Saturday, July 27, 2013

Dr. Zayner and Other Stuff

So I defended my thesis which I am glad is finally over! It was really nice to be able to share my Science everyone. I have so many friends and we rarely talk about what we actually do because we usually spend 8-12 hours a day doing Science and talking with co-workers about it. It was really nice to be able to show my love for Science to people.

It is also fun to be a Ph.D. I have only been one for a few days but whenever I start to feel down I always just remind myself that I have a Ph.D. and it can't ever be taken away. I know lame right? But I still have a kick out of it.

I am still waiting to hear back from my NASA fellowship and have a Skype interview with Ed Boyden next week but otherwise not much going on.  I am really interested to see stuff Ed has to say, hear what he is interested in.

I am working on two cool projects at the moment. One is developing the Chromochord into a new sound sensitive instrument. We have talked to some people at the business school and plan on doing a Kickstarter or some such thing to raise some money for it. I will post on here when that goes down.

I just need to find a job now.

I also did an interview with Nona Griffin that will be published online hopefully soon. I will post when it is up. She was really great. If you have a great Science project that you are working on I encourage you to look her up online and email her.

Thursday, July 4, 2013

Solidoodle 3 Beginner's Tutorial

Here I will provide a Solidoodle Getting started Guide this is done with Linux but most of the stuff should transfer over to Windows:

Things you should do after opening your Solidoodle 3

  1. Install Software & Test Printing
  2. Calibrate Filament Feed
  3. Calibrate Temperature on Extruder
  4. Level Bed
  5. Tape the Bed

1. Installing Software & Test Printing
The software I use on Linux is Slic3r in repetierhost and pronterface.

RepetierHost is what I use for visualization/centering/slicing it seems to do much better than the pronterface/skeinforge package. It can be found at

Pronterface is from the PrintRun software package at . It is built off of python so make sure you have python installed (sudo apt-get install python).

Goto Thingiverse and pick something really simple to print

Download the stl file and load it up in repetierHost
If it doesn't look like below the object in 3D there is something wrong with the file so you should try another. Or you can run the file through the netfabb service that automatically repairs stl files (

So the Slic3r config files provided by Solidoodle are for version 2, hah! So we need to update those for use. Basically we just need to change the bed size to 205, 200 and the print center to 102.5, 100.
You can download mine here:

Open up the Slicer tab in repetierHost and click on the first configure button.
Then in Slic3r click on "File" then "Load Config"
Remember that anytime you change anything in the Slic3r config, like adding an extrusion multiplier or something. You need to save those changes in the config before you close the Slic3r window or they won't take effect in your print.

Now we are ready to slice so click on "Slice with Slic3r"

This should eventually output a g-code file and bring you to the "g-code editor" tab click on the save icon and save this g-code file for use with pronterface.

Open up pronterface and connect to your printer and click on the "Monitor printer" box.
Turn on your bed and heater(extruder heater) and let them warm up.
Load your g-code file from Slic3r.

Before you click on print make sure the filament is in and extruding properly. Keep clicking on extrude till something comes out.

Click "Print" and sit back for a few hours.

2. Calibrate Filament feed
This is fun and easy what you need to do is plug-in your printers USB cable to your computer and open up pronterface and connect to the printer. Heat-up your extruder to 190C or so. Remove all filament from the extruder by backing it out and blow out any filament dust. Sometimes this causes extruding problems. Reinsert filament until it starts coming out of the extruder.

Now take a ruler and measure 100 mm (use 100 mm because small errors will add up and be visible) of filament say from the top of the extruder and mark this point with a sharpie or marker. Type in 100 mm in the extrude box and click extrude. Now measure how much is left if the mark is not almost exactly near the top of the extruder.

We need to calculate the extruder multiplier. The extruder is set to extrude at an arbitrary extrudeness of 1 extrude multiplier. If however 1 extrude multiplier is greater than what is actually needed we need to increase of decrease this value. If your Solidoodle extrudes less than what you want i.e. You want 100 mm and it extrudes 90 we need to change the extrude multiplier. We calculate it like so:

(Amount we want it to extrude) / (Amount actually extruded)

So in the above case: 100 mm / 90 mm = 1.11

This extrude multiplier we enter into our Slic3r config in repetierHost under the "Filament Settings" tab.

3. Calibrate Temperature on Extruder
Open up pronterface. In the bottom right corner there should be a command entry text box and a "Send" button.

Enter and press Send:
M303 S200 C5

This  should run an automated temperature calibration process that when finished should output 3 values: Kp, Ki and Kd.

