A Cheap Source of Platinum Wire for Gel Electrophoresis Boxes
EJ
meeting. I remembered that in the Diamond District there is a little
store that deals mostly in jewery-making supplies but also in precious
metals with very little middleman charge (his prices reflect the
current index prices and change daily, sometimes twice a day). It's on
my way to work, so I stopped by this morning and asked about thin
platinum wire (I told them either 29 gauge or 1/100th inch). They had
it and the price was great- I bought TWO FEET for $36. That's enough
for at least 4 minigel boxes for DNA analysis. They said there was NO
minimum purchase, so I could have bought even less and paid less too.
They will also mail the wire just about anywhere in the world. When I
told the guy behind the counter what it was for, he said they sell
platinum wire to lots of places like MIT and companies for all sorts
of similar scientific applications.
Myron Toback Inc.
25 W 47th Street
New York NY 10036
212-398-8300
www.MyronToback.com
Bryan Bishop
> The NYC DIYbio group is planning to try to build a gel box at our next
> meeting. I remembered that in the Diamond District there is a little
> store that deals mostly in jewery-making supplies but also in precious
> metals with very little middleman charge (his prices reflect the
> current index prices and change daily, sometimes twice a day). It's on
Are you using the schematics from our gel box project? And if not, how
about you upload some of the CAD files to describe the projet that you
are implementing? That would be really nice. Alternatively, there's
the electrophoresis.py script that was released on the list last
year-- and it even outputs in SVG format, which would be a suitable
format to attach in an email.
EJ
simple to make. Two wells joined by a shallower bridge part where the
gel goes. I'm just going to glue some plexiglas scraps together, run
the electrodes along the bottom of each well, anchored with silicone
caulk at both ends. For the part of the electrode wire that will have
to run down the side of the box to get to the bottom, I'll cover it
with the caulk so the only current will becoming from the wire along
the bottom. For our first attempt, since I have not procured a power
supply yet (looking for used ones now), I'll just use banana clips and
attach them to 9V batteries. And make sure everyone keeps their
fingers well away from the thing when its running! Later I can modify
it with banana plugs and a safety lid. I'm not going to bother with a
gel tray- as I recall you can just sort of seal each side of the
bridge with Scotch tape when you pour the gel, then remove it when
it's gelled. I found a fast food container that has a polyethylene rim
that seem a good thickness to cut a comb out of.
And sorry, but I have no idea how to use CAD or what the heck a .py
script is, LOL. We'll be posting a video of the gel box construction
on our new YouTube channel after Monday's meeting:
http://www.YouTube.com/DIYbioNYC
On Mar 4, 11:00 am, Bryan Bishop <kanz...@gmail.com> wrote:
> > The NYC DIYbio group is planning to try to build a gel box at our next
> > meeting. I remembered that in the Diamond District there is a little
> > store that deals mostly in jewery-making supplies but also in precious
> > metals with very little middleman charge (his prices reflect the
> > current index prices and change daily, sometimes twice a day). It's on
>
> Are you using the schematics from our gel box project? And if not, how
> about you upload some of the CAD files to describe the projet that you
> are implementing? That would be really nice. Alternatively, there's
> the electrophoresis.py script that was released on the list last
> year-- and it even outputs in SVG format, which would be a suitable
> format to attach in an email.
>
>
> - Bryanhttp://heybryan.org/
> 1 512 203 0507
Jason Morrison
On Mar 4, 2009, at 12:17 PM, EJ <ellenjo...@aol.com> wrote:
> And sorry, but I have no idea how to use CAD or what the heck a .py
> script is, LOL.
prickly) command line script like that to run from google appspot, or
something similar, with a web interface?
Meredith L. Patterson
script under mod_python or simply cgi.
--mlp
Bryan Bishop
<clon...@gmail.com> wrote:
> Yeah, should be pretty easy to throw a web front-end on it and run the
> script under mod_python or simply cgi.
I'd suggest django for rapid web prototyping with python. You can even
expose the function signature as an HTML form automagically IIRC if
you just throw the parameters to the script into a class/object of
their own.
- Bryan
Daniel Singh
Daniel C.
> I'd suggest django for rapid web prototyping with python.
Django is the Bees Knees if you're making a web site, but probably
overkill if you're doing nothing more than putting a web front end on
a python script.
Not to discourage anyone from doing it as an exercise, of course. But
if a novice is reading this, they should be aware that digging into
Django to accomplish the task at hand is going to get them more than
they bargained for.
