OpenTrons BioBot: Open-Source DIY Liquid Handling Robot!

[Will Canine]

Hello from the OpenTrons team!

It is an exciting day! We have been getting ready to show you all the open-source DIY liquid handling robot we have been developing at Genspace for a long time. Couldn’t be more excited to announce the DIY BioBot 1.0 to the DIYBio list!

We are hosting the BOM, control app, assembly instructions, and getting-started guide on Synbiota: Check out how you can make one yourself for under $2000USD!

Hardware: All the parts for a DIY BioBot are off the shelf (buy them from OpenBuilds or Inventables, etc) or 3D printed (print in ABS -- stronger than PLA and autoclavable), so you can make it all yourself. You use your own hand micropipette for the liquid handling -- with most pipette brands, every size, any number of channels will fit in the BioBot with minimal modification.

Electronics: BioBot uses the TinyG motor controller, an awesome piece of tech from Syntheos, to run the robot’s six stepper motors.

Software: We are using Cordova for this BETA version of the OpenTrons control app: HTML5 interface on top of an Android plug-in sends the TinyG motor controller JSON wrapped g-code over Bluetooth serial. The source code is right here.

We are also working on an open BLE service for automation modules -- things like centrifuges, incubators, spectrometers, etc -- as part of the OpenTrons automation platform. We are hoping that other developers will be interested in building on the OpenTrons with their own modules and tools!

OpenTrons’ mission is to provide open, affordable, and easy to use automation equipment and empower a new generation of biodevelopers with the tools to change modern biotech. To that end, we are spending the summer working with factories to develop a plug-and-play BioBot liquid handler that we will be selling for under $2000 starting in 2015 -- keep an eye out for our crowdfunding/presale campaign this November!

Please dont hesitate to reach out to in...@opentrons.com with any questions, comments, ideas, advice, to be added to the early-bird sales list, or whatever! We are always interested in hearing what the community has to say.

Thanks!

Will

[Bryan Bishop]

On Thu, Jul 10, 2014 at 10:09 PM, Will Canine <willc...@gmail.com> wrote:

open-source DIY liquid handling robot we have been developing at Genspace

What's the license on the CAD parts, and the cordova javascript stuff?

Are there source files available for these?

https://github.com/Opentrons/OpenTrons/tree/master/3D-Print-STL/CAD%20Drawings

Also, is there a way to export the synbiota.com page to another format? Saving the html dump w/ images will miss a lot of the other non-image files linked from the page. I see that the synbiota.com page has a Creative Commons logo that seems to be CC-BY only, and not CC-BY-SA, is that right?

Thanks.

- Bryan
http://heybryan.org/
1 512 203 0507

[Will Canine]

Hi Bryan,

Glad your excited about the BioBot!

The Cordova app is under the Apache 2.0 license. 

The parts are not really licensed so much as just there for you to use... We would like to use the CERN license or similar, but because we are using the TinyG (which does not open its .brd file) and that is the only electronics that could be open-source, it does not really fit. Would welcome any advise on this!

I think we can provide the design files for the 3D printed parts, didn't occur to me, let me get back to you on that. 

You'll have to ask the Synbiota folks about their site. 

Thanks!

[John Griessen]

On 07/10/2014 10:34 PM, Will Canine wrote:
> because we are using the TinyG (which does not open its .brd file) and that is the only electronics that could be open-source, it
> does not really fit. Would welcome any advise on this!

TinyG has a nice low price. I like the generic nature and fully open design of the smoothieboard
project that uses low power 32 bit ARM microcontroller better. The smoothieboard does not lock
you into any particular size or kind of motor -- it can drive larger drivers to control kilowatt
stepper motors if desired.

The code of TinyG and Smoothie both started from grbl, so are similar.

Other code on their wiki is also free and open. I'll ask about their board -- if it is an open design
that can be modified easily. Hmm.... here is maybe the non-answer paraphrased from their wiki:
https://www.synthetos.com/about/

"Do you have any plans to release the tinyg board with the step/direction/enable pins broken out? If not, is there any chance you
would release the circuit design so I can have a crack at modifying it to replace the onboard stepper drivers with such pins? "

No response...

About outline for fitting in enclosures:

" No we do not have a cad file available. Sorry about that." RileyApril 18, 2013

It seems possible to graft on larger drivers from a forum entry here:
https://www.synthetos.com/topics/about-external-stepper-drivers/

https://www.synthetos.com/topics/eagle-files-gerbers-bom/
TinyG source is open source. We also provide the schematics. TinyG hardware is not OSH.
February 19, 2014 at 7:30 am Riley Keymaster

https://www.synthetos.com/topics/license-question/
I have a question about which license your TinyG Hardware actually uses. You seam to have a few versions. Maybe you could clarify?
February 4, 2014

No response...

