Category: Skunkworks

Product Review: BioTek Microflo liquid dispensing machine

Posted by – December 20, 2009

A couple of pictures of the BioTek Microflo liquid dispenser.

Device with hatch open and spring tension unlocked:

BioTek Microflo cartridge in place

BioTek Microflow cartridge in place. Spring tensioner open. Eight silicone tubes run in parallel, across the pump axle.

Device with hatch open and spring tension locked:

Biotek Microflo with tensioner locked

Biotek Microflo with tensioner locked. Tension is placed across the silicone tube liquid lines. Tension is adjustable with a set screw parallel to each line (screws not shown here, they are vertical and can be seen in a top-down view). The axle rotates clockwise or counterclockwise to move liquid forward or backward with peristaltic action. It is very fast.

This machine has both serial RS-232 and USB; however, the communication link is a proprietary protocol which is only compatible with BioTek’s Microsoft Windows software. The machine is not Unix compatible. So unfortunately, I won’t be using this device in my lab automation setup.

U.S. Office of Science and Technology Policy soliciting your feedback on “Improving Public Access to Results of Federally Funded Research” until Dec 20, 2009

Posted by – December 12, 2009

The U.S. Office of Science and Technology Policy, under directives from the President Obama administration, is soliciting public feedback. Note the deadline!  (Dec. 10th-20th)

Policy Forum on Public Access to Federally Funded Research: Implementation

Thursday, December 10th, 2009 at 7:25 pm by Public Interest Declassification Forum

By Diane DiEuliis and Robynn Sturm

Yesterday we announced the launch of the Public Access Forum, sponsored by the White House Office of Science and Technology Policy.  Beginning with today’s post, we look forward to a productive online discussion.

One of our nation’s most important assets is the trove of data produced by federally funded scientists and published in scholarly journals. The question that this Forum will address is: To what extent and under what circumstances should such research articles—funded by taxpayers but with value added by scholarly publishers—be made freely available on the Internet?

The Forum is set to run through Jan. 7, 2010, during which time we will focus sequentially on three broad themes (you can access the full schedule here). In the first phase of this forum (Dec. 10th-20th) we want to focus on the topic of Implementation.   Among the questions we’d like to have you, the public and various stakeholders, consider are:

  • Who should enact public access policies? Many agencies fund research the results of which ultimately appear in scholarly journals. The National Institutes of Health requires that research funded by its grants be made available to the public online at no charge within 12 months after publication. Which other Federal agencies may be good candidates to adopt public access policies? Are there objective reasons why some should promulgate public access policies and others not? What criteria are appropriate to consider when an agency weighs the potential costs (including administrative and management burdens) and benefits of increased public access?
  • How should a public access policy be designed?
    1. Timing. At what point in time should peer-reviewed papers be made public via a public access policy relative to the date a publisher releases the final version? Are there empirical data to support an optimal length of time?  Different fields of science advance at different rates—a factor that can influence the short- and long-term value of new findings to scientists, publishers and others. Should the delay period be the same or vary across disciplines? If it should vary, what should be the minimum or maximum length of time between publication and public release for various disciplines? Should the delay period be the same or vary for levels of access (e.g. final peer reviewed manuscript or final published article, access under fair use versus alternative license)?
    2. Version. What version of the paper should be made public under a public access policy (e.g., the author’s peer-reviewed manuscript or the final published version)?  What are the relative advantages and disadvantages of different versions of a scientific paper?
    3. Mandatory v. Voluntary. The NIH mandatory policy was enacted after a voluntary policy at the agency failed to generate high levels of participation. Are there other approaches to increasing participation that would have advantages over mandatory participation?
    4. Other. What other structural characteristics of a public access policy ought to be taken into account to best accommodate the needs and interests of authors, primary and secondary publishers, libraries, universities, the federal government, users of scientific literature and the public?

We invite your comments [...]

Give government your feedback on how to release data and publications from publicly funded research.

More information is in the U.S. Office of Science and Technology Policy video:

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Add Streaming Video to any Bio-lab!

Posted by – October 16, 2009

Combining an inexpensive (under $15) USB webcam with free VLC media player software, it is simple to add password-protected internet streaming video for remote users to any lab.  VLC includes the ability to capture from a local webcam, transcode the video data, and stream the video over the web.  It’s available for OS/X, Unix, Linux, and Microsoft systems.