-Dan
Meredith L. Patterson
backend, so if your application doesn't need a database backend, using
Django is sort of silly.
OTOH it has some very nice templating facilities, so if you have one
or more database-backed apps and want to generate an identical look
and feel easily, Django is great. It also does a brilliant job of
sanitizing form input and generally just providing a sane programming
API for web-application tasks.
--mlp
EJ
sincerely trying to be helpful, but I am a molecular biologist and I'm
afraid that the following suggestions are complete Greek to me:
"wire a command line script like that to run from google appspot"
"throw a web front-end on it and run the script under mod_python or
simply cgi"
you just throw the parameters to the script into a class/object of
their own"
programming
API for web-application tasks"
lipofectamineLTX vs FUgene for tx into H1299s to generate permanent
KIs using an ATF3 delta102-139/neo vector?
How about I just draw a picture of what I'm doing in Microsoft Paint
and email it to you :-) ?
On Mar 5, 10:22 am, "Meredith L. Patterson" <clonea...@gmail.com>
wrote:
> backend, so if your application doesn't need a database backend, using
> Django is sort of silly.
>
> OTOH it has some very nice templating facilities, so if you have one
> or more database-backed apps and want to generate an identical look
> and feel easily, Django is great. It also does a brilliant job of
> sanitizing form input and generally just providing a sane programming
> API for web-application tasks.
>
> --mlp
>
>
>
> > On Wed, Mar 4, 2009 at 4:16 PM, Bryan Bishop <kanz...@gmail.com> wrote:
> >> I'd suggest django for rapid web prototyping with python.
>
> > Django is the Bees Knees if you're making a web site, but probably
> > overkill if you're doing nothing more than putting a web front end on
> > a python script.
>
> > Not to discourage anyone from doing it as an exercise, of course. But
> > if a novice is reading this, they should be aware that digging into
> > Django to accomplish the task at hand is going to get them more than
>
> - Show quoted text -
Bryan Bishop
> You guys crack me up- you all must be programmer types. I know you are
> sincerely trying to be helpful, but I am a molecular biologist and I'm
> afraid that the following suggestions are complete Greek to me:
How about you ask for help in interpreting what these mean?
> "wire a command line script like that to run from google appspot"
Google AppSpot hosts applications on their cloud/cluster, so a
developer can register an account and upload some applications, it's
kind of like virtualization.
> "throw a web front-end on it and run the script under mod_python or
> simply cgi"
The mod_python package is an addon for apache, there are many mod_*
packages for the apache web server. CGI is an ancient, though still
useful gateway interface method, and you either tell the apache in the
/etc/apache2/sites-available/000-default or /etc/apache2/httpd.conf
file that a certain directory is to be run as CGI or not (and then you
get to use your #!'s to say what particular interpreter should be
running the script, blah blah blah).
> "expose the function signature as an HTML form automagically IIRC if
> you just throw the parameters to the script into a class/object of
> their own"
Well, that's django-specific. What django does is take a class
definition and export that to a backend database like MySQL or
PostgreSQL- or really whatever other plugins the developers for django
have written- and for each of the variables there is a column in the
table, and then it knows the maximum lengths and so on to specify in
the HTML form elements per the W3C standards blah blah blah.
> "sanitizing form input and generally just providing a sane
> programming
> API for web-application tasks"
Haven't you ever had to deal with crappy data before? :-)
> Would you understand me if I discussed the realtive merits of
> lipofectamineLTX vs FUgene for tx into H1299s to generate permanent
> KIs using an ATF3 delta102-139/neo vector?
Yes.
> How about I just draw a picture of what I'm doing in Microsoft Paint
> and email it to you :-) ?
That would be like me keeping ethidium bromide gels with my food in
the refrigerator.
EJ
much background you have that some of the rest of us do not. I was
trying to say that in a humorous manner, but I guess it did not come
across that way. I have never taken a programming class (they were
using Fortran when I went to college and there were no PCs), and my
experience with computers is pretty much limited to PCs loaded with
Microsoft products. So even your explanations make no sense to me,
though they may seem really dumbed-down to you- and almost like you
are laughing at my ignorance.
Hey, I'd love to know more about computer stuff, but the level that I
need to start with to come up to yours is a lot lower than you are
assuming. For instance, I do not know what cloud/clusters, CGIs,
apache servers, gateway interfaces, plugins, backend datasets, and
interpreters running scripts are. I probably know less than a 12-year-
old when it comes to this stuff- do you really want me pestering you
with questions and tying up this board or do you want to know how I'm
making a gel box?
