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F.Lab's DIYbio Centrifuge

by F_Lab_TH, published

F.Lab's DIYbio Centrifuge by F_Lab_TH Dec 7, 2015

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Summary

This is our DIYbio 3D printed centrifuge.

We have instructions below, but you can also check out our Instructables via ProgressTH here: http://www.instructables.com/id/3D-Printed-DIYbio-Mini-Centrifuge/

We are currently using it for DNA extraction. If built and operated carefully it is a safe and fun piece of lab equipment. Just by building it you can learn a lot about how it works and perhaps get inspiration to design your own lab equipment in the future (and hopefully share it with others!)

It uses a 1806/2400 brushless DC motor taken from a drone and its accompanying ESC (electronic speed control), an Arduino Nano, and some other parts common at makerspaces. It is a great project to build at a makerspace. See the custom section below for instructions, parts, and more details.

We've also included a SketchUp 8 file so you can easily edit it to meet your requirements (like making the case taller to hold a larger Arduino board).

See it in operation here: https://www.youtube.com/watch?v=LXfSYA7idDM

Print Settings

Printer Brand:

MakerBot

Printer:

MakerBot Replicator 2

Rafts:

No

Supports:

No

Resolution:

Low

Infill:

10%


Notes:

10% infill seems to have worked well. Please make sure the print comes out well, at least for the rotor, because it will be spinning at high speeds and needs to be strong.

How I Designed This

SktechUp Design Tips

We use SketchUp almost exclusively. It is easy to teach, intuitive, and very flexible. With experience there is almost nothing you can't do.

For this project, we used a caliper to carefully measure the parts. We gave each part 0.3mm tolerance to fit together. That means if you are using an 80x80 mm computer fan, you must create a space that has an extra 0.3mm on each side, or an 80.6x80.6 mm space.

When designing anything, especially a case for electronics, it helps to build a case-less prototype to see how everything is assembled.

Our centrifuge project had two versions. The first failed to account for how we would actually mount the motor. When it was printed out and in the process of assembling we realized it was impossible to do! The second version fixed this problem.

It is not enough to make a case that fits your components well, you must also consider what order and how it will be assembled! Keep in mind wire lengths and tolerances needed to account for pins, connectors, and other parts. Measure carefully and double check everything.

And remember -- it takes experience and lots of failures before you become good at this -- so don't be afraid to try, and especially don't be afraid to fail. We have a mountain of failed projects we use for spare parts and prototyping!

Custom Section

Project: Build your own DIYbio Centrifuge for DNA Extraction

Objectives: Learn how basic lab equipment works by building it yourself, then use it to explore the process of DNA extraction, perfect for DNA barcoding. The centrifuge serves as a perfect example of how 3D printing enables regular people to create otherwise very expensive and inaccessible scientific equipment.

Audiences: High School or above. Perfect for makerspaces with an abundance of spare parts from drone and Arduino projects.

Preparation: People should be familiar with how to use an Arduino and basic electronics.

Steps: Print out the components using 10% infill, no supports required. Make sure that the print comes out properly. The spinning rotor may fail if layers are not properly fused.

  1. Assemble the necessary electronics (see picture) which include -- Arduino Nano or microcontroller of similar size, a brushless DC motor (used with drones) and accompanying ESC (electronic speed controller), a DC adapter, a 12V wall adapter, hobby potentiometer. and hobby electronics toggle switch (optional).

NOTE: You can use any Arduino for this project to test it, but only a Nano or smaller will fit in the case.

  1. Assemble the electronics. The ESC has a positive and negative (red and black) wire which must go to your power adapter's '+' and '-' terminals. It also should have 3 wires to connect with your 1806/2400 brushless DC motor. Mount the motor using 4 screws (usually come with the DC motor) before hooking up the ESC wires which must run through the case of the centrifuge. There is also a positive, negative, and signal cable leading out of the ESC. These go to your Arduino's 5v, GND, and pin 9 (see wiring diagram above).

  2. Upload code to your Arduino (See here: http://83.56.32.125/sierrademesaI.html).

  3. Fasten your project together using screws through the bottom, a nut to secure the rotor onto the DC motor, and another nut and bolt to secure the cover on the back. The knob that affixes to the potentiometer has a few ways to secure it. Gluing it is not recommended in case you need to open the centrifuge in the future. Instead, use a piece of cardboard, cut and folded aluminum (be careful of sharp edges).

