DIYbio:Notebook/Open Thermal Cycler/Specifications

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Current revision (02:35, 15 April 2009) (view source)
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== "the brain"==
== "the brain"==
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#(fenn)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 addition of some inexpensive external electronics; intermediate difficulty to program $2.58 @ digikey
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can be configured as an insecure webserver and/or USB device with the
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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 implement encryption protocols if you knew what you were doing $12.58 @ digikey
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addition of some inexpensive external electronics; intermediate
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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 to make sure that the included AES encryption code is actually secure $109.00 @ http://makezine.com/controller
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difficulty to program $2.58 @ digikey
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#TS-7200 full blown linux server running debian, in a tiny package, easy to program, perhaps too $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 already soldered to the board; with usb connector $30 @ sparkfun + $45 for ethernet module
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#AT91SAM7S256, an ARM system on chip with integrated ethernet and usb
+
#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)
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"slave" support, rather advanced programming/development, might be able to
+
-
implement encryption protocols if you knew what you were doing
+
-
$12.58 @ digikey
+
-
 
+
-
#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
+
-
 
+
-
#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
+
-
 
+
-
#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
+
-
 
+
-
#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 ==
== the interface ==
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#I don't see much use for pictures or animations but something similar
+
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...
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to an HTML form might make a lot of biologists happy.  Drop down
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Step 1: "95C" "00:30"
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boxes, text fields, etc.  That way I could enter numbers into boxes...
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Step 2: "55C" "00:30"
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Step 1: "95C" "00:30"
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Step 3: "72C" "02:00"
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Step 2: "55C" "00:30"
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Goto Step1 25 times
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Step 3: "72C" "02:00"
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Step 4: "4C" forever
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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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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
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suffice just as well.  Anything involving a full QWERTY keyboard would
+
-
be a huge improvement over most thermocycler interfaces. -- Cory Tobin
+
-
# 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
+
2. 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

Current revision

"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
  2. 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
  3. 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
  4. TS-7200 full blown linux server running debian, in a tiny package, easy to program, perhaps too $149 @ http://embeddedarm.com/products/board-detail.php?product=TS-7200
  5. 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
  6. 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

2. 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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