Science

GUIs in python are pretty easy too. Here's some old code I wrote to plot spectrometer data in python:
https://github.com/nmz787/open-spectrometer/blob/master/desktop-software/openSpectrometer.py

I've been working with wxpython lately for GUIs, and would have to look at the pygtk forums and bug tracker to see if it would be worth switching to wxpython or not in any future updates/forks of this. I kind of forgot about it when I was looking at GUI toolkits a few months ago.

Excel read/write in python is easy.

On Thu, Jul 31, 2014 at 5:10 PM, John Griessen <john@industromatic.com> wrote:
> What format of data do your colleagues want? Or, (even worse), is there a
> specific
> vendor and app they use?

The Nanodrop software can export your data as an Excel spreadsheet. I
know plenty of people who would whine for days if this was no longer
an option. Not because Excel is particularly useful but because
that's the way they've done it for years. Some biologists are
obstinate.

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On 07/31/2014 05:52 PM, Cory Tobin wrote:
> It doesn't report data to a computer so you have to resort to
> recording your data into your notebook with a pen. I don't mind but I
> know this would be a deal breaker for some of my colleagues.

What format of data do your colleagues want? Or, (even worse), is there a specific
vendor and app they use?

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wouldn't you use protein SDS gel electrophoresis to separate the
protein? or is that too analytical and you want preparative (i.e. you
need a lot of your pure protein)?

I guess how much protein do you need? I seem to recall Josiah posting
on biocurious that he was cleaning up a F/H-PLC to try and get
working... so I presumed he has some experience with them. I've some
HPLC and GC once in a class, and according to wikipedia ion exchange
chromatography is also considered FPLC sometimes if used for protein,
so when I used the Carolina kit for GFP I guess I was doing FPLC :)

These terms are all a bit overlapping, kinda like the act of walking,
whether you have sandals or boots on. A lot of similarity, but
differences around the edges.

normal phase vs reverse phase (is the buffer (mobile phase) polar or
the resin (solid phase) polar?). You can also have different phases
than solid and liquid. You could say that your lungs filter oxygen and
repel CO2, that would probably be something like gas to liquid to
solid... but that might be stretching it for an /easy/ example :)


On Thu, Jul 31, 2014 at 6:09 AM, Mega [Andreas Stuermer]
<masterstorm123@gmail.com> wrote:
> Hi!
> Again to my question, there seem to be little guys dealing with FPLC here.
>
> https://groups.google.com/forum/#!topic/diybio/24PZTzije98
>
> Is there a way to do this cheaply at my university, without buying an FPLC
> machine?
>
> Thanks god those berberine derivatives are all fluorescent. So detecting
> will not be a problem.
>
> What we want to do is: preparing a cell protein extract. Separate those
> proteins. Add the fractions to berberine, let it incubate, and do
> photometry see which turns it into the derivative we want.
>
> Best,
> Andreas
>
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--
-Nathan

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I recently bought an old Eppendorf Biophotometer. I have access to a
Nanodrop at my university's campus and the Biophotometer reports DNA
concentrations within one 1 or 2 ng/uL of what the Nanodrop reports.
There are a few downsides to the Biophotometer, though.

1) It only reads at fixed wavelengths (230,260,280 and a few others)
so you can't get a full spectrum measurement like on the Nanodrop.

2) By itself it does not handle microliter volumes. It takes a
cuvette like usual. But it can also handle the Hellma TrayCell or the
Eppendorf uCuvette G1.0. Those are sold separately but allow for
using 1-2uL samples. These devices fit into the cuvette receptacle
and focus the light through a small point where the sample sits. I
have a Hellma TrayCell and it works just fine. It's a little more of
a pain to clean out the old sample compared to the Nanodrop but I
don't mind.

3) It doesn't report data to a computer so you have to resort to
recording your data into your notebook with a pen. I don't mind but I
know this would be a deal breaker for some of my colleagues.

4) The TrayCells are hard to find (occasionally one will show up on
ebay) and the uCuvette G1.0 costs around ~2,000 USD.

The positives are

1) Way cheaper than a Nanodrop.

2) Works just as well as a Nanodrop.

3) Can also do OD measurements so you don't need a separate device.

-cory

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On Jul 30, 2014 10:45 PM, "Jonathan Cline" <jncline@gmail.com> wrote:

> I guess a piezo starter might work but I would think it would be rather imprecise.  Nature is imprecise too.  But you want to ensure a good result and/or a good yield.

Months ago I got no/little response when I posted a paper theorizing lightning strikes as potential for horizontal gene transfer (i.e. electroporation)

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On 07/31/2014 12:13 PM, Cathal (Phone) wrote:
> I like the graphite/paper concept!
+1

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On 07/31/2014 11:26 AM, Simon Quellen Field wrote:
> the idea I like best is to draw two lines on paper with a pencil and let a drop of critters soak into the paper. You can make the
> lines quite close together, and graphite isn't toxic. Then cut the paper and drop it into some nutrient broth.
>
> No cleaning electrodes.
> You can control the volume quite easily.
> Nothing dangerous.

Hmm... that idea even upgrades from DIY to a low cost product! How about ink jet printed conductors
with some large lands that spring contacts connect to on your electroporator-with-safety-features?
The paper could come from the clean and pure sources used for old school analytic filter paper.

It could come in sealed sterile packs. Hey Nathan -- want to do some testing of that starting with
hand drawn graphite papers? The extra volume of critters outside the lines may not matter.
For apps where a tiny volume is all you have the paper could be trimmed away just outside the conductive lines
and dip it in a microdrop of bugs to load your bugs into the "zap chamber"

Fantastic lateral thinking Simon!

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I expect you'd get greater efficiency with steel as copper ions are pretty cytotoxic. I like the graphite/paper concept!

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The nanodrop /is/ just a plain old spectrometer, with two fiber optic cables leading to and from the microdrop stage. Search Google for TakeItApart nanodrop to see pics of the inside.