Hint: Video formats are confusing.  Even video professionals have a tricky time figuring out the standards and compatibility issues.  Today’s web browsers also have limitations in what they can display (mime types and such) — which simply means both sides need to use VLC.  Figuring all this out using the VLC documentation takes some work.  Transcoding the video is required and a proper container must be used to encapsulate both video and audio.  Once debugged, it’s good to go.

Here’s how it worked in the lab:

Webcam for Biotech Lab Automation

See the setup below to get it running.

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Low Cost Microcontroller-based Digital Microfluidics using “Processing”

Posted by – July 1, 2009

I’ve now tested the digital microfluidics board via microcontroller. The digital microfluidics board moves a liquid droplet via Electrowetting-on-Dielectric (EWOD).  The microcontroller switches the high voltage via a switching board (pictured below, using Panasonic PhotoMOS chips), which controls the +930VDC output by the HVPS (posted earlier), and runs over USB using no cost Processing.org software.  This is alpha stage testing.. cleaner version to be built.  The goal of course is to scale the hardware to allow automation of microbiology protocols.

Labview is quite expensive, and industrial-grade high voltage switching boards are also quite expensive.  So I built my own hardware and the Processing.org language is an easy way to test things.  The Processing.org language is a free, open source graphics/media/IO layer on top of Java (as posted previously here).

What follows is the super simple test software written in Processing.org & Java.

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

Posted by – 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

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

Posted by – 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.

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

Posted by – 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

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Make some simple biology lab tools

Posted by – February 3, 2009

Sometimes biology lab tools are really simple, and ridiculously obvious (i.e., a petri dish?).   Yet most of the general public form the idea that biology, chemistry, or even nanotechnology, is impossible because we don’t have high-tech tools. Maybe it’s because the research papers always use big words, half of which are some form of Latin, or the tools are named after a dead guy with a crazy name (erlenmeyer flask anyone?).

Look at some of the tools used in most biology labs for proof.  Cheap office supplies are re-used as laboratory supplies.  Many biology tasks only need the most basic tool for pouring, scraping, mixing, holding, or electrocuting something.  These are easy jobs which only require simple tools.

A few more examples are provided in The Scientist article, Let’s Get Physical -
How to modify your tools to prevent pain at the bench
.   (Free registration might be required to view the article.)

Maybe some of the Makers out there will read this article and Make me something.  (Meredith wants to make something; I need simple lab tools.)

Build a Spectrophotometer (Schematics included) as a DIY Project

Posted by – December 26, 2008

I recently ran across this published paper.  Most skunkwork types seem to buy used equipment via ebay.    This article explains how to build a spectrophotometer with schematics, illustrations, and photos.  The circuit is simple:  a photoresistor, op amp, and some mechanics for the optics.

The article even includes a Bill of Materials  (component price list); for the electronics, anyway, and it’s cheap (less than $20 for single quantities through Digikey).  The article is geared towards having undergraduate students build their own laboratory equipment as an educational exercise — and if undergrads can do it, anyone can do it (the article says that a science camp of kids aged 13 to 16 found success).

Education in Chemistry

Build your own spectrophotometer

Summary

  • Take a 100 W light bulb, a light-dependent resistor and op amp, a prism or grating in front of a slit, and a curtain – and voilà , a DIY spectrophotometer.
If you build this project or a similar one, leave a comment below.

We Make the News Headlines: “Amateurs are trying genetic engineering at home”

Posted by – December 25, 2008

As a nice holiday surprise for me this week, my project (Melaminometer) & a team member (Meredith L. Patterson) made it into Associated Press science news: “Amateurs are trying genetic engineering at home”.  The article is accurate, and quoted below.  For the melaminometer project, we are also collaborating with Taipei National Yang Ming University.

http://news.yahoo.com/s/ap/20081225/ap_on_sc/do_it_yourself_dna

Amateurs are trying genetic engineering at home

Meredith L. Patterson, a computer programmer by day, conducts an experiment in Meredith L. Patterson, a computer programmer by day, conducts an experiment in the dining room of her San Francisco apartment on Thursday, Dec. 18, 2008. Patterson is among a new breed of techno rebels who want to put genetic engineering tools in the hands of anyone with a smart idea. Using homemade lab equipment and the wealth of scientific knowledge available online, these hobbyists are trying to create new life forms through genetic engineering – a field long dominated by Ph.D.s toiling in university and corporate laboratories.
(AP Photo/Noah Berger)

SAN FRANCISCO – The Apple computer was invented in a garage. Same with the Google search engine. Now, tinkerers are working at home with the basic building blocks of life itself.

