Open Hardware for Open Science – Interview with Charles Fracchia

Open Science has been a long-standing ideal for many researchers and practitioners around the world. It advocates the open sharing of scientific research, data, processes, and tools and encourages open collaboration. While not without challenges, this mode of scientific research has the potential to change the entire course of science, allowing for more rigorous peer-review and large-scale scientific projects, accelerating progress, and enabling otherwise unimaginable discoveries.

As with any great idea, there are a number of obstacles to such a thing going mainstream. The biggest one is certainly the existing incentive system that lies at the foundation of the academic world. A limited number of opportunities, relentless competition, and pressure to “publish or perish” usually end up incentivizing exactly the opposite – keeping results closed and doing everything to gain a competitive edge. Still, against all odds, a number of successful Open Science projects are out there in the wild, making profound impacts on their respective fields. HapMap Project, OpenWorm, Sloan Digital Sky Survey and Polymath Project are just a few to name. And the whole movement is just getting started.

While some of these challenges are universal, when it comes to Biology and Biomedical Engineering, the road to Open Science is paved with problems that will go beyond crafting proper incentives for researchers and academic institutions.

It will require building hardware.

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Mediated Matter at the MIT Media Lab

Few things have managed to capture the imagination of hackers and engineers around the world the way Synthetic Biology did over the last couple of years. The promise of “applying engineering principles to designing new biological devices and systems” just seemed way too sci-fi to missed out on, and everyone jumped on the bandwagon. All of a sudden, the field which used to be restricted to traditional research organizations and startups found itself crowded with all sorts of enthusiasts, biohackers, and weirdos alike. Competitions such as the International Genetically Engineered Machine (iGEM) paved the way, and the emergence of community spaces like GenSpace and BioCurious finally made DNA experimentation accessible to anyone who dares to try. As it often happens, the Sci-Fi itself did not go untouched, and a whole new genre called “Biopunk” emerged, further fueling people’s imagination and extrapolating worlds to come.

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Take Your Samples for a Spin with the RWXBioFuge

We have a confession to make: we love centrifuges. We’ve used all shapes and sizes, for spinning bags of whole blood into separate components to extracting DNA, and everything in between. Unfortunately, these lab staples are too expensive for many DIY-biologists unless they buy them used or build them themselves. [Pieter van Boheemen] was inspired by other DIY centrifuges and decided to make his own, which he named the RWXBioFuge.

[Pieter] designed the RWXBioFuge using Sketchup, OpenSCAD, and InkScape. It features a Thermaltake SMART M850W ATX power supply, an R/C helicopter Electronic Speed Controller (ESC), and brushless outrunner motor. For user output it utilizes a 16×2 LCD character display with an I2C interface.The frame is laser-cut from 3mm MDF while the 3D-printed PLA rotor was designed with OpenSCAD.

An Arduino handles the processing side of things. [Pieter] used an Arduino Ethernet – allowing a web interface to control the centrifuge’s settings and operation from a distance. We can see this being useful in testing out the centrifuge for any rotor/motor balance issues, especially since [Pieter] states that it can be configured to run >10,000 rpm. We wouldn’t want to be in the room if pieces start flying off any centrifuge at that speed!  However, we feel that when everything’s said and done, you should have a centrifuge you can trust by your side when you’re at your lab bench.

While there are similarities to the Openfuge, the larger RWXBioFuge has rotor capacities of eight to twenty 1.5-2.0ml microcentrifuge tubes. Due to the power supply, it is not portable and a bit more expensive, but not incredibly so. There are some small touches about this centrifuge that we really like. The open lid detector is always a welcome safety feature. The “Short” button is very handy for quick 5-10 second spins.

A current version of the RWXBioFuge is being used at the Waag Society’s Open Wetlab. [Pieter’s] planned upgrades for the next version include a magnetic lid lock, different rotor sizes, an accelerometer to detect an improperly balanced rotor, and optimizing the power supply, ESC, and motor setup. You can never have enough centrifuges in a lab, and we are looking forward to seeing this project’s progress!

Check out a few more pictures of the RWXBioFuge after the break.

