$25 is a bit too much. How about $10? :-)
What for? We're suggesting versions that would cost less than 1%-
hell, somebody throw together a grant application, get on it. :-)
> A gel box costs $250-$500
How is it worth $250 ? Really? Is that including the power supply?
> An illuminator for seeing DNA in a gel box costs
> $1135: http://tinyurl.com/dzfhwd
So, what about a raster scanning UV LED and diode setup?
No power supply. I recently got a new one from BioRad. Medium sized.
300 bucks. It is pretty excessive for a few pieces of acrylic and
some platinum wire. But as long as academic and commercial labs are
willing to pay the price rather than build their own boxes, BioRad is
going to charge as much as they can.
It really comes down to a matter of time. Most university biology
labs would rather spend the money and save the time rather than spend
the time and save the money.
For SYBR dyes I usually stain the gel afterwards rather than mixing
the dye into the gel. If the solution it was sent in says "1000x"
then first you need to dilute it down to 1x. So if you think 10mL is
enough to submerge your gel, then mix 10uL of the dye into 10mL of
water. Then put the gel in some sort of container and pour the 1x dye
on the gel (completely submerging it). Let it sit in the dark for ~15
minutes. Take the gel out and transilluminate.
SYBR Gold and SYBR Green seem to make the bands run slower. I've
never used SYBR Safe though. I just assumed it was the same.
So if that's true, if anyone likes doing cell phone application
development (meh, I stay away from it, just because I have better
things to do), it would be neat to be able to take a photo and then
analyze the migration distance with respect to some marker in the
photo, which is a simple image processing or analysis trick. At the
very least, this could be something submitted to the bioperl project,
or bioruby project or something, using programs like imagemagick.
"ImageMagick(R) is a software suite to create, edit, and compose
bitmap images. It can read, convert and write images in a variety of
formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF,
PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate,
flip, mirror, rotate, scale, shear and transform images, adjust image
colors, apply various special effects, or draw text, lines, polygons,
ellipses and Bézier curves."
Oops. Turns out somebody beat us to it.
"Flicker is an open-source stand-alone computer program for visually
comparing 2D gel images. Two-dimensional polyacrylamide gel
electrophoresis (2D-PAGE) gels are often difficult to compare because
of rubber-sheet distortions. Flicker allows you to visually compare
your gel images against each other or against those found in Internet
databases. Many published Internet gels have a subset of spots
identified which may make them useful to compare with your gels. Some
of these Internet gels are active maps that you can click on a spot to
inquire of its identity. You may be able to draw putative conclusions
as to the identification of some spots in your gels that visually
appear to be the same spots as in reference gels. The Flicker program
integrates these various needs to help you try to make putative spot
identifications. See the Quick start examples below for a short list
of some of these methods."
Now just throw that on to a cell phone app, and suddenly thousands of
biology students all over the worl-- ah, pipe dreams.
Nokia S60-series phone (comes with a Python interpreter) + biopython +
Python Imaging Library = win.
Sigh. I've been meaning to get one of those phones for a while now, I
suppose this is just one more reason.
Surely there's a paper on this out there?
> The above image processing algorithms are very simple and would amount
> to under 500 lines of well-spaced C code. Note: No JPEG libraries
> required since it should use the raw bitmap. In comparison, python
> interpreter+related libraries+kitchen sink GNU library+imagemagik
> addon library+etc,etc are >100k lines of code. Not to mention
> slow. As an iPhone app, it would be very simple using all standard
> libraries. Is a 2 Megapixel camera sufficient to differentiate/
> discriminate the lines?
Can somebody check please? The next gel you do, snap a few photos, or
take a few photos out from your archive.
> Originally I was thinking about using a phototransistor approach for
> building a read-head which could be manually scanned or motor-scanned
> across the gel. It's pretty much the same concept as the line-
> following robots I used to build, except in reverse. The line-
> detection side is very easy - even adding a bluetooth transmitter to
> it for wireless operation, it's still easy (serial output to bluetooth
> dongle). There is no need to take a digital image of the gel from the
> data processing standpoint, except for the warm fuzzies or glam cover
> publishing in Nature.
I'd be concerned about manual scanning- there's no way you're going to
be able to do that at a reasonable constant rate with your hands. And
the motor-scanning mechanism is also kind of complex to set up in this
case. The cell phone idea, I think, is a cheap solution. But ideally
one that doesn't require a cell phone is even better. The cheap
image-bed scanners from garage sales, perhaps. Any way you can get the
data into a camera, or scanner, I think, will be sufficient.