I soldered the IC and components together point-to-point [note, my holes were incredibly off-center but I bent the pins to fit and it worked fine].  That was probably my first "board".  I didn't have a schematic, I drew one on a spare piece of graph paper based on the circuit I saw in the datasheet and a project idea I read in a magazine.  I didn't have an electronics soldering iron, I used an automobile-grade type, I didn't have access to the chemicals for etching.  I think I was 12 at the time.  I had no guidance.  I didn't have instruction from school or a mentor.   I didn't have youtube videos to watch as a guide.  I didn't have new components, I ripped them out of an old radio and tape player.  I didn't have datasheets for anything in the world available via a mouse click.   I didn't have a digital logic probe or O-scope.  Look at how much easier CAD and fab technology and component procurement has become since then and all the examples and videos online!  It is much easier now if anything.  It is not difficult even for a "novice".  Do the homework.  RTFM.  End the "must spoon feed them" mentality.  It doesn't take "excessively long" and you don't "need to get it done right now".  Any biology protocol will take longer to incubate than to design and build the electronics.   It's all good experience and not wasted.   BTW that circuit worked, I still have it, I found it in a move a while back, quite a trip to find.  Today, use the latest and greatest tools available for the newbie, and why not start with the professional tools compared to starting with the lego kit, or at least, quickly switch over to the professional tools and ditch the toys, take off the training wheels as soon as possible.

A complete beginner without ever having touched any electronic component can easily download kicad and draw out a schematic from other examples found elsewhere [online, datasheets, magazines, whatever], can absolutely do a layout, then very easily print out the copper traces and etch a board and drill the holes and even bake on the surface mount parts to complete a new board.  I am not saying this is necessary, I am saying, drop the idea that it is sooooo hard and sooooo complex.   It is no more complex today than brewing beer in the kitchen or making a batch of yogurt from scratch or canning jam.  I hope everyone does those things too.  They will be helpful skills to have for when the zombies come.

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

On 3/25/15 5:13 PM, Simon Quellen Field wrote:

I respect you, and your engineering talents.

But are you really are recommending that the electronics novice design his own PC board using a CAD system, ship it off to a PC board manufacturer, and solder in all the parts of the power supply and microprocessor and clock system, and program the chip on a separate programmer board?

My recommendation would be to use a ....

 

[Jeswin]

On Thu, Mar 26, 2015 at 3:21 PM, Jonathan Cline <jcl...@ieee.org> wrote:
> The trap you guys are falling into is called "jumping to implementation
> before design". The suggestion to throw away the existing board elicited
> immediate reactive responses to pick a new one. Be proactive on the design
> instead. Do not propose implementation solutions before deciding what the
> device is even going to do, for simple example, what LED's it is using to
> show heating/cooling cycles. Jumping immediately to "OK let's pick a board!
> Let's pick a chip!" (and "Let's use arduino!") is a classic type mistake.
> Compare designs of peers. Look at the strengths and goals of the designs.
> I already mentioned that there is not a "one size fits all" with embedded
> boards so attempting to find one is not likely to reach a conclusion.
> [Note Simon I would suggest if you're giving away boards to random people,
> maybe try handing out Teensy 3.x's or Teensy LC's instead of the nano's.]
>

Is it just me or are the two sides in this argument not seeing on the
same level? It seems Jonathan is looking at the problem through a
"mass production" viewpoint, which would require a somewhat good
design of all components in the device, i.e., circuit boards, casings,
components, etc. Everyone else seems to be thinking through the
DIY/hobby design viewpoint, i.e., simple-to-build. The former will be
more elegant in terms of circuitry, software, and even the enclosure.
If you're a hobbyist (any level of skills), then it won't really
matter if it's a kludge build, as long as the basic components do
their job and you can get "up n' running" quickly.

--
In necessariis unitas, in dubiis libertas, in omnibus caritas.
-Marco Antonio Dominis

[John Griessen]

On 03/26/2015 02:59 PM, Jeswin wrote:
> it won't really
> matter if it's a kludge build, as long as the basic components do
> their job and you can get "up n' running" quickly.

