Fred Hapgood, Shawn Finney-Manchester, Marc Rogers, Laura, Keegan Cooke, John at sprout.

Keegan explains the basics of Microbial Fuel Cells

Before the meetup, Keegan said

“I’ll bring some ingredients to put in the MFCs (soil, sugar, etc.), but I think it would be fun if you told people to bring some leftovers from their refrigerator (no more than a cup of it) and we’ll see who’s leftovers the microbes like the best (i.e. who’s leftovers generate the most power).”

What food or compost products will be converted into the most power? Can’t wait to find out. Keegan took the assembled MFCs back to his workshop for measurement. It takes a week or so for the anode’s environment to become oxygen-free, at which point the electrogenic microbes from the collected soil start colonizing the anode and “breathing” their electrons onto it.

Later, I hastily assembled the latest design for the two-axis computer-controlled slide holder. It’s designed to work with webcams that have been hacked into microscopes. Here’s a video:

More photos are available on flickr: mine, yours.

See you next time!

DIYBio brand petri dishes!

We had our first DIYBio workshop in Broad Hall on the UCLA Campus over the weekend. The student community from both north and south campus were involved, which included art and science/math majors.

Romie Littrell started things off with a short presentation on the concept and history of DIYBio. His talk kicked off discussion focusing on the safety and security of biotechnology that is open to the public.

Romie (middle, blue) presents to DIYBio attendees.

Big discussion on safety and terrorism issues of biotechnology

The highlight of the workshop included an extraction of DNA from everyday food products, akin to the extraction of DNA from strawberries.

DNA from a cup of green tea!?

lysing cells through a syringe

Everyone is in awe

Looking for the nucleic acid precipitate

Homemade centrifuge

Other demos at the workshop included a sampling of a biological polymer made from cornstarch and other products found in every kitchen.  The red color and taste reminded me of Twizzlers.

Tor Nowlan and Max Belasco explain to us the elegance behind this!

DIY bio Los Angeles Workshop at UCLA! February 27th, 2010 from Kenneth Wei on Vimeo.

We had a diverse group of visitors throughout the workshop over 4 hrs.  Other than science and art professionals,  a lawyer and stay-at-home mother with toddler came to participate.

Check out our Flickr page for more pictures from this specific event.  Stay tuned for an exciting announcement in the coming weeks on the next workshop and the start of our long term project!

Rendering of ASPEX's tabletop scanning electron microscope.

You can see a gallery of some of the scans they have made on their website. My favorite sample is an old stir bar some folks from chemistry-blog.com sent in. The SEM can also use x-ray fluorescence (a byproduct of electron bombardment) from the samples for elemental composition analysis (called EDS or XFR) – in the case of the stir bar, the analysts found a microscopic chunk of Chromium stuck to the surface! Leftovers from some experiments, I guess. Wow.

a microscopic chunk of a Chromium-containing compound on the surface of an old stir-bar.

They emailed us recently inviting us to take advantage of their offer. It sounds pretty cool and I’m going to mail in a sample of one of Paul Stamet’s LifeBoxes.

I CAN HAZ SEM?

I also casually asked if I could possibly borrow on of their tabletop SEMs for a couple of weeks to play with here in Boston, pretty please with sugar on top? They wrote back and said yes!

So sometime this spring they are going to drop off a demo unit for a couple of weeks and we are going to have a scanning electron microscope bonanza. Hopefully it will be so cool that ASPEX will be happy to lend the unit to other local diybio groups too.

DEETS

So to mail a sample to ASPEX, check out their online instructions, print this PDF, and mail your sample to:

ASPEX Corporation
Free Sample Submissions
175 Sheffield Dr.
Delmont, PA 15626

Do-it-yourself biology on the rise - 20 Dec 2009 - SF Chronicle (pdf)

SF Chronicle reporter Juliane Guthrie interviews Tito Jankowski, Phil Ross, Jason Bobe, and Raymond McCauley about the DIYbio projects they are working on. They also interviewed Drew Endy about safety and regulatory concerns.  The article is online at SFgate.com.