Rather than having to educate me up to your level maybe it would be
more efficient to find some common ground in programs that are readily
available to the average home user without the need to modify them.
For example, when my computer tried to open that schematic of yours
with a .py extention, it freaked out and did not know what to do. I'm
sure there's a program out there somewhere that will open it, but why
not just a drawing? Why, if a simple blueprint-type drawing is good
enough for a university machine shop to make a gel box, is it
comparable to storing mutagens with food? I'm guessing there must be
some advantage in doing the way you want to, but the since
biolotechnology portion of this DIYbio movement seems so down-to-earth
and uncomplicated, the preference for complicated computer stuff seems
puzzling to me.
On Mar 5, 11:56 am, Bryan Bishop <kanz...@gmail.com> wrote:
> 1 512 203 0507
Daniel C.
> You guys crack me up- you all must be programmer types. I know you are
> sincerely trying to be helpful, but I am a molecular biologist and I'm
> afraid that the following suggestions are complete Greek to me:
*chuckle* Point taken, Ellen. However, since the discussion in
question was over the best way to accomplish a specific programming
task, and was held largely between programmers, I think that the use
of programming gobbledygook was justified. (Yes, gobbledygook is the
right word here. Yes, I am a word geek.)
If you'd like to learn to program, I can point you to several
tutorials aimed at non-programmers. It's not hard.
> For example, when my computer tried to open that schematic of yours
> with a .py extention, it freaked out and did not know what to do. I'm
> sure there's a program out there somewhere that will open it, but why
> not just a drawing?
.py files are programs written in a language called Python. (Named
after Monty Python, not the snake.) The program that was suggested
will create a new blueprint for you based on certain parameters - the
thickness of the plastic you're using, etc.
> biolotechnology portion of this DIYbio movement seems so down-to-earth
> and uncomplicated, the preference for complicated computer stuff seems
> puzzling to me.
The biotech portion of the DIYbio movement seems complicated to me,
and the computer stuff seems simple ;-)
-DTC
Bryan Bishop
> On Thu, Mar 5, 2009 at 9:09 AM, EJ wrote:
>> For example, when my computer tried to open that schematic of yours
>> with a .py extention, it freaked out and did not know what to do. I'm
>> sure there's a program out there somewhere that will open it, but why
>> not just a drawing?
>
> .py files are programs written in a language called Python. (Named
> after Monty Python, not the snake.) The program that was suggested
> will create a new blueprint for you based on certain parameters - the
> thickness of the plastic you're using, etc.
I encourage anyone to do as much drawing as they like. There has been
a long history of blueprints and drawings in mechanical engineering
and for machine shops and craftsmen, even hobbyist craftsmen. There
are even international standards for drawing blueprints too, there's
all sorts of standards from ASCII, ASME, IEEE, tons of specialty
associations, and so on. But these days, computers describe hardware
more accurately and better than engineers can with pen and paper--
blueprints are of course still a cultural tradition, and if that's
what you're comfortable contributing, that's fine, but let the rest of
us package it up into a better form, or let us help you install Python
so that you don't repeat unnecessary work, etc.
EJ
On Mar 5, 3:50 pm, Bryan Bishop <kanz...@gmail.com> wrote:
> But these days, computers describe hardware
> more accurately and better than engineers can with pen and paper--
> blueprints are of course still a cultural tradition, and if that's
> what you're comfortable contributing, that's fine, but let the rest of
> us package it up into a better form, or let us help you install Python
> so that you don't repeat unnecessary work, etc.
>
> 1 512 203 0507
I would be grateful if those of you who are versed in this stuff would
"package it up" for me if I come up with something that folks want to
reproduce. Learning more about programming is on my life to-do list
(along with getting better at blues guitar, learning to drive a
speedboat, and firguring out how to cut my own hair without ending up
looking like the Bride of Frankenstein), but realistically my most
useful contributions to DIYbio will be on the biotech side of this
equation.
That said, I got an email from the people who are making the gel box
you referred to in your first post. They are not just making a box,
they are improving on currently available designs by incorporating the
visualization light into the box. That's a step up from what I am
doing, so I don't know if there's any reason to formalize my design.
My first box will be rather crude- I need to get it ready for Monday-
so I might just cut the plastic imprecisely and stick it all together
with silicone bathroom caulk for my first effort :-) But it will
definitely be functional.
Daniel C.
> I would be grateful if those of you who are versed in this stuff would
> "package it up" for me if I come up with something that folks want to
> reproduce.
That's actually what the discussion was about earlier =)