Re: [DIYbio] Re: Electronic requirements for redesign of Arduino PCR thermal cycler

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  ## jcline@ieee.org  ## Mobile: +1-805-617-0223  ########################    

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

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)!

On 24/03/15 20:44, John Griessen wrote:

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...

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to diybio+unsubscribe@googlegroups.com.
To post to this group, send email to diybio@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio.
To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/5512FB3C.1040406%40ieee.org.

For more options, visit https://groups.google.com/d/optout.