One of the article’s main thrusts is concerned with safety and regulation, or the lack thereof. I know diybio-nyc has been thinking about it and is organizing a round-table in a month or so, and I’ve been throwing a couple of ideas around with people here in boston. Maybe it’s time to set up a safety working group to synthesize the community’s thoughts on the issue with pointers to relevant resources. Is anyone doing this already (there’s some info in the faq).

Happy holidays, Mac

Shaunalynn Duffy, Alec Resnick, and David Thompson lean closer as the ucam's image comes into focus. The camera cost $10 and took 5 minutes to hack.

We hacked $10 webcams into microscopes, a la Hackteria.org at the bosslab + sprout. Yashas Shetty, Jason Bobe, Rich Pell, Myself, and others are planning a worldwide webcam hacking day on January 30th, in conjunction with the UCLA “Outlaw Bio” symposium.

@molecularist (Charlie Schick) posted a great writeup with some photos on his blog.

hello world, ucam style

@jasonbobe was the first to have a cam connected to his laptop and the lens unscrewed and inverted.

Jason testing the ucam: lens unscrewed and inverted, clipped to laptop screen, with an alligator clamp holding a microscope slide above the camera (consider vibration and focal point).

A droplet of saliva dripped onto a microscope slide held above the webcam/microscope (microcam? u-cam? ucam?) showed up as amorphous blobs: Hello World! The inverted lens resting on top of the camera chasis seemed to have a focal plane somewhere inside the lens body.  This is when we realized we should screw the lens into the chasis in reverse.

detail of Jason Bobe's laptop w/ skype; soon this ucam will be broadcasting microscopic images all across the world...

@jayunit & David Thompson built an ad-hoc microscope slide holder out of a block of insulator foam, a pencil, two black binder clips, a bolt, a nut, and a washer. By rotating the nut (or holding the nut and rotating the bolt), we could raise and lower the height of the microscope slide.

the nut on the bolt controls the height of the slide above the camera. Unscrew the lens from this particular $10 usb webcam, open the camera body, reverse the lens and screw it back through the camera body inside out, and voila, instant microscope.

I hacked together some rudimentary processing code to access the usb microscope. It seemed to be more reliable than quicktime (or skype) and I was excited about using my favorite blob-detection library on the microscope feed.

You can grab the source here: ucam.

To get the focal plane outside of the lens assembly, we unscrewed the 2 small machine screws holding the camera body together to open the camera then and screwed the camera lens back into the housing from the inside-out such that the the lens was reversed. The part of the lens that had originally been closest to the CCD was now outside the camera body. Then screwed the housing back together.

By rotating the lens and and the nut on the slide holder, we were able to intersect the focal plane of the ucam with the microscope slide. it works!

ucam hello world: looking at streetwater and blood from mac cowell on Vimeo.

12 Dec 2009 – wiki notes.

hplusmag - winter 2009 - cover "Hi there, Ray"

Parijata Mackey wrote an article for the Winter 2009 h+ magazine about diybio titled “diybio: a growing movement takes on aging.” She provides an overview of diy -hardware, -software, and -wetware, and gives shoutouts to some of the projects listed at diybio.org/projects (man we gotta develop a better system for collecting projects).  Overall she provides an overview of where diybio came from and where it’s going in an optimistic manner consistent with h+. She also provides tantalizing interview coverage with John Schloendorn concerning his DIY SENS lab and biotech co-working space in the Bay Area.

Andrew Hessel wrote another article called “Why DIY Bio” in which he explains his vision, based on open source & synthetic biology principles, for a distributed, open anti-cancer research collective. He calls it Pink Army.

UPDATE: slashdotted on 26 Jan 2010.

@molecularist blogged about the 22 Nov 09 diybio-boston meetup at sprout and recently posted a great little video of the tour. You can see us setting up Sprout and touring through the mobile lab. Read Charlie’s full post for more info.

The Boston Open Source Science Lab (BOSSlab.org)

Hey DIYbio-Boston peeps,

It’s been a while!

