[Open_electroporator] promoting culture shock progress

Mitchell Altschuler mitchellalt at gmail.com
Tue Jul 11 15:10:29 UTC 2017


Thanks so much !

I have been looking through your culture club GITHUB site and READ Me's
this morning, as about the STM32F401 boards etc, and and figuring my next
steps.
After scanning through your email it looks like reading that more carefully
will be helpful for me going forward.

So far I need to :
1) re attach the Cap with solder ( important for the EP function, but not
sure that is needed for get the program to function however)  Never used
such Caps (not leads)
It seems like it has some strips that line up with the position on the
board.  My plant is to heat a little solder on the strip on the board and
place the  cap on top while its hot.
If you have a better suggestion, pleas let me know...

2) Upload the files using my mac.  From reading the various texts the board
is supposed to show as a USB drive.

3) from the various emails I have looked over,  I get the impression you
are suggesting we will need to test the variables to optimize for EP.

Once i get the device it working  I can look into what we can vary and
decide what is the best things to change and then plan a controlled Ecoli
transformation.  .....
My hope is to get this in shape in 2perhaps 3 weeks.



 Mitchell










On Tue, Jul 11, 2017 at 9:42 AM, John Griessen <john at cibolo.com> wrote:

> On 07/11/2017 05:52 AM, Mitchell Altschuler wrote:
>
>> Thanks John,
>>
>> (see attachments)
>>
>> I assume I can superglue that Cap back on the board as long as the
>> contacts are aligned?
>> It doesn't look like it was soldered.
>>
>
> It needs solder.
>
>
> I see two potential positions to do place the cap, does it make a
>> difference on where I place it ?
>>
>
> either is fine.
>
> Also attached are the pictures of the wiring from the board.  One wire was
>> loose, I reinserted the wires into the wire connector
>> so if you can please confirm that its right as it is, or let me know how
>> the wires should be attached it would be appreciated.  I
>> have limited electronics experience with arduino and RaspPi etc.
>>
>
> If one of the wire nut connectors was still attached, then connect the
> loose, (and only loose), one again.
>
> If both fell off, this will need using a volt meter before attaching to
> get the DC polarity correct.
>
> You could just reconnect the loose things, then run the old original
> program to see how it does.
>
>
>> I quickly looked over README directions about loading up micropython.
>>
>
> Is that the Readme.md of https://github.com/kanzure/culture_shock?
> (I don't have a Mac, I use debian linux.)
>
> From the git repo:
> Now the code needs loading by following the instructions in
> kanzure/culture_shock/micropython_timer_code_lowlevl/micropython_compile_G30TH.txt
> Next step depends on which code you want to run, so follow README.md in
> kanzure/culture_shock/micropython_timer_code_lowlevl or
> kanzure/culture_shock/micropython_pulser_code as they will be different
> code and different platforms possibly.
>
> Micropython_compile_G30TH.txt is written for debian or ubuntu linux.  You
> won't need to do that until the micropython install
> breaks, or we decide to start using a more recent version.
>
> https://github.com/kanzure/culture_shock/tree/master/micropy
> thon_pulser_code  is the newer code you want to load into your machine.
>
> You will need any kind of Mac terminal program for using a USB to serial
> port to talk to a running micropython installation.
> Mac OS X: use the command: screen /dev/tty.usbmodem* is what Nathan uses.
>
> The other thing you need is a Mac file manager app, (one of which probably
> pops up automatically when the USB device, [culture shock], is plugged in).
>
> I use a mac and saw the readme in which you have some
>
>> direction on how to upload that via a mac and then there are two programs
>> to load.  That is something I plan to do later this
>> morning.  If you have any suggestions or tips before I do that it would
>> be appreciated.
>>
>
> Nathan's program is in files:
> tim3_enable_tim1_tim2_tim5__tim1_shuts_down.py
> boot.py
> stm_low_level.py
> nvic.py
> pybcdc.inf
>
>
> These files all need to be copied to the virtual drive created by the USB
> connection to culture shock.
> The virtual drive comes up as /flash on a linux system, not sure about
> Mac.  It will probably be visually obvious though.
> That virtual drive directory, /flash will already contain boot.py main.py
> and the old program hv_pulser_orig.py
> main.py is default and can be left as is.  Copy in all the rest in the
> list above.
>
>
>
> If we can load up Nathan's tim3_enable_tim1_tim2_tim5__tim1_shuts_down.py
>  program, it still is not optimized for doing a range of strengths of zaps
> for testing purposes.
>
> It will do though, so loading it is a good goal.  The pulse shape it can
> do will be either a (1 - exp) up then (1 - exp) down, or a (1 - exp) up to
> a plateau, then (1 - exp) down..
>
> tim3_enable_tim1_tim2_tim5__tim1_shuts_down.py  has a couiple of
> variables you can change iwth a command,
> and a "fire" command.  I'll reread the source and get back to you on that
> soon.  Breakfast now.
> What time zone are you in Mitchell?  Pacific coast?
>
> --
> John Griessen
> cibolo.com  Austin TX  building lab gear for biologists
> _______________________________________________
> open_electroporator mailing list
> open_electroporator at cibolo.us
> https://cibolo.us/mailman/listinfo/open_electroporator
>



-- 
Mitchell Altschuler
925 212 2296
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