We also friction welded the feet onto the bottom before applying a ring of hot glue to the bottom of the feet. You can superglue the feet as well if you think that is easier. The hot glue, when cooled, acts like "rubber feet" to keep the centrifuge stable when in operation.

  1. Operation -- ALWAYS make sure the lid is fully closed and secured with a 3-4mm bolt before turning on your centrifuge. When first testing it, go as slowly as possible in case you assembled it incorrectly and something is not balanced or one part is making contact with another. Our centrifuge is well-balanced, vibrates very little, and no part makes contact with another. If yours is not like this, please double check your connections, bolts, alignment etc.

The ESC, because it is supposed to be used with RC aircraft, goes through a quick, automatic calibration when first switched on. After this, you can go ahead and use it, but wait for the beeps indicating the calibration process stop before turning the potentiometer.

Results: Your working centrifuge is now ready for use. Following this basic protocol () using items you can find at your local store, you can extract and see DNA from virtually any living organism including yourself!

Follow this protocol available on F.Lab's blog: http://f-labth.blogspot.com/2015/12/basic-dna-extraction-protocol.html

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PLEASE FIX THE V2 BODY STL FILE. ORPHANED TRIANGLES AND LOTS OF BROKEN SIDES. Printer loses it's mind when trying to print! Thanks!

First, saw the article in MAKE magazine and thought this was fantastic. Great job.
This may be a problem with Slic3r but maybe you can help. When I generate the GCODE it seems to be missing the front hinge of the V2_body.stl . The .stl file I downloaded views fine in Slic3R and does show the front hinge. Any idea why this might happen. The part printed perfectly otherwise.

I was wondering how safe it is using a 1A 12v adaptor is to power the system. Most brushless motors need at least 6A to operate reliably, otherwise the motor is at risk of burning out.

Great design! I have two things that I would like to ask:

1: How about a safety interlock that only allows it to operate when the lid is closed? That rotor seems to be going a good RPM and could hurt someone I imagine if they got too close. This could just be a NO switch on the power supply for simplicity.

2: How about substituting a simple tiny45 with a basic program reading a pot then using PWM to control a MOSFET into a lower cost motor perhaps? This could lower overall cost, is there a minimum RPM that must be reached for this to operate properly?

Great points. Very soon we'll be working on V.2 and it will have a safety switch (we didn't know how much interest this would have when we first designed it and it was just for us to use/abuse/and take risks with). It does hurt really bad if you hit your finger with it when it is spinning.

Simplifying the electronics is also on the to-do list. Interesting that you mention ATtiny. We got our hands on some decent developer boards that cost under a dollar and are much smaller. One from TAMI (https://telavivmakers.org/index.php/ATtami) even has a diode for added protection which other ATtiny boards lack.

The RPM question is also a very good one. We'd like to figure out several things. The RPMs, the RPM bursting point of the rotor, and a way to get it set optimally for the DNA extraction procedure it was designed to do (and does well when we set it to maximum) as well as a quick-spin option when mixing the contents of test tubes and especially smaller PCR tubes (which will require a second sort of rotor).

Stay in touch and if you decide to build this or improve upon it, please let us know. We'd love to see it.

Hello again!

I never even thought about the bursting point of the rotor, that would not be a good thing to see at all! I wonder if you could coat the rotor with one of those special poly coatings they make for 3D prints to help reinforce it.

After reading your feedback, it could use an AT tiny84 and have more programming options with a few pre-programmed routines for some of the options you outlined above. With the added program space and I/O pins it may be a good route to explore. Could design either a light disc or a magnetic tach to get RPM readings from, this may be useful from not only a safety standpoint but also a research standpoint. I imagine other fields of science could benefit from an open sourced centrifuge such as chemistry or botany , especially looking at developing nations.

It is nice to see projects like this in the pipeline which have the potential to help reshape the world.

Feel free to ask for any advice or assistance in the tiny45 or 84 area, those are my favorite devices to program for!

Thanks for the advice. We're working on an electrophoresis system at the moment. When it is done we will begin on V.2 of the centrifuge and will definitely ask you about the ATtiny as it is of great interest to us for a variety of projects.