He got that quick is desirable. I just wish he could maintain the tone
in his writings as just now in describing how novices *CAN* build electronics
that will function and be reliable with a lower learning curve than
before.

Let's stop the flaming and/or ignoring and make apologies for ugly outbursts that went by
yesterday.

[Jonathan Cline]

"it won't really matter if it's a kludge build" - yes, it will matter,
as I described before, it matters quite a lot to hackers:
http://en.wikipedia.org/wiki/Hacker_ethic

It also matters quite a lot in terms of a clean implementation having
tangible long term value, even to others:
http://en.wikipedia.org/wiki/Broken_windows_theory

Bandying about the term "agile" as it was mentioned before is no excuse
for finalizing junk (even if the term is misapplied). Why not just
label it a Microsoft product then? And if that metaphor isn't
understood then nothing else I'm describing will be understood either.

## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

[Simon Quellen Field]

Andy said he was an undergraduate genetics student who wanted to put together a lab to get hands-on experience in doing biology.

If he had said he was a novice who wanted to learn how to build his own circuit boards and design his own microcontroller systems, then I would certainly agree with Jonathan. What I got from Andy's original post was that he wanted some lab equipment, and was forced to build his own due to lack of funds. If someone donated a thermocycler to his cause, he would likely be done, as his goal is to use the thermocycler, not to build one.

Nothing in the "hacker ethic" says you have to etch a PC board, or even know how to do that. But I wouldn't let someone's statement of their principles be my straight-jacket anyway. If I want a hole dug, it doesn't have to be beautiful. I build spectrographs out of plumbing parts. What the hacker ethic page does say is that important resources should not be wasted. The time of a genetics student is an important resource. Telling a fencer he has to learn how to forge his own sword will not help him learn how to fence.

I like the Teensy boards. But they are overkill for the thermocycler, and the cheapest one costs $11.65, so I won't be handing them out to my students instead of the $2.54 Arduinos that do the job. And Andy's thermocycler will work fine on a solderless breadboard.

There is nothing wrong with Jonathan's point of view. He makes good points, and he's obviously bright, capable, and educated. He is just trying to apply someone else's "ethic" to people who don't share it. That's OK. His designs will be beautiful, robust, and they will work. They will take longer to build and be more expensive, and that is the way he likes to make the tradeoffs. There is a lot to be said for that. But it is expensive thermocyclers that were the problem we're trying to help Andy solve.

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[Simon Quellen Field]

Yes, a very nice little board.

I love that we're getting so many cheap Linux systems.

The Internet of Things really needs cheap.

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[Andy Morgan]

Having watched this thread for awhile, I figured now would be a good time to jump back into the discussion.

Jonathan does make some good points. Inevitably if you do want to scale up your design and potentially market it as a viable alternative to mainstream products then maybe it would be worthwhile to move away from using Arduino and the like.

But as Simon has pointed out, I'm primarily using this because I'd like to do some bio experiments at home that I wouldn't be able to readily do at Uni. I certainly don't have the experience (read: zero experience) nor the intention to scale my design up (though I'll probably document how I made it incase it interests others).

Adding the Arduino definitely adds to the complexity of something that could be much more "simple" in design, but rather than adding to the complexity, the Arduino (using the code already written) actually makes things easier for me. But thats me personally.

[Andrew Barney]

just found this thread. There is some VERY interesting ideas in this one that i need to go back and read in greater detail.

On Wednesday, February 25, 2015 at 5:49:50 AM UTC-7, Andy Morgan wrote:

Hey, so I'm currently an undergraduate genetics student and I'd like to do some diy biohacking to really get lots of hands-on experience while I'm studying. At the moment I'm just setting up a basic lab by building some lab equipment based off plans on the internet.

So, I've slightly redesigned the Arduino PCR thermal cycler (http://www.instructables.com/id/Arduino-PCR-thermal-cycler-for-under-85/?ALLSTEPS) to make it a bit better, by replacing the two wiremound resistors (100watts) with a cartridge heater (300watts) (http://www.ebay.com.au/itm/Cartridge-Heater-3-8-Diameter-3-2-Length-220VAC-300W-/380898256650?pt=AU_B_I_Electrical_Test_Equipment&hash=item58af4e270a).