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OpenFuge: an open-source centrifuge

openFuge

Biohackers, fire up your laser cutters. [CopabX] has developed OpenFuge: a (relatively) low-cost, open-source centrifuge from powerful hobby electronic components. If you thought the VCR centrifuge wasn’t impressive, trolls be damned— OpenFuge can crank out 9000 RPM and claims it’s capable of an impressive 6000 G’s. [CopabX] also worked in adjustable speed and power, setting time durations, and an LCD to display live RPM and countdown stats.

And it’s portable. Four 18650 lithium cells plug into the back, making this centrifuge a truly unique little build. The muscle comes from a DC outrunner brushless motor similar to the ones that can blast you around on a skateboard but with one key difference; an emphasis on RPMs over torque. We’re not sure exactly which motor is pictured, but one suggestion on the bill of materials boasts a 6000 KV rating, and despite inevitable losses, that’s blazing fast at nearly 15V.

You’ll want to see the demonstration video after the break, but also make time to swing by Thingiverse for schematics and recommended parts.

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VCR Centrifuge

vcrCentrifuge

VCR’s practically scream “tear me open!” with all those shiny, moving parts and a minimal risk that you’re going to damage a piece of equipment that someone actually cares about. Once you’ve broken in, why not hack it into a centrifuge like [Kymyst]? Separating water from the denser stuff doesn’t require lab-grade equipment. As [Kymyst] explains: you can get a force of 10 G just spinning something around your head. By harvesting some belt drives from a few VCR’s, however, he built this safer, arm-preserving motor-driven device.

[Kymst] dissected the video head rotor and cassette motor drive down to a bare minimum of parts which were reassembled in a stack. A bored-out old CD was attached beneath the rotor while a large plastic bowl was bolted onto the CD. The bowl–here a microwave cooking cover–acts as a protective barrier against the tubes spinning inside. The tube carriers consist of plastic irrigation tubing fitted with a homemade trunnion, which [Kymyst] fashioned from some self-tapping screws and a piece of PVC. At 250 rpm, this centrifuge reaches around 6 G and best of all, gives a VCR something to do again. Take a look at his guide and make your own, particularly if your hackerspace has a bio lab.

Your Hackerspace needs a biology lab; here’s the inspiration

biology-hackerspace

When you think of Hackerspaces what pops to mind? For us it’s electronics first, then machining related stuff (3D printing, CNC milling), followed by welding, woodworking, auto mechanical, we could go on and on. But biology hacking doesn’t really make that list. The New York based Genspace is a strong case on why we should add a biology lab as a viable hackerspace option.

What are Hackerspaces other than a collection of tools and skilled members that helps to bring the mad scientists of the world out of their basements and into the light? Pretty much every Hackerspace teaches classes that are open to the public. This is basically a requirement of being a non-profit, but is also driven by the virtue of making knowledge open and available. Offering biology themed classes is an incredible tie-in for helping to see our young learners through to a career in the sciences.

Vice-President and Co-Founder [Daniel Grushkin] was inspired by college students who hack organisms for a one semester long project. He wanted to try his hand at it, but needed help with the resources. He gathered a few others who were interested and, with encouragement from NYC Resistor, they got Genspace up and running in Brooklyn. The organization holds safety as a top priority. Each new member learns about the Biosafety Level 1 guidelines used by the space. For less involved experiments they even use tools of their own making, like a glovebox similar to this one.

 

Genetic testing with Lego

From the dark recesses of the Internet circa 2009 comes the BioBrick-A-Bot, a liquid handling system for molecular biologists.

The 2009 iGEM competition was a student competition to build devices for synthetic biology. The BioBrick-A-Bot’s goal is to build a simple, low-cost liquid handling system that sucks liquids out of petri dishes and into vials.

Like most lab equipment, the commercial version of this tech is insanely expensive – about 10 grand for a commercial liquid handling robot. The BioBrick-A-Bot is made nearly entirely out of LEGO parts, so the cost of the entire system was brought down to about $700.

There are two main parts to the BioBrick-A-Bot. The Alpha module holds four pipette on a delta platform We’ve seen this type of robot built out of LEGO before, but moving liquids is new territory. The Phi module contains all the mechanics to suck microliters of liquid into a pipette and spit them out into vials.

The BioBrick-A-Bot didn’t win the 2009 iGEM competition (that honor was taken by students from Heidelberg Cambridge), but we’d take a LEGO robot any day of the week. Check out the demo after the break.

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