The bursting point of the rotor is just a matter of curiosity. The current rotor/motor arrangement + the 2mm cover should be more than adequate. But we'd like to look into it just to assuage the concerns of some of the more cautious people following our project.

You can use a Servo Tester instead of the Arduino and Potentiometer.
It its simpler and cheaper :)
http://www.banggood.com/Wholesale-EK2-0907-Updated-Version-Servo-Tester-Server-Electronic-Speed-Controller-p-66240.html

Really nice work - this is the best of the OS centrifuges I have seen yet. - -I took the liberty of adding yours here http://www.appropedia.org/Category:Open_source_centrifuges

Thanks a lot for that, much appreciated. We learned a lot from previous attempts and took the next step. We plan another version soon and hope others take this design and build upon it too.

A small bar of 7 segment displays or maybe even an LCD display to show the current RPM would be a great addition to this. As far as i remember there are different RPM settings for different experiments...
If you go for an LCD you could also display how long it is switched on so you don't need a stopwatch next to it.
Sure this would have to be configured to fit the motor used, but that should not be too hard.
An emergency stop button would also be nice (instant motor off, reset kill command once pot is turned down next time) would also be a nice feature.

All good points. We're debating whether to add these functions in with displays or through a single app that can connect and give us metrics about all of our hardware we plan on developing. It is a good point you make about the RPMs, in biology labs you will see something like ours with no RPMs displayed for very simple spinning, while others have impressive suites of controls for timing, Gs, and RPMs.

Consider this the light version. A function-heavy version might be in the cards depending on how well this one and its version 2 does. Thanks for the feedback.

Apr 23, 2016 - Modified Apr 24, 2016

Cool! I want to make one when I have the time, I have most of the spare parts for this. I have a 2207 2100KV motor and a few ESC's laying around. I would have to make some minor changes to the wheel for my motor with the taller stator. Have you considered adding a resistor for limiting the current draw on the PS? Brush-less motor driving ESC's can demand a LOT of current, and many people with small-medium fused power supplies will be blowing fuses or burning them out; even at part throttle, they will draw full load and emit a timed PWM signal.

This is entirely dependent on the parts one uses for this build, if they're purpose bought, or just laying around in the workshop.
This design would benefit from some ESC programming as well, with functions like slow start, low timing (if no motor sync issues arise), and the removal of LVC since the application calls for a hard wired PS. Just my thoughts!

Thank you for sharing, can't wait to make one!

Edit: Also, disable phase braking on the ESC, this will prevent turbulent stops.

Thanks for that. Yes, we need to rethink this design and will take this and other very helpful comments to heart when doing so. The main design here was based around what we had laying around the makerspace and only decided to share it on Thingiverse after it was finished. Knowing that people are interested in making this, we'd like to make one as simple, cheap, safe, and as efficient as possible.

Please do share some pictures of the one you make, we love to see others making our designs. If you need any help with redesigning let us know. We've included the SketchUp file as well to make it easier to edit with the same software it was designed in.

Apr 24, 2016 - Modified Apr 24, 2016
wubwub89 - in reply to F_Lab_TH

Not a problem, I will post results when I get the chance. I will try the files without editing if there is enough headroom for it. My spare motors are only a few mm taller than the recommendation.

Edit: You could add this for people that need a specific G force per Vin calculated by their choice of parts without an actual measurement, given, it's ballpark, not perfect. Where R should be taken as the centerline distance from the end of the capsule to the center of shaft;
G=1.12 x R x ([KV(n) x Vin]/1000)²

For anyone asking about RPM, KV(n)*Vin=Max no load RPM

If you thought this wasd cool. I reccomenf checking out this thing made by a user.

http://www.thingiverse.com/thing:1322841

Vise (Fully 3d printed)
by jdog13

Interesting thnig. To get DNA out of stuff, but what can a DIYer do with it then? What are the possibilities in the future? Are there any?

Good question. You can use that DNA to then barcode the sample. So say you want to know for sure what is in your hamburger, you could do a barcode protocol and determine if it is really beef, or something else, like horse. DIYbio labs in England actually did this during the horse-meat situation a while back. You could also extract and ship samples for more detailed sequencing at local or overseas labs.

Ok. Thought I can't go and make a potato that is hairy because it is related to me or sth:) Joke;)

Neat project, thanks for sharing.

