[Open_electroporator] promoting culture shock progress

[Nathan McCorkle]

On Tue, Jul 11, 2017 at 6:49 PM, Mitchell Altschuler
<mitchellalt at gmail.com> wrote:
> Nathan,
>
> Thanks for your input !  I just want to confirm the following.  As an FYI I'm using a mac and can see the board when the USB is plugged in as
>  Pybflash....
>
> So I can copy over the files however you mentioned in this last email that without the modifications to the end of the file  I might need to keep the computer connected for the EP to work

Right, if you don't modify it, you'll then need to connect to the
board (which in addition to micropython showing up as a storage
device, it also shows up simultaneously as a COM port, serial port,
tty, etc...). So you need a terminal program to connect to it, and you
often need to specify the baud rate. I found these MAC instructions,
they seem to lack baud rate options, so maybe the default is correct
(or MAC is somehow smart enough to understand the correct baud):
http://docs.micropython.org/en/v1.8.4/pyboard/pyboard/tutorial/repl.html#mac-os-x

> or was that  i need to do those code modifications to be able vary the EP attributes (variables) when testing ?

the pulse() and a(...) functions are available in the file I
mentioned, or from the interactive terminal. From the terminal, to
start, you can just try calling pulse() and it should fire. If you
have an oscilloscope, you can check the GPIO pins on the
microcontroller sub-board to see them toggling at low voltage. I have
a 40kV arc rated 1 GigaOhm resistor that I used to connect the HV side
of the cuvette holder to my oscilloscope. I believe John has a
professional HV probe to do essentially the same thing.

>
> In any event I'm going to start without modifying the file, then if I can't see anything working make those modifications.
>
> I assume I can use textrangler to update the code then reload that to the board

Sounds good! Just use whatever text editor to open the "USB drive" and
edit the files in-place. Save, then hit CTRL-D (or MAC-D I guess for
you???)  to 'refresh' the filesystem and soft reboot the
microcontroller.

>
> To get the signal traces I have seen I assume that was done with an oscilloscope?  I think I heard something about using a resistors when testing ?

Yeah, see above.

>
> It also seems that the old EP process was changed from what was done in the past I assume because of the cost and safety issues ... some of those capacitors seemed extremely dangerous if the charge was not discharged ....

It was hard and expensive to find the required capacitors... they were
also very large in general, and not being adjustable means they would
be overkill if a given user needed much less voltage than normal, say
for microfluidic experiments. At least not without changing the
capacitors, or getting a capacitor extension box (which they
commercially do sell). Programmability opens up all sorts of
experimental possibility, even outside electroporation.

>
> Since I am new to this project it would be useful to know why we think these new parameters will still work?  Is that documented anywhere?

There are some links in the archives of this mailing list, here's
something recent:
https://cibolo.us/pipermail/open_electroporator/2017-April/000500.html

Best,
-Nathan