So, it's not open to modify/integrate into a low cost product without angering the creators and maybe getting in a lawsuit.

So, I advise looking at Smoothieboard to see if you could port your code to it. Much more product
evolution friendly for your ongoing automation suite plans. And the parts cost is easy just like
TinyG, but more processing power and better microcntroller prices than Atmel, and low power consumption
and more generic/open C coding than AVR C code and compilers.

John Griessen

[Will Canine]

Bryan,

I have some more information for you!

If you sign in to synbiota and join the BioBot project, you can export the lab book, STLs and all, and download it. If you dont want to join synbiota etc, here is a link of the already exported lab book (thanks Connor Dickie!): http://files.synbiota.com/ot4bb/opentrons-biobot-1-0-assembly-guide.zip

Just keep in mind the above file is just a snap-shot and wont update if/when we change stuff.

And you're right we were not using the share-alike clause, which we should be doing. Fixed it :)

Would love to hear about your process if you are building a BioBot! Excited to see what people do with it!

Thanks,

Will

[Will Canine]

Hi John!

Sorry have been out of touch for a little while, we are settling in to Shenzhen, China, where we are working with factories and distributors in preparation for our kickstarter in the fall.

Thanks for this! We have also been looking at the smoothie board for a long time, and have been excited to try it out after releasing this first version of the software. Right now we are putting together a next prototype that uses browser --wifi--> R-Pi + Smoothie instead of Android --BT--> TinyG to see how we like it.

Its good to hear your feedback vindicating our interest in the smoothie -- it seems like a really great piece of tech, and love how open and well documented it is. Thanks for the thoughts, would love to hear any more you have!

[Bryan Bishop]

On Wed, Jul 16, 2014 at 10:20 PM, Will Canine <willc...@gmail.com> wrote:

If you sign in to synbiota and join the BioBot project, you can export the lab book, STLs and all, and download it. If you dont want to join synbiota etc, here is a link of the already exported lab book (thanks Connor Dickie!): http://files.synbiota.com/ot4bb/opentrons-biobot-1-0-assembly-guide.zip

yoink.. mirrored:

http://diyhpl.us/~bryan/irc/opentrons-biobot-1-0-assembly-guide.zip

[Michael Shamberger]

Hope things are going well in China.

I am preparing to build an opentrons.  Some improvements I am planning are to base it on Shapeoko 2, use all metric parts, and really take a look at reducing the 3d printed parts with standard ones.    I also want to try R-Pi & Smoothie.  

I am also building a microscope to attach to it so it would be good to know which way you are going with the technology.  People will be reluctant to develop for the platform if you have not decided on the hardware/software platform.

[Will Canine]

Michael,

Awesome!

We are working on the transition to Rpi + Smoothie right now; will keep everyone up to date when we've ported things over fully. 

We're also switching to 100% metric and cutting down the number of custom parts needed -- making it easier to make and less expensive!

Platform wise, it is safe to say that we will be on the Rpi + Smoothie, with the Rpi running a Node.js server to handle communication over both bluetooth 4.0 and wifi. We are also making a BLE service for easy integration of Arduino and Node based peripherals; we are starting with a centrifuge that can be used in BioBot automation jobs, but a microscope is also a great thing to integrate. The BLE service/API is still in the very early stages, but I will let you know as it progresses! 

Keep us up to date with your progress, and let me know if you have any questions! So excited you're building a BioBot!

Thanks,

Will

[John Griessen]

On 07/24/2014 04:16 AM, Will Canine wrote:
> Platform wise, it is safe to say that we will be on the Rpi + Smoothie, with the Rpi running a Node.js server to handle
> communication over both bluetooth 4.0 and wifi. We are also making a BLE service for easy integration of Arduino and Node based
> peripherals

When you say Smoothie, do you mean a smoothieboard by Arthur Wolf, ( http://shop.uberclock.com/products/smoothieboard),
or just the Smoothie code? Smoothie is a real time OS in its own right, so my guess is not running on the R-Pi.

I'm interested in using platforms like the R-Pi to run ROS, (Robot Operating System), to orchestrate microcontroller
based bots using smoothie on STM32 micros.

BLE means Bluetooth Low Energy or something else?