Would be nice to include schematic and code in the archive though.

But do like the idea of the servo tester mentioned below.

Actually, we have included all the instructions (below the summary under Thing Details, sort of hidden but it's there we promise). There is a link leading off to the code we used as well. There is also an image showing how to wire everything together. You're right about the servo tester. There is a better way to do this and we plan on making a second version.

Check out our instructions and if you have any other questions, we'll be happy to answer them.

What´s about Gel Electrophoresis ?
This would be the next step- a seperated dna made with this machine is nice, but only the foundation.

Yep, i know the manual from the university of utah- they have a good knowledge base for dna stuff :)
But i´ll wait until there is a nice print file for the box.

Yes, you are correct. We are working on one right now as a matter of fact. Have lots of testing to do before we put it up. Stay tuned! We also want to make a better version of this centrifuge.

Great idea. We are looking into ways of making motor control easier and cheaper for the next version.

neat! I won't be building because I actually have a huge 3L refrigerated IEC centrifuge in my house (long story) but this is really cool!

How many RPMS do you spin at and do you have an estimate of Gs generated? also, do you have any data on rotor failure? Has it happened? any plans to do teeny swinging buckets??

The rotor seems pretty solid. We have not calculated the RPMs but have confirmed it is pulling enough Gs to create a decent DNA pellet at the bottom of a test tube which is why we made it. Future modifications may include a means to measure and also set RPMs/Gs.

We won't be doing any other rotor configurations unless the need arises, mainly because of the potential of failure increasing with complexity when 3D printing.

We always operate it with the lid closed just in case!

How do you guys produce STL files from Sketchup?

Thanks
Clive

Depending on what version of SketchUp you have, there are different ways to do it. If you download the most recent version, there is an "extension warehouse" under your "window" option. Go there, and in the search box, type in STL and you should get a SketchUp team extension that you can download for free that will import/export STLs.

Also, I am guessing that the red cables are 12v, the black cables are ground, and the orange and green cables are signal?

Yes. On a real ESC you might have an orange or white wire for signal (or maybe even another color) but the other two, black and red are negative and positive respectively.

Can you give any details on the brushless drone motor and electronic speed control you used? Can you buy one new? Or what model drone did you get yours from so I can get the right speeds?
Do you have an estimate of the RPM you can get to?

We're not sure about the RPM's yet, we just know that it is more than enough for a 1 minute spin to create a DNA pellet.

The 23mm diameter motor we have is taken from an old drone project. On the case it says: 1806/2400.

The mounting holes fit this one, and several others of similar size we had on hand. If you cannot fit yours using the mounting holes, we've included the SketchUp file so you can edit it. Let us know if you have any problems.

Thanks! I'll spec a new motor and ESC and figure out how to adjust to it once I have it.

I just test-printed the rotor, and one area that strikes me as weak is the central disk - in between the 6 holes for the tubes. It is so thin that any lamination issues and any weakness due to infill structure would be exposed there. I wonder if there's a way to adjust that design? Maybe printing the bottom 10 layers solid, then having infill for the rest... You don't want too much mass up above! (do you? I'll explore the physics)

Dec 10, 2015 - Modified Dec 10, 2015
F_Lab_TH - in reply to prispin

We have had no problem with ours. We used a MakerBot Replicator 2 and a 10% infill. As long as it is printed properly, it should be strong enough. If you are using different software or a different printer it might be a different story. Always be careful when testing it out, and always make sure to have the lid down or some sort of solid barrier between it and people while testing.

Could you post photos when you are done printing it out? We are very eager to see others make this project. Thanks!

Can you please provide details on the power supply setup? Like, did you power the arduino using the 5v, 1amp usb and the esc with the 12v wall adapter? Or how? I would also like to know what the amperage of the wall adapter is.

Thank you,
Eric

As promised, we've added the wiring diagram above.

And anyone who sees a better way to do this please feel free to give us your suggestions! We are hackers not electrical engineers. Thanks in advance.

The adapter we're using is 12V 1A. The Arduino Nano's Vin can handle 12V in. We were powering the Arduino via a USB because we were still working on the code, but it is now powered by 12V and seems to be ok.

We'll post up a diagram of the wiring soon.

Let me know when the code becomes available!

Thanks!

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