LavaAmp: cheapest pocket PCR thermocycler dreamed for DIY biologists

The LavaAmp is a portable PCR thermocycler that has the potential to become the default garage biology (home biology, bioDIY, DIYbio) tool once it hits the market. Think of Apple II for personal computing or MakerBot for 3D printing.

The 1st LavaAmp prototype was shipped this week from Biodesic to Gahaga Biosciences and the process is documented and engineering details uncovered in Rob Carlson’s post.

The people behind are mainly ex SciFoo Campers and open science advocates: Guido Nunez-Mujica, Joseph Jackson, Rob Carlson, Jim Hardy and a cool engineer Rik Wehbring.

Here’s the pic of the prototype:

lavaamp-thumb-500x375In the 2007 proof-of-concept paper, entitled A Pocket-Sized Convective PCR Thermocycler, authors Nitin Agrawal, Yassin A. Hassan, and Victor M. Ugaz wrote:

Herein, we introduce an innovative thermocycling system that
harnesses natural convection phenomena to amplify DNA rapidly by the PCR in a greatly simplified format. A key element of this design is an architecture that allows the entire thermocycling process to be actuated pseudo-isothermally by simply maintaining a single heater at a constant temperature, thereby enabling a pocket-sized battery-powered device to be constructed at a cost of about US$10.

PocketThermocyclerAgrawalpic

Realizing the potential of the device and thinking about how to build a digital thermocontroller for it with the Arduino I contacted Victor Ugaz this January and was informed that they only built the proof-of-the-concept  devices testing them in the lab interested mainly in ‘understanding the physics of the thermally driven flow and its effect on the reaction’. But it was obvious to me that somebody will produce those devices for the market and make them affordable to people as it seemed to me as the familiar case of the low(est)-hanging-fruit.

So when Joseph Jackson mentioned to me his grandiose open science plans and the groups’  ‘super affordable pcr’ project I became instantly interested. As Rob Carlson writes:

The intended initial customers are hobbyists and schools.  The price point for new LavaAmps should be well underneath the several thousand dollars charged for educational thermocyclers that use heater blocks powered by peltier chips.

Why the Dyna-Vision G1 Android Telemedicine App can only be used by licensed physicians???

Let us assume that you are a technological early adopter, a maker, a hacker, a geek. Your software/hardware skills and experiences are much better than the bulk of licensed physicians. You also have a G1.

Now imagine a mobile application/gadget-in-a-belt-pouch that is the most advanced telemedicine solution in the market. With this application/gadget you were able to non-invasively monitor vital signs of the people that matter you the most at anytime from anywhere around the world. You were able to quickly recognize life threatening heart and respiratory problems of the people you care about and maybe save their lives.

The problem is that such a product exists according to this press release (via androidguys) but you are not allowed to legally use it (no information on the details of purchase yet) unless you are a registered and licensed physician. The press release does not offer any reasonable (legal?) explanation on why this is the case.

The Dyna‐Vision© G1 Android Telemedicine Application by RS TechMedic B.V (“specialized in creating very easy-to-use user interfaces”) will be officially launched during the CeBIT starting today:

Dyna‐Vision© is a small light weight and portable device, with the dimensions of a PDA. The patient wears this device in a belt pouch. This reliable and sophisticated medical device monitors up‐to 10 clinical parameters through non‐invasive sensors attached to the skin. The measurements include 12‐lead ECG, Heart Rate, Heart Rate Variability, RR‐times, Respiration, Plethysmogram and Oxygen
Saturation.

Dyna‐Vision© automatically transmits cardiac events and even continuous real‐time ECG recordings to a secured server. Besides using a computer or laptop, physicians can now also monitor a patient’s real‐time vital signs on a G1 Android mobile phone. Physicians can use the application at anytime from anywhere around the world.

The Dyna-Vision G1 Telemedicine Application can only be used by licensed physicians after registration with RS TechMedic B.V.

Practical DNA: Hugh Rienhoff’s got a story to tell

After the Nature cover article Hugh Rienhoff and the story of My Daughter’s DNA is now covered by Wired magazine. I wrote about Hugh (a fellow SciFoo Camper) as an example of any future bioDIY effort in The conditions of a mass biotech DIY movement and now the Wired piece gives us more context and details concerning how things were actually done. This is really a story that cannot be overemphasized by simply telling it again and again. 

By making inquiries with local surplus brokers, Rienhoff discovered he could buy a secondhand PCR machine for less than a MacBook. He ended up purchasing a full working model for just $750.
Obtaining additional supplies, like the PCR reagents, for his experiment was tougher. Some chemical companies didn’t want to ship to a private address, so Rienhoff pretended his house was the headquarters of the fictional Institute for Future Study.

