Month: June 2009

Comments Re: Woodrow Wilson International Center’s Talk on Synthetic Biology: Feasibility of the Open Source Movement

Posted by JonathanCline – June 26, 2009

The Woodrow Wilson International Center for Scholars hosted a recent talk on Synthetic Biology, Patents, and Open Source.  This talk is now available via the web; link below.  I’ve written some comments on viewing the talk, also below.

WASHINGTON – Wednesday, June 17, 2009 – Synthetic biology is developing into one of the most exciting fields in science and technology and is receiving increased attention from venture capitalists, government and university laboratories, major corporations, and startup companies. This emerging technology promises not only to enable cheap, lifesaving new drugs, but also to yield innovative biofuels that can help address the world’s energy problems.

Today, advances in synthetic biology are still largely confined to the laboratory, but it is evident from early successes that the industrial potential is high. For instance, estimates by the independent research and advisory firm Lux Research indicate that one-fifth of the chemical industry (now estimated at $1.8 trillion) could be dependent on synthetic biology by 2015.

In an attempt to enable the technology’s potential, some synthetic biologists are building their own brand of open source science. But as these researchers develop the necessary technological tools to realize synthetic biology’s promises, there is as yet no legal framework to regulate the use and ownership of the information being created.

Will this open source movement succeed? Are life sciences companies ready for open source? What level of intellectual property (IP) protection is necessary to secure industry and venture capital involvement and promote innovation? And does open source raise broader social issues? On June 17, a panel of representatives from various sectors will discuss the major challenges to future IP developments related to synthetic biology, identify key steps to addressing these challenges, and examine a number of current tensions surrounding issues of use and ownership.

________________________________
Synthetic Biology: Feasibility of the Open Source Movement
Presenters:

  • Arti K. Rai, Elvin R. Latty Professor of Law, Duke Law School
  • Mark Bünger, Director of Research, Lux Research
  • Pat Mooney, Executive Director, ETC Group
  • David Rejeski, Moderator, Director, Synthetic Biology Project

Synthetic Biology: Feasibility of the Open Source Movement

While viewing the webcast (which we are all lucky to have viewable online), I wrote some comments.  Since others were interested in the comments, I’ll post ’em here.
More→

Playing with the $100K Robots for Biology Automation

Posted by JonathanCline – June 26, 2009

The Tecan Genesis Workstation 200: It’s an industrial benchtop robot for liquid handling with multiple arms for tray handling and pipetting.

The robot’s operations are complex, so an integrated development environment is used to program it (though biologists wouldn’t call it an integrated development environment; maybe they’d call it a scripting application?), with custom graphical scripting language (GUI-based) and script verification/compilation. Luckily though, the application allows third party software access and has the ability to control the robotics hardware using a minimal command set. So what to do? Hack it, of course; in this case, with Perl. This is only a headache due to Microsoft Windows incompatibilities & limitations — rarely is anything on Windows as straightforward as Unix — so as usual with Microsoft Windows software, it took about three times longer than normal to figure out Microsoft’s quirks. Give me OS/X (a real Unix) any day. Now, on to the source code!

More→

HVPS for Systems Biology: A Low Cost, High Voltage Power Supply with Schematics + Board Layout

Posted by JonathanCline – June 22, 2009

I have designed this high voltage, low current power supply for various experiments in systems & synthetic biology. I have cleaned up the design and I am placing the schematic and board layout online below!  This circuit outputs up to +1,866VDC at under 1 mA or can be tapped at various points for +622VDC or +933VDC. This is useful for either DIY Biology or institutional research experiments such as:

  • capillary electrophoresis
  • digital microfluidics using electrowetting-on-dielectric
  • possibly electroporation
  • various electrokinetic experiments, such as dielectrophoresis
  • (other uses?? Let me know)
  • and, lastly of course:  making huge sparks that go PAHHHHH-POP

Below is the schematic; read the full post below for the board layout information.  Click on the schematic for the full sized version.  The schematic operates in stages, so leaving out or bypassing before the 2nd final stage will yield only +933VDC, and leaving out that stage will yield only +622VDC, etc.

Schematic for the HVPS "Tripler1"

Schematic for the HVPS

More→

Don’t Train the Biology Robot: Have the Machine Read the Protocol and Automate Itself

Posted by JonathanCline – June 3, 2009

Imagine reading these kinds of instructions and performing such a task for a few hours: “Resuspend pelleted bacterial cells in 250 µl Buffer P1 and transfer to a micro-centrifuge tube. Ensure that RNase A has been added to Buffer P1. No cell clumps should be visible after resuspension of the pellet. If LyseBlue reagent has been added to Buffer P1, vigorously shake the buffer bottle to ensure LyseBlue particles are completely dissolved. The bacteria should be resuspended completely by vortexing or pipetting up and down until no cell clumps remain. Add 250 µl Buffer P2 and mix thoroughly by inverting the tube 4–6 times. Mix gently by inverting the tube. Do not vortex, as this will result in…” (The protocol examples used here are from Qiagen’s Miniprep kit, QIAPrep.)

Wait a minute!  Isn’t that what robots are for?  Unfortunately, programming a bioscience robot to do a task might take half a day or a full day (or more, if it hasn’t been calibrated recently, or needs some equipment moved around).   If this task has to be performed 100 or 10,000 times then it is a good idea to use a robot.  If it only has to be done twice or 10 times, it may be more trouble than it’s worth.  Is there a middle ground here?

If regular English-language biology protocols could be fed directly into a machine, and the machine could learn what to do on it’s own, wouldn’t that be great?  What if these biology protocols could be downloaded from the web, from a site like protocol-online.org ?   It’s possible! (Within the limited range of tasks that are required in a biology lab, and the limited range of language expected in a biology protocol.)

Biology Protocol Lexical Analyzer converts biology protocols to machine code for a robot or microfluidic system to carry out

Biology Protocol Lexical Analyzer converts biology protocols to machine code for a robot or microfluidic system to carry out

The point of this prototype project is this: there are thousands of biology protocols in existence, and biologists won’t quickly transition to learning enough engineering to write automated language themselves (and it is also more effort than should be necessary to use a “easy-to-use GUI” for training a robot). The computer itself should be used to bridge the language gap. Microfluidics automation platforms (Lab on Chip) may be able to carry out the bulk of busy work without excessive “training” required.

More→

DIY Digital Microfluidics for Automating Biology Protocols (sub-microliter droplets)

Posted by JonathanCline – June 3, 2009

Systems biologists and synthetic biologists spend a large amount of time moving small liquids from one vial to another. I would say it makes up the majority of their work day, even in a technologically cutting-edge lab which has robotics.  Strange, isn’t it, that the most advanced biological science labs in the world are dependent on a human physically moving small drops of liquid samples and reagents around a lab?

Microfluidics aims to move liquids without humans, under computer control.  A small flow of DNA in water, for example, might trace a path between two glass plates, within a tiny, etched microchannel.  The movement of the flow is controlled by numerous micro-mechanical valves connected to electronics.

Digital microfluidics aims to move liquids without humans, under computer control, using only single droplets under electrical control: no micro-mechanical valves. It works by using electric fields (electrowetting-on-dielectric properties, abbreviated “EWOD”), which polarize water atoms enough to move a very small water droplet across the surface of a computer board.  Droplets on the board can split into two, or join together into one.

Standard PCB etching techniques can be used to make low-tech digital microfluidics devices

Standard PCB etching techniques can be used to make low-tech digital microfluidics devices

More→