Using homemade lab equipment and the wealth of scientific knowledge available online, these hobbyists are trying to create new life forms through genetic engineering — a field long dominated by Ph.D.s toiling in university and corporate laboratories.

In her San Francisco dining room lab, for example, 31-year-old computer programmer Meredith L. Patterson is trying to develop genetically altered yogurt bacteria that will glow green to signal the presence of melamine, the chemical that turned Chinese-made baby formula and pet food deadly.

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The Fundamental Problems in Open Source — What’s the Bio Fix?

Posted by – December 3, 2008

Synthetic biology aims to create biological parts which can be connected together to form larger functional devices, and many hope the most poplar library of parts will be “Open Source”.  Openly publishing large collections of biological parts is great, as it would rapidly accelerate engineering progress and rapidly diseminate the technology.

There’s one big drawback to open source though:  Where do you go when it doesn’t work? This is called the support issue. Presumably, there’s a “community of experts” who monitor problems and provide fixes for others. More often, though, the users themselves have to become expert, or they abandon the project.   (A secondary question is:  Who do you sue when it does something wrong? which is a question I posed in my licensing discussion.)

I recently ran across the following blog article from a popular web hosting company (bluehost.com) describing their use of Linux (properly called GNU/Linux, since Linux is only a small part of the operating system, and a tapestry of GNU software makes up more than 90% of a “Linux system”).  This web hosting company is very popular with many individuals and small companies, and it’s profitable existence owes much to open source software (although it’s reported that their servers experience unhealthy downtime).  Without open source software, the company couldn’t exist; the cost of their software would make their service very unprofitable.

The following quote is telling [1]:

“Whenever we see ANY bottleneck in the system whether it be CPU, I/O Block Device, Network Block Device, Memory, and so on we find out EXACTLY what is causing the problem. When I say we find the problem, I mean we go down to the actual code in the kernel and see exactly where the issue is. Sometimes that gives us the answer we need to the solve the problem and other times it is a bug in the kernel itself that we need to create a patch for.” (The full article is quoted below)

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Genetically Engineer Bacteria and/or Yeast using Sound (Ultrasound, Sonoporation)

Posted by – November 20, 2008

Almost everyone in the BioBricks realm seems to use a standard method for modifying their organisms: chemical transformation. Yet there is another method which is very promising.

In chemical transformation [3], some standard bacteria is grown, purified, mixed with some chemicals which cut open the bacteria, the new DNA plasmid is added to create some modified bacteria, the new DNA plasmid flows through the cut into the bacteria, everything is mixed with some more chemicals, allowed to heal & grow, and purified. (My naive translation of the process)

Note all the chemicals used? Chemicals can be expensive. And the amount of modified bacteria which results from this process is pretty low.

There’s an alternative method used more for yeast than bacteria: voltage-based transformation, electroporation [1]. With electroporation, some standard bacteria is grown, mixed with some simple chemicals, the new DNA plasmid is added, everything is given a quick high voltage zap (like lightening) which cuts open the bacteria, the new DNA plasmid flows through the cut into the bacteria, the bacteria is allowed to heal & grow, and purified.  (Again, my naive translation of the process)

This eliminates some chemicals, although the process still requires some specialized equipment which can be troublesome (and expensive) — the voltage can be as high as 5 kV at 20 mA. (As high as the internal components of a CRT television, which, if accidentally touched, can be easily fatal.)

There’s another method though, that I haven’t seen mentioned: sonic transformation, sonoporation [2]. In sonic transformation, some standard bacteria is grown, some chemicals are added, optionally producing small bubbles, the new DNA plasmid is added, everything is given a loud blast of ultrasound (for example, at 40 kHz) which cuts open the bacteria, the new DNA plasmid flows through the cut into the bacteria, the bacteria is allowed to heal & grow, and purified.

In the research quoted below, sonoporation has shown to be much more effective at modifying bacteria than either chemical transformation or electroporation; plus, this is done without the expensive chemicals necessary for chemical transformation and without high voltage equipment necessary for electroporation.

From [2]:
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