[Open_electroporator] What does it look like when you use an electroporator with finesse and programability?

Nathan McCorkle nmz787 at gmail.com
Tue Mar 11 18:59:33 UTC 2014


See below.

On Tue, Mar 11, 2014 at 7:31 AM, John Griessen <john at industromatic.com> wrote:
> On 03/10/2014 10:41 PM, Nathan McCorkle wrote:
>>
>> my interest is in using them with great
>> finesse and programability. We both want to get it done, right?
>
>
> Only if we agree what "it" means in context.  If what we want is too far out
> of alignment, I start on
> other projects instead, and this gets back burner on the 2nd stove status.

I want more than nothing, but comparable to what exists on the market
(tweakable time constant seems to be the 'first' feature across them
all, then it moves to AC). If this could be augmented easily (it seems
like it could be) to run at constant current or power then I think it
would double for a gel electrophoresis power supply for capillary
gels, and maybe small student sized gels (5 or 6 cm square) (but the
voltage for these is centivolts, not kilo). For the gel supplies, HV
the next step up is AC and adding channels so you can have electrodes
in many positions to change the vector direction of the electric field
relative to the gel and sample.

I'm trying to be easy, because I'm quite sure any work done on this
will be very helpful to other community members who are unaware of
this list or who simply don't have the time/devotion to getting such a
complex electrical magic box to work.

>
> On 03/10/2014 10:44 PM, Nathan McCorkle wrote:> I guess what can I do to
> help motivate you in any way? I could plan a
>> trip to TX...
>
> Oh, let's not be dramatic.

I wasn't trying to be! Its a bit far-fetched, but I actually have 2 or
3 other items on a TX trip plan. Adding more people/stops/plans only
increases the likelihood for me to get down there! I'm serious in case
you are better fleshing out projects in-person with a white board and
a pot of coffee.

>
> What is it you want?  What does it look like when you use an electroporator
> with finesse and programability?
>

I guess I just mean its either stable enough without A/D or comparator
feedback to be repeatable for experiments, and that the pulse duration
and voltage were computer-controlled or at least quantized and
displayed on two 7-segment displays with a non-crappy potentiometer to
adjust and record successful settings (I'd keep track of the bad ones
too).

> USB port? Ethernet port?  Lab DC supply?  Self contained power supply?  To
> deliver enough power for
> the longer pulse methods used on lower impedance gels?

I bought some Arduino Mega 2560s for $13 last year, I wouldn't mind
burning a few of them up, but maybe a DIP processor during testing (if
you think initial testing is likely to fry a bunch of them) would be
cheaper and more replaceable.


Remember that electroporation usually doesnt happen in a gel, that's
electrophoresis. If you did electroporate in a gel, well I can quickly
imagine the gel matrix tearing the cells apart, but a quick google
shows that gel immobilization prior to electroporation does work.


> Lower impedance automatically has higher power and thus higher parts cost,
> danger, and complexity.

I don't think you should be concerned with that, all the
electroporation instruction manuals I've seen mention ensuring the
salt content is low enough that it doesn't 'spark', I don't know if
they're saying the solution would spark, or if small air gaps between
the electrodes (due to not being totally flat) would spark simply
indicating the conductivity was too high.

>
> I can help you with parts of the process that make sense and you can hack
> the rest to suit yourself for
> speed.  I can probably advise you how to stay safe even using hacked
> together one of a kind equipment,
> but that's obviously not something that would benefit many others, or
> generate any income to cover my expenses.

Thanks, I guess that's a point of divergence for us... I want one of
these things to help me in experiments that could make money, you want
one to directly make money. I only need 1 decent non-lethal reasonably
reproducible device to get me through to prove my ideas, after that my
business plan would be to either sell devices, but I'm increasingly
thinking I'll just sell a service using the device (which includes but
isn't limited to an electroporator).

> One thing I am leery of in dealing with you is your dropping some things in
> the past we were talking about,
> and your admitted taking on more debt and probable need for a job to avoid
> bankruptcy soon.  That makes
> you a  little desperate, short cut motivated, and so not easy to deal with.

What projects did I drop out on, wasn't this the same one we've been
talking about for a few years?

Also, I think you're misconstruing my situation, I guess from the DNA
synthesizer thread where I mentioned that has been my goal for many
years now. I'm not in bankruptcy or anyway close to that. I've got
some jobs and a few backup plans. I'm not looking for any shortcut
because I'm trying to be cheap, I look for shortcuts when I feel they
are the best route. This electroporator project is no shortcut, its
something that I knew I wouldn't need for a few years and so started
trying to work on developing one. eBay or Amazon.com or biotech
equipment dealer would be much faster at getting me to a solution. I'd
like to avoid that route, just as a matter of principle because I
think getting the information laid out online truly would be helpful
for the greater community. At this point I am starting to get
concerned with this open electroporator project not really going
anywhere, because I'm approaching the time where I will need to
actually use one.

My reason for wanting the design (and wanting to understand it) is
also because my requirements for power may decrease significantly
enough to warrant a redesign for a smaller lower-voltage unit, which
don't really exist on the market. My thinking this whole time has been
with microfluidics in mind, likely the design would be significantly
different due to requiring ones or tens of volts, not 1000s. Not as
much market for someone like you in that market, unless I can get a
microfluidic production kit to sell along with it (which I plan on
figuring out this summer).

> On the other hand, thanks for considering me as a collaborator.  There are
> very few people willing to collaborate
> on open hardware.

I owe the same thanks to you, that electronics expertise makes you
quite desirable to have on the team! I like you I emailed the X-ray
HEI guy, maybe he'll stop by and add some ideas.


> That said, I am still busy with the apartment construction project, but we
> just asked for plumbing final and
> building final and they may pass soon and I could wrap up in 2 more weeks of
> interior furnishings work.

Yes and I've got tons of other things going on with various projects,
software and microfluidics and a spectrometer project. Starting a new
job next week, but also finishing a chemistry class... so gaining and
losing time with that deal, but also gaining some extra income, which
means experiments are funded a little better too!
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