Re: [DIYbio] Open Gelbox/Transilluminator Source Files

[Cory Tobin]

I don't know anything about the Open Gelbox 2.0 but IORodeo has a gel
box which they give away the design files for (
http://www.iorodeo.com/content/mini-gel-electrophoresis-system )
including the spec sheet, Open SCAD files and laser-cutting files.
They also have python scripts in one of their Bitbucket repositories (
https://bitbucket.org/iorodeo/transilluminator_enclosure/src ) which
allow you to input different dimensions and it will generate the SCAD
files automatically. So if you want a larger or smaller box than the
default, you can easily make that happen.

As for the blue and amber filters for an LED illuminator, I had good
luck using gel filters (the colored things you see covering lights at
theater performances or movie sets). I got them from this guy on ebay
http://www.ebay.com/itm/390061292911?ssPageName=STRK:MEWAX:IT&_trksid=p3984.m1423.l2649
They have a huge selection of colors and they are very cheap ($6 for
4sq ft). If you want I can go through my notebook and find which
specific colors worked best.

No need to use an arduino to control the LEDs. If you have a DC power
supply, hook a few LEDs in series with a resistor and add a switch if
you want. Much cheaper.

Also, if you're interested in making a UV illuminator, IORodeo has
design files for that as well
http://www.iorodeo.com/content/transilluminator-enclosure


-cory

[Pieter]

The full instructions can be found on instructables:
- http://www.instructables.com/id/Gel-electrophoresis-system-mini/?ALLSTEPS
- http://www.instructables.com/id/UV-Transilluminator/?ALLSTEPS

Following these steps would probably also lead you to a fine gelbox: http://learn.genetics.utah.edu/content/labs/gel/build_gel_box.pdf

The instructables are pretty nice, but it is sometimes hard to get all the components. Perhaps we should make a kit, as a supplement to the OpenPCR

[Ravi]

Thanks all for advice/links. As I continue to work on this I will evaluate feasibility of kits, but I will definitely document. I know IOrodeo has kits but I think $300 is a little out of budget. Thanks to IOrodeo though for making there schematics completely available. 

Anyone have the Gelbox 2.0 laser cut schematics - I found the sketch up 3d files, but no laser files. 

Ravi

[cameron]

We built the whole system including camera, filters, integrated gelbox etc at BIocurious. Email me off line and I can send you pics, designs for laser cutting etc.  We never managed to put any documentation together, but the whole thing without the $90 camera is $100 or less. It works beautifully. We also designed gel cartridges that use a fraction of the reagents because we use channels instead of a full gel.  Each lane uses 2ml. It also allows you to load dry without loading dye so it's fast and easier.  You can experiment with it yourself to see if you like it. I can send you pics of the gels from the doc station. We use the Logitech c910 camera.

Cameron

[Mac Cowell]

The design is excellent, I would love to see it replicated.

Mac

231.313.9062 // @100ideas // sent from my rotary phone

--
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To view this discussion on the web visit https://groups.google.com/d/msg/diybio/-/OH83b597gEUJ.
To post to this group, send email to diy...@googlegroups.com.
To unsubscribe from this group, send email to diybio+un...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/diybio?hl=en.

[Roger Stager]

There were a few parts that were difficult to acquire.  LED assemblies ($12), amber Acrylic and stainless steel wire.   I ordered extra, so If there is sufficient interest, we could put together a few kits.

[Tristan Eversole]

You know, I always meant to mention that the cassette-gel idea has been around for a while, but never caught on, for some reason. I remember seeing them for sale in a Carolina catalog ages ago. I think maybe the company just charged an arm and a leg for them.

http://www.westburg.eu/en/site/products/genomics-research/dna-gel-electrophoresis/lonza-flashgel-precast-gel-electrophoresis-systems/flashgel-dna

T.

[John Griessen]

On 06/09/2012 04:21 PM, Tristan Eversole wrote:
> the cassette-gel idea has been around for a while, but never caught on

All the cassettes I have seen are complex, partly sealed with many pieces made by injection molding.

An open topped tray or set of channels that all have contacts and get
volts as a group when you load them would be enough, and it could be a simpler shape
than any cassette parts. I'm not sure 3D printing is ready for the low prices you'd want,
but a combination of laser cutting of plastic like polycarbonate or the UV clear acrylic,
plus some CNC milling out of wells and channels is. Contacts might be a batch run of metal
rectangles folded into a C shape that clips around the ends of channels. One leg of the
C would contact cast gel, one leg would contact another metal contact that is
part of the electrophoresis volt source module that hold the channels during a run.

[Nathan McCorkle]

On Jun 5, 2012 11:28 PM, "cameron" <selur...@gmail.com> wrote:
>
> We also designed gel cartridges that use a fraction of the reagents because we use channels instead of a full gel.  Each lane uses 2ml.

> Cameron

2mL is still pretty much on par with gel consumption in non-cassette gels, using 30mL of agarose solution with a 10 or 14 well comb...

[Zebedee Boy]

But not if you only have three lanes to run :-)
 
Zeb
 

---

Date: Sat, 9 Jun 2012 20:39:19 -0400

Subject: Re: [DIYbio] Open Gelbox/Transilluminator Source Files

From: nmz...@gmail.com
To: diy...@googlegroups.com

--
You received this message because you are subscribed to the Google Groups "DIYbio" group.