I’ve been making progress on getting us a lab space here in the Boston area. I’ve acquired a shipping container that has a molecular biology lab built inside of it and am spinning up an organization to take care of it. It’s called the Boston Open Source Science Lab, or the BOSSlab (cred for the awesome name goes to a brilliant volunteer at the recent iGEM Jamboree). Some basic info about it online athttp://bosslab.org.

My vision for the space is to develop it into a volunteer research center where PhDs and amateurs can work together to develop and document low-cost, low-waste “open source” tools and techniques for biotechnology and synthetic biology. 12-month goal: build and distribute one unencumbered (IP-free or freely-licensed) BioBrick under the new BioBrick Public License to the DIYbio community, preferably a device with an obvious and fun phenotype. In the process develop comprehensive and practical resources and protocols for DIY biobrick creation and use that bridge the gap between high-school and PhD-level lab instructional material. Along the way, we’ll figure out how to make it all financially sustainable with a combination of workshop tuition, membership fees, donations, and grants. We might even be able to put together some DIY kits.

For now, the BOSSlab is chilling out on a low-cost industrial lot near Fresh Pond (NorthWest Cambridge) until we can find a space for it closer to public transportation, universities, utility hookups, etc.

The fine folks at Sprout (http://sproutward.org) are coincidentally in the process of setting up a community wetlab space as well and are excited to host us until the BOSSlab is ready to open its doors.

I propose we meet up at Sprout this coming Sunday at Noon to:

• set up Sprout’s wetlab space
• review the great projects that were brought up during the iGEM Jamboree DIYbio meetup
• and finish with a tour of the BOSSLab, which is about 15 minutes away

You can get directions to Sprout here: http://thesprouts.org/contact

Check out the diybio-boston mailing list for updates and watch @bosslab on twitter.

Cheers! Mac

• Yashas Shetty wants to organize an international DIY microscope building session and subsequent videoconference for early December based on his DIY Microscope guide.  See http://hackteria.org/wiki/index.php/DIY_microscopy for instructions


• Alex Hornstein told us he had just been diagnosed with Type 1 diabetes and wanted to synthesize his own insulin, DIY-style. Would we help? Hell yes! A grad student from Harvard who had dropped in pointed out that the Registry of Standard Biological Parts already has an insulin-generating biobrick. Alex and the grad student went off to talk.This is radical self-actualized DIY theraputics. Extremely controversial.


• A variety of brave souls volunteered to start writing for the (so far, low-volume) blog at diybio.org in an attempt to amplify the signal that inevitably gets lost in the noise on the diybio mailing list and in the DIYbio ecosystem of blogs. Want to help? Email contact@diybio.org for an account.


• volunteers from each DIYbio region present (Ellen from NYC, Tito from SF, Paul from MIT & myself from Boston) thought it would be useful to describe the organizational blueprint for the local group in a central place, perhaps on the new forums, for comparisons sake and to help new groups bootstrap more intelligently and more quickly.


• Alec Nielsen, myself, Jason Bobe, David Thompson, and iGEM volunteer from MSU, and the DIYbio-NYC folks all were excited about developing a standard DIY-friendly DNA barcoding protocol. 16s rDNA sequencing of soil microbes was the initial suggestion, followed by interest in plant barcoding, in which sample collection and genome isolation may potentially be easier (using the COI gene).


• I announced the Boston Open Source Science Lab, a volunteer research center where PhDs and amateurs can work together to develop and document low-cost, low-waste “open source” tools and techniques for biotechnology and synthetic biology. 12-month goal: build and distribute one unencumbered (IP-free or freely-licensed) BioBrick under the new BioBrick Public Agreement to the DIYbio community, preferably a device with an obvious and fun phenotype.  In the process develop comprehensive and practical resources and protocols for DIY biobrick creation and use that bridge the gap between high-school and PhD-level lab instructional material.  Along the way, we’ll figure out how to make it all financially sustainable with a combination of workshop tuition, membership fees, donations, and grants.  We might even be able to put together some DIY kits.