While Rienhoff could spring for his own PCR machine, a used gene sequencer (assuming he could find one) would cost around $100,000. So he found a university lab (which he declines to identify) that would sequence the genes he had amplified, for $3.50 per 50-microliter sample. In spring 2007, Rienhoff mailed in more than 200 samples.

Rienhoff compared Beatrice’s DNA with the information on Ensembl, looking for any base-pair variants that hadn’t been previously recorded on Ensembl. Continue reading

1st UK Maker Faire, Newcastle, March 2009, makers wanted!

The first Euro Maker Faire in Brussels was an evening event but now with the first UK Maker Faire makers have a chance to hang around for 2 days and develop or deepen their DIY skills similar to the original US events (we enjoyed Austin Maker Faire in 2007). Let me know if you’re interested.

from my mailbox:

We are shortly to publicly announce the first UK Maker Faire but thought you would appreciate advanced notification.
The Make team forwarded me your names and email addresses as they believe you might be interested in the Newcastle upon Tyne Maker Fair on March 14th-15th 2009.

The first UK Maker Fair will take place in Newcastle 14-15 March as part
of Newcastle ScienceFest – a 10 day festival celebrating creativity and
innovation.

This two-day, family-friendly event celebrates the Do-It-Yourself (DIY) mindset and features interactive exhibits organized by individual enthusiasts, hobbyist groups and clubs as well as student groups. It’s for creative, resourceful folks who like to tinker and love to make things. Maker Faire is an opportunity to share what you do with others. Continue reading

Low budget, high tech: Microfluidics device out of a $50 plotter!

7550AplotterBuilding and using low budget but high tech devicesplotterink at home is a main motivation behind hacking. A Harvard Chemistry Research Group now created a microchannel producing device using a Hewlett Packard 7550A Graphics Plotter (see some eBay prices) to perform a diagnostic protein assay with it amongst others. /See my SciFoo microfluidics coverage./

According to the current Nature by Tim Lincoln:

“The system works like this. By replica moulding, the pens of the plotter are replaced with PDMS versions that can deliver various types of ‘ink’. The purpose of the ink, when cured, is to create channels in a filter-paper substrate, and after experimenting with the possibilities Bruzewicz et al. found that a syrupy mixture of 3:1 PDMS:hexane did just fine. Having chosen the appropriate paper, the trick then is to use the plotter to draw channel shapes, with the PDMS syrup penetrating the full depth of the paper to create water-tight chambers in various patterns.”

Hardware-Software Specs from the supporting information:

Computer.
• Computer: Dell Dimension 4100, Pentium III Processor (1 GHz)
• Plotter: Hewlett Packard 7550A Graphics Plotter
• Operating System: OpenSuSE Linux 10.1, Novell Corporation. Available for free download
• Additional Software:
1. Inkscape – vector drawing program, for design of channels. Included in OpenSuSE, also
available for free.

The HP Computer Museum highlights this particular plotter: Continue reading

Biotech DIY for aging/life extension research: the double future?

“The best way to predict the future is to invent it.” – said Alan Kay, computer legend in 1971.

Recently I had a comment dialogue with Chris on whether state-supported research or industrial business enterprises can (or should) lead to big progress in robust and healthy life extension technologies. Besides the government and corporation coin the research breakthrough could come from an aging focused foundation like the non-profit Methuselah Foundation behind the SENS approach, which supports research projects (like MitoSENS and LysoSENS) and scientists (like Mark and John) through cooperation with university labs. And finally, there is going to be another option to contribute:

agingbioDIYtoast

Imagine the following future scenario: biotech DIY is becoming an accepted home activity so geeks are setting up private labs and conduct basic in vitro (but not in vivo) research. Continue reading

First DIY RFID experience: Arduino controlled Parallax reader

RFIDParallaxArduinoiBookIn the last couple of weeks I became heavily interested in RFID (Radio Frequency Identification) technology probably because the dangerous idea of all pervasive computing and the opportunities to build sg from the bottom-up. So here is a how-to to my first installed low frequency, read-only RFID system hopefully followed by a more juicy stuff in the ultra high frequency range up to 9 meters.

Hardware:

Parallax RFID reader with 2 tags ($49.99+shipping, Radio Shack)

9-Position Female Crimp D-Sub Connector($1.99, Radio Shack)

4 hook-up wires

Arduino Diecimila microcontroller ($34.99)

Macbook, iBook

Software, code:

Code in C programming language for using the Arduino with the Parallax RFID reader but in order to upload it to the Arduino board and make it actually work I had to put the reader activator line:

 digitalWrite(2, LOW);                  // Activate the RFID reader

into the

 void loop()

function just like in the the sample Wiring tutorial

Arduino software: different packages for Intel based Macbook and PPC iBook

Here is a screenshot on the Serial Monitor reading the tags on iBook: Continue reading