[John Griessen]

On 06/11/2012 09:40 AM, Zebedee Boy wrote:
> But not if you only have three lanes to run :-)
>
> Zeb

What do you think of the open topped channels idea I described the other day for this?

An open topped tray or set of channels that all have contacts and get

volts as a group. Contacts might be a batch run of metal

[Zebedeeboy]

Traditional gel rigs are pretty inefficient in terms of agarose use, mostly because they are just that 'traditional'. From my experience they haven't really changed much in design since they were first made for the nascent mol bio field. 

So there is lots of scope for redesign, high resolution cameras are everywhere these days so I think miniaturisation is def the way to go as you suggest. Avoiding too much edge effect is going to be the key I think, but I haven't started playing around with this yet so that's only opinion.

Zeb

Sent from Samsung Mobile

-------- Original message --------
Subject: Re: [DIYbio] Open Gelbox/Transilluminator Source Files

[John Griessen]

On 06/12/2012 11:01 AM, Zebedeeboy wrote:
> I think miniaturisation is def the way to go as you suggest. Avoiding too much edge effect is going to be the key

By that do you mean the thinness of the starting point well where you
add your sample? So as to not yield a blurry group of same sized molecules,
but rather a sharp and discernable one?

We've seen some cartridge designs where they have a plastic funnel slot in the top for adding your sample,
but no control on how much. There seems to be a skill factor in your results -- too much
sample and get a blurry set of lines likely. A thin well made by a comb shape in the gel
seems best to me from a 3D fields and movement point of view. Then don't overfill it.

Does electrophoresis gel ever need to be sterile? how long will it keep at what temps? -- the cartridge
folks may be providing sterile, or with antibiotic preservative to keep from growing mold..

[Nathan McCorkle]

The injected/pipetted sample height in the column/gel should ideally approach 0 thickness for optimum separation resolution. So the thinner the better, but then your DNA concentration needs to be sufficiently high to visualize it. Potentially two glass plates 1mm apart with a well a few cm deep could work for improving resolution but I'm not sure that would reduce gel consumption.

(1 mm) * (25 mm) * (150 mm) = 3.75 milliliters

Also we could just use capillaries and and a photodiode detector at the end of he channel, which is the next step towards current day tech.

On Jun 12, 2012 9:29 AM, "John Griessen" <jo...@industromatic.com> wrote:

[Avery louie]

Get some blue less off ebay.  Works very well with gelgreen.  Go to www.bosslab.org if you want to see pictures.

On Aug 2, 2012 6:24 PM, "AMD" <amdu...@gmail.com> wrote:

OP wanted a blue light transilluminator, not a UV transilluminator.

--

You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diy...@googlegroups.com.
To unsubscribe from this group, send email to diybio+un...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msg/diybio/-/EoWUZ_Pr7j4J.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[Nathan McCorkle]

I think Avery meant "blue LEDs off ebay"

--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Avery louie]

yees.  I got something like this: http://www.ebay.com/itm/24cm-Blue-LED-Flexible-Neon-Strip-Light-for-Car-or-Van-/330770420346?pt=Motors_Car_Truck_Parts_Accessories&hash=item4d0374127a&vxp=mtr

--A

[SC]

Dear Cameron,

I'd love to see your design for a gel cartridge for running a few lanes.  Is the design available online anywhere, or would you consider sharing it here?

Also, can anyone offer advice for sources of blue and amber filters?  My little Pearl Biotech transilluminator works great, but I've been unable to find a source of acrylic or lighting filters with just the right wavelength in order to build a larger one.

Wishing you all sharp bands,

Stacy

[Cory Tobin]

> Also, can anyone offer advice for sources of blue and amber filters?

Lee Filters makes blue and amber filters that are very cheap. They
sell sheets which are 4 square feet, so you could make a bunch of gel
boxes with just a single piece. You can usually find them for under
$10 each. If I remember correctly, Lee filters #15 and #21 (
http://leefilters.com/lighting/colour-details.html#015 and
http://leefilters.com/lighting/colour-details.html#021) both worked
well for the amber and #716 worked well for the blue.

Bulbtronics has the entire collection of Lee filters
Blue #716
http://www.bulbtronics.com/Search-The-Warehouse/ProductDetail.aspx?sid=0010305&pid=GLLE716SHEET
Amber #21
http://www.bulbtronics.com/Search-The-Warehouse/ProductDetail.aspx?sid=0010034&pid=GLLE021SHEET
Amber #15
http://www.bulbtronics.com/Search-The-Warehouse/ProductDetail.aspx?sid=0010028&pid=GLLE015SHEET

-cory

[Nathan McCorkle]

Cory,
was this determined from a data sheet or database somewhere (the
wavelength response), or just by experiment?

[Cory Tobin]

> was this determined from a data sheet or database somewhere (the
> wavelength response), or just by experiment?

Oh, right. On the Lee Filters website you can see a list of all the
filters they offer here:
http://www.leefilters.com/lighting/colour-list.html

Scroll through and find ones that look approximately the right color
and click on it. Then click on the little image that looks like a
color spectrum and it will pop up a window that shows the transmission
spectrum in nanometers.

Since they are so cheap I purchased a couple different colors and just
tested them to find which ones work the best.


-cory

[Alan Durbin]

Hi- I'm working on this now, have some stuff on the way, will report back.

-Alan

--
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diy...@googlegroups.com.
To unsubscribe from this group, send email to diybio+un...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msg/diybio/-/1Q3TFt6r_DsJ.