DIYbio:Notebook/Open Thermal Cycler/Specifications

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"the brain" and their costs (fenn):
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== "the brain"==
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ATmega48 20MHz microcontroller, easy to interface to sensors and relays;
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#(fenn)ATmega48 20MHz microcontroller, easy to interface to sensors and relays;
can be configured as an insecure webserver and/or USB device with the
can be configured as an insecure webserver and/or USB device with the
addition of some inexpensive external electronics; intermediate
addition of some inexpensive external electronics; intermediate
difficulty to program $2.58 @ digikey
difficulty to program $2.58 @ digikey
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AT91SAM7S256, an ARM system on chip with integrated ethernet and usb
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#AT91SAM7S256, an ARM system on chip with integrated ethernet and usb
"slave" support, rather advanced programming/development, might be able to
"slave" support, rather advanced programming/development, might be able to
implement encryption protocols if you knew what you were doing
implement encryption protocols if you knew what you were doing
$12.58 @ digikey
$12.58 @ digikey
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makezine controller; same as above but already soldered and comes with a
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#makezine controller; same as above but already soldered and comes with a
simple operating system and connectors, fairly easy to program; you'd have
simple operating system and connectors, fairly easy to program; you'd have
to make sure that the included AES encryption code is actually secure
to make sure that the included AES encryption code is actually secure
$109.00 @ http://makezine.com/controller
$109.00 @ http://makezine.com/controller
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TS-7200 full blown linux server running debian, in a tiny package, easy to
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#TS-7200 full blown linux server running debian, in a tiny package, easy to
program, perhaps too easy.. but you can use ssh and ssl for encryption
program, perhaps too easy.. but you can use ssh and ssl for encryption
$149 @ http://embeddedarm.com/products/board-detail.php?product=TS-7200
$149 @ http://embeddedarm.com/products/board-detail.php?product=TS-7200
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i should add Arduino to this list; basically the same as atmega48 but  
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#i should add Arduino to this list; basically the same as atmega48 but  
already soldered to the board; with usb connector
already soldered to the board; with usb connector
$30 @ sparkfun + $45 for ethernet module
$30 @ sparkfun + $45 for ethernet module
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Tom: What about the linux "wall wart?"
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#Tom: What about the linux "wall wart?"
http://www.linuxdevices.com/news/NS9634061300.html
http://www.linuxdevices.com/news/NS9634061300.html
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ben: it has no i/o so you're back to square one (equivalent to a laptop with  
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Response by fenn: it has no i/o so you're back to square one (equivalent to a laptop with  
USB port and ethernet)
USB port and ethernet)
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== the interface ==
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#I don't see much use for pictures or animations but something similar
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to an HTML form might make a lot of biologists happy.  Drop down
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boxes, text fields, etc.  That way I could enter numbers into boxes...
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Step 1: "95C" "00:30"
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Step 2: "55C" "00:30"
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Step 3: "72C" "02:00"
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Goto Step1 25 times
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Step 4: "4C" forever
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I guess a progress bar wouldn't hurt but a count-down timer would
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suffice just as well.  Anything involving a full QWERTY keyboard would
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be a huge improvement over most thermocycler interfaces. -- Cory Tobin
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# When you feel like just clicking, use your "Biobricks" profile that you download from igem.org. It's preconfigured to the Taq you're using. Click the profile and go! The same with the "Bioweather Maps" profile that you get from Jason Bobe -- amplify ribosomal RNA. Or, if you're amplifying another sequence, you copy/paste in your primer sequences and the PCR machine does the rest of the calculations. -- Tito Jankowski

Revision as of 02:28, 15 April 2009

"the brain"

  1. (fenn)ATmega48 20MHz microcontroller, easy to interface to sensors and relays;

can be configured as an insecure webserver and/or USB device with the addition of some inexpensive external electronics; intermediate difficulty to program $2.58 @ digikey

  1. AT91SAM7S256, an ARM system on chip with integrated ethernet and usb

"slave" support, rather advanced programming/development, might be able to implement encryption protocols if you knew what you were doing $12.58 @ digikey

  1. makezine controller; same as above but already soldered and comes with a

simple operating system and connectors, fairly easy to program; you'd have to make sure that the included AES encryption code is actually secure $109.00 @ http://makezine.com/controller

  1. TS-7200 full blown linux server running debian, in a tiny package, easy to

program, perhaps too easy.. but you can use ssh and ssl for encryption $149 @ http://embeddedarm.com/products/board-detail.php?product=TS-7200

  1. i should add Arduino to this list; basically the same as atmega48 but

already soldered to the board; with usb connector $30 @ sparkfun + $45 for ethernet module

  1. Tom: What about the linux "wall wart?"

http://www.linuxdevices.com/news/NS9634061300.html Response by fenn: it has no i/o so you're back to square one (equivalent to a laptop with USB port and ethernet)

the interface

  1. I don't see much use for pictures or animations but something similar

to an HTML form might make a lot of biologists happy. Drop down boxes, text fields, etc. That way I could enter numbers into boxes... Step 1: "95C" "00:30" Step 2: "55C" "00:30" Step 3: "72C" "02:00" Goto Step1 25 times Step 4: "4C" forever

I guess a progress bar wouldn't hurt but a count-down timer would suffice just as well. Anything involving a full QWERTY keyboard would be a huge improvement over most thermocycler interfaces. -- Cory Tobin

  1. When you feel like just clicking, use your "Biobricks" profile that you download from igem.org. It's preconfigured to the Taq you're using. Click the profile and go! The same with the "Bioweather Maps" profile that you get from Jason Bobe -- amplify ribosomal RNA. Or, if you're amplifying another sequence, you copy/paste in your primer sequences and the PCR machine does the rest of the calculations. -- Tito Jankowski
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