[Will Canine]

John,

Yes indeed, the smoothieboard by Arthur Wolf and Mark Cooper. 

The ROS is awesome but overkill for our purposes -- we are just using a Node.js server on the Rpi to create g-code and send it to the smoothieboard. 

And yes, BLE stands for Bluetooth Low Energy, aka Bluetooth 4.0. 

[Michael Shamberger]

I have been thinking about some other design changes that would be good for a bio bot.

- Enclosure to maintain specific environment.   This allows it to be used as an incubator.  Cooling would allow it to be used for printing microarrays.  The enclosure would be made of correx and could be paired with a HEPA filter.

See http://users.ox.ac.uk/~atdgroup/technicalnotes/TE300%20incubator%20enclosure.pdf for an initial design that is compatible with the current opentrons.

- Computer vision for self calibration and "Pick and Place".  I am planning on using a downfacing Raspberry PI camera.  I think I will start with the vision library made my guys working on the Firepick delta (www.firepick.org) which is a pick and place machine.  See the code at github https://github.com/firepick1/FireSight.  It is a layer on top of opencv and runs on Raspberry PI.  The computer vision can recognize the plates being used for experiments.

- Automatic tool change needs more thought

I haven't started my build yet because I have been investigating these design changes and will make CAD drawings before physical assembly.

[John Griessen]

On 08/03/2014 03:47 AM, Michael Shamberger wrote:
> The enclosure would be made of correx and could be paired with a HEPA filter.

The hollow shapes of correx will collect dust that can be blown loose as flow is forced if not sealed perfectly.
Solid wall parts have fewer hollows or cracks to seal, so better for the low cost/high performance purpose.

[Michael Shamberger]

>>The hollow shapes of correx will collect dust that can be blown loose as flow is forced if not sealed perfectly.
>>Solid wall parts have fewer hollows or cracks to seal, so better for the low cost/high performance purpose.

Thanks for that.  The correx solution works for incubating bacteria but a sterile environment for printing microarrrays is more difficult.

[Will Canine]

Michael,

Thanks for this! Great ideas.

Camera: We are on 100% the same page here. We are planning on incorporating an Rpi camera for auto calibration and job-monitoring for the BioBot One that we will be Kickstarting in November. We're currently finishing up the physical design for manufacture, and  porting the software from Android/TinyG to Rpi/Smoothieboard. We should talk more off-list about developing the computer vision software going forward! 

Enclosure: this is certainly an awesome idea, and we have been playing with it ourselves. It adds a ton of cost however, and would require a lot of testing to get right, so we've decided to hold off and include this in later models of the 'bot. But that is no reason to stop you from experimenting! Would love to hear about anything you discover. Out of curiosity, what are you hoping to use the 'bot for that you'd want environmental controls like this? 

Automatic Tool Change: This is something we actually have made some designs for, but it is also a feature that is going to have to wait for the next version. But to compensate for not having auto tool changes on the BioBot One, we are including three active heads so you can have two differently sized micropipettes and a test-tube gripper all at the same time -- hopefully this makes it flexible enough to be useful. 

AND-- 

Open Source Protocol Scripting and Sharing: We are including compatibility with PRPR -- an open-source liquid handling robot scripting language alternative to the proprietary Tecan EvoScript or similar -- in all of our labtools. This means that you can write code to do biotech protocols on your bench top. We are developing a community hub for sharing and creating these scripts as well as a node.js API/Library. We think that enabling crowdsourced optimization and quick download and run capabilities could be really awesome for empowering biodevelopers and improving scientific reproducibility -- but this is just getting started, and it would be amazing to hear anyone's thoughts on sharing scripted protocols like this! 

THANKS!!!!!!

Will 

[Otto Heringer]

These are awesome news, Will! Congratulations!

The documentation on synbiota is great! This is what I was looking for some months ago. :)

Hope to help on the crowdfunding on this November!

Best,

Otto

[Will Canine]

Hey Otto!

Good to hear from you again! How is hacking liquid handlers in Brazil going? I know you have quite a good team down there!

Glad the DIY documentation looks good to you too -- sorry we couldnt make it any faster ;) Excited to hear what you all ended up working on! 

And thanks for the offer on crowdfunding help, we're going to need all the help we can get. We really want provide these machines as cheaply as possible, but if we dont get enough pre-orders we are in trouble. Any thoughts on good ways to reach out to folks who could use affordable, scriptable liquid handling automation down in Brazil (or anywhere) would be greatly appreciated!  

Thanks! 

Will