Interview to Open Trons

By on July 11, 2014
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Biology labs today are where computers were in the 1950s and ‘60s — they exist in huge, climate controlled spaces behind security guards that only allow trusted experts with white lab coats inside. But, like the personal computer revolution in the ‘70s, the open science and DIY biology movements are breaking the lab free of stogy institutions.

Community labs like Genspace in Brooklyn and open-source biotech tools like the OpenPCR have done a ton of work to accelerate the democratization process. And now biohackers are reaching beyond the basics. OpenTrons are making professional grade lab robotics and automation systems at a maker scale.

Liquid handling — moving around tiny and precise solutions containing DNA, enzymes, and the other chemical components of biology experiments — is the most common and time-consuming task of a molecular biology. In order to scale up production in biotechnology, it is crucial to automate this process. But today, liquid handling robots cost at least $30,000 and only big, well-funded labs can afford to automate. OpenTrons plan to sell their BioBot for around $2000, making automation accessible for everyone who needs it.

 

Few days ago, we spotted OpenTrons, a self dubbed  “affordable, easy to use biotech tools that can be connected together to make a modular lab automation system”.

will canine

As I’m particularly interested in the developments in science-related open source projects I was amazed by OpenTrons vision and I decided to followup and get in touch with Will Canine, one of the project founders.

 







[Open Electronics]: Ciao Will! Can you describe the vision behind OpenTrons in few word? What is the mission? The problem you’re aiming to solve with this platform?

[Will Canine]: OpenTrons’ mission is to empower a new generation of biodevelopers with powerful, open, and affordable biotechnology tools.

Until recently, if you had an idea for the next amazing genetically engineered machine, you’d need a PhD and a a ton of lab equipment to make it a reality. Today, the DIYBio movement is making it more and more possible for individuals outside of big institutions to innovate in biotech. Imagine if you could download a complicated lab procedure designed by an expert, set-up your machine (like you home a CNC mill), and then run the protocol and get the product? That is the dream — to create an open, affordable automation platform for reproducing cutting edge life science.

This would begin to emancipate the means of production in one of our most closed-off and important industries: biotech. Food, medicine, environmental security — these are the things that biotechnology produces, and the means of this production have been in the hands of too few for too long. OpenTrons is part of a growing movement to empower individuals with the ability to make innovative biotech products and solve real world problems for themselves.

 


[Open Electronics]: Can you also give us a more clear understanding of the scope of use cases the machines you’re building will be able to enable?

[Will Canine]: The BioBot is a modular, extensible platform for automating any number of processes done in a wetlab. Some examples include serial dilutions to assay engineered proteins, repeat electroporations to transform linear DNA, plasmid preparations, and heat-shock transformations.

But really, you can use OpenTrons to do a ton of different repetitive tasks. We are making every effort to be open and modular to the core, so you can use our app and hardware to do whatever you want — the only limits are your own ambitions and abilities! If you want to make a module for the bench or the active head and automate something completely outside of lab work, you can do it. Just design around our forthcoming hardware specs and Bluetooth 4.0 service/API to easily integrate your unit into the OpenTrons ecosystem.

So far we have made a centrifuge and a heater/cooler unit for the benchtop, and a gripper and liquid handler for the active heads, but you can make anything you want ( besides labwork, I am personally really excited about the chess robot possibilities…).

 

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[Open Electronics]: what strategy are you thinking to pursue when it comes to creating a community around this project? and what are the more exciting plans with regards extending functionalities and make it a “platform” for innovation?

[Will Canine]: As I alluded to above, in addition to the OpenTrons’ hardware and software being as open and modular as we can make it, we are developing an open automation protocol library. Think of it as a Thingiverse for biology protocols.

This protocol library provides two really important functions:

  1. Reproducibility. Today, the reproducibility of protocols and replicability of results can be a scientific problem. A common platform for designing protocols and executing labwork solve everything from wasteful research false-starts (like the one experienced in stem cell production last spring) to the day-to-day headaches of deciphering other people’s protocols.
  2. Abstraction. One of the biggest barriers to entry into biotechnology is wetwork skills. The ability to download and remix complicated lab protocols and then run them on your own robot opens the door to biotech innovation for interdisciplinary problem solvers without a lab background. Abstracting protocol complexity lets people focus on their design instead of their labwork.

 

[Open Electronics]: I can imaging this project can not only aim to DIY bio hackers but also to established research institutes looking for more innovation in the lab. Is it true? In this case do you have a particular plan on how to reach out to them and involve them?

[Will Canine]: Absolutely! It turns out scientists are constantly rigging up their own robots and automation machines to avoid the the closed platforms and ridiculous price tags of the robots out there today. After talking with us, tons of them are excited that they don’t have to do all the mechanical and software designs from scratch anymore!

We have been doing outreach at hackathons and community labs, and at this point, people are contacting us faster than we could ship out DIY BioBot kits! We are now focusing on designing a plug-and-play BioBot, so we aren’t shipping any more DIY kits. But you can still make your own! Just 3D print what you can’t order online — The STLs, BOM, and assembly instructions are all right here.

Our next version of the OpenTrons software will be released July 8th.







 

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[Open Electronics]: Did you guys start from an existing open source platform? if yes can you please tell us more about what are the basic contributions that allowed you guys to start from a foundation of works?

[Will Canine]: Yes great question! We could never have done any of this without already existing open-source projects.

We use the Shapeoko carriage assembly plan for the XYZ chassis of our BioBot. The Inventables MakerSlide project has really made this type of three-axis robot so easy to make, and the Shapeoko folks have a fantastic assembly guide.

The TinyG motion controller by Synthetos is amazing. It can accept g-code commands packaged as JSON objects, so we easily get our tablet controlling the robot over bluetooth. It also has all the physics algorithms and jerk control you could ever want in a professional motion controller — could not be more grateful for this wonderful piece of technology.

We are also using Apache Cordova for the next version of the OpenTrons control app (we have been native Android). This means that we can write a responsive HTML5 interface that you can use in a browser, Android app, or whatever else you want to use to control the BioBot. Javascript robotics, here we come!

But it is not just about the open technology, it is also about the open community. I have been a member of Genspace, the community biolab in Brooklyn, for over a year. Without Genspace’s open lab space, open science resources, and the individuals that openly share their expertise and passion there, OpenTrons could never have happened.

We could not be more grateful to the Open Source community, and we are equally excited to give back.

 

[Open Electronics]:  What’s the plan with OpenTrons? Are you looking for venture funding and maybe turn this initial idea and prototypes into final products? Are you looking into crowdfunding maybe?
Do you want to keep it only as a participative platform? What’s your sustainability model?

[Will Canine]: We are beginning the process of designing for manufacturing and working with factories for delivery of a plug-and-play BioBot in early 2015. Keep an eye out for our Kickstarter late this fall!







About Boris Landoni

Boris Landoni is the technical manager of Open-Electronics.org.
Skilled in the GSM field, embraces the Open Source philosophy and its projects are available to the community.