Write these down.
Send the command(where X equals the value of Kp, Y equals Ki and Z equals Kd) :

We need to permanently save these values by sending the command:

4. Level the bed
Purchase a small level if you don't have one and place it on the bed in the middle. There are three screws on the Solidoodle bed that can be rotated to change the pitch and height of the bed. They are very sensitive. Make sure you rotate the level 90 degrees and place it in multiple places on the bed to have the best levelling.

After you level your nozzle might be raised or lowered a bit. There is a screw in the on the back wall of the Solidoodle pointing down that looks like it is not doing anything. It is in fact a stop for the bed. The bed height is what controls the height not the nozzle.

If after leveling your bed you feel you changed the height significantly adjust the screw at the back. There are lots of techniques people suggest to try and find the proper 0.1mm height. Some say place a piece of paper underneath the nozzle on the bed and move the nozzle if it drags the paper it is too low. I suggest just printing the bottom layer of something. And optimizing it so you have the smallest layer that is not see through. 3D printing is much trial and error. If you print to thick of layers the nozzle will catch on the object and knock it out of place or deform it. Practice printing by printing something easy and once everything is tuned nice go onto something bigger.

5. Tape the Bed
Nothing sticks to the kapton bed and this can be quite annoying for a beginner as it was for me. Solidoodle say everything sticks but they are wrong. One reason stuff does not stick and warps is because of temperature. The bed does not reach the temperatures that Solidoodle says it does because it is exposed. I wrapped my Solidoodle in aluminum foil.

This allows the bed temperature to become 5 or 10 degrees warmer but it still only helps a little. What you need to do is cover the bed in painter's tape or masking tape such as

It becomes alot harder to remove things from the bed(the tape can actually help though by using it to help remove the printed product) but everything actually sticks!

Wednesday, July 3, 2013

A Cheap Simple DIY Electrophoresis Power Supply

As most people trying to run Gel Electrophoresis in their apartment know generating greater than 100V of DC so you can run your gel in a reasonable amount of time can be expensive. Most of these power supplies can run in the >$100 even for ones that are 30 years old. I started messing around with some stuff and came up with a way to build a "power supply" that can output > 100V DC for less than $5.

All our outlets in North America output ~120V AC. Using this for most applications is not plausible because AC is not continuous current. What we usually want for most electronics and gel electrophoresis is DC. People have tried AC with gel electrophoresis and it just screws up the mobility because of the wave constantly changing sign. The beauty of the system here is that is uses AC just rectified. So you still can output >100V.

Full-Wave rectification converts an AC into a oscillating DC. This removes the negative portion of the AC and makes a perfect electrophoresis power supply because we don't care if our DC current oscillates.

What I used :
Small prototyping breadboard
which can be purchased off of eBay for at like 10 for $2
A 200V bridge rectifier. $0.29
Remember 120V is RMS voltage for AC so it can reach up much higher. Go with at least 200V. I choose 1A to keep gel heating down. If you are in Europe you need a much higher rectifier.
A power cord
If you don't have one laying around here is one for $2.25
Banana jack if you need/want them.
Use shrouded banana jacks so you don't shock yourself or burn down your house.

DISCLAIMER: you are going to be working with AC mains voltage. If you don't know how to work with this safely please don't do this.
This is simple. Connect with solder the positive and negative wires/banana jacks to the pins marked + and - on the bridge rectifier diode. Then connect the white and black wires of the power cord to one each of the other pins on the diode(it doesn't matter which ones you connect them to) they should be labeled with a ~. I soldered the green wire off by itself as a "ground"!

Make sure all the components are covered before you plug it in to prevent spectacular shorts and electrocution. I used duct tape for the tests because I am cheap and simple. A good idea for an enclosure would be an old pipette tip box with holes cut in the sides. 

Putting a 250V 250mA or so fuse in the circuit is a good idea to protect yourself.

I also have another connector in between the bridge rectifier and the banana jacks for my home built electrophoresis setup. So ignore the black and green connectors.

That's it.
Plug in your positive(red) plug to the red banana jack and the negative(black) plug to the negative banana jack of your gel box and plug your power supply into the outlet. Plugging and unplugging the jacks is best done while disconnected from AC mains to prevent any accidentally shocks.

The short circuit reading from my multimeter is 108V. Obviously in Europe with 240V AC your voltage is going to be >200V. You can step this down using a voltage divider in the output of your circuit.

Here is the test. I ran a 1% agarose gel in TAE. What I ran is DNA ladder(lane 1) a plasmid(lane 3) and some ~75bp primers(lane 5 hard to see) at 100V for 20 minutes using a Fischer brand power supply from our lab.

~100V for 20 minutes using Fischer Power Supply

I did the same test with my rectified supply.

As you can see the images are almost identical.

And here it after 37 minutes:

Any questions feel free to ask.