• 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.

Then you pull out your iPhone, magnify the sample 100 x and snag a photo. Doesn’t look like anything familiar but…

Maybe #diybio on Twitter would know?

“#diybio, I’m at the salt flats outside San Francisco. Any idea if I’m looking at something like red tide, or is this just algae?” – DIYbioGuy, N 37^o 50′ 55.5” – W 121^o 55′ 53.0”

Fellow citizen scientists take interest…

“@DIYbioGuy — Those algae look active, and wow look at the chambers on that Foraminifera! It looks like it may be ornamenting itself. #diybio” – wreinhardt

Make this happen — a portable, web-enabled 100x microscope that plugs into an iPhone. The purpose of this article is to document my attempt. To be sure, I had an idea and I tried it out. I did not refine the idea or do very much planning. In place of refining the idea, I used lots of tape. I also didn’t get very far.

Cellscope demo at Critter Salon (SF)

Inspiration: A few weeks ago at the CRITTER Salon in downtown San Francisco, I talked with Amy from UC Berkley about a project called “CellScope“.  Their mission — diagnosing diseases in remote areas by hooking a simple microscope up to a cell phone. Snag an image, and send it off to some professions for diagnosis of sickle cell and TB, and other diseases.

I love the idea, I dislike squinting into microscopes (and maybe you do to?). Though I won’t be diagnosing diseases, a portable, web-enabled microscope would be very useful. Extending this project to connect to an iPhone seemed like the obvious choice, so I gave it a shot.

Day 1 – I bought a RadioShack pocket scope tonight. Lining up the microscope with my iPhone while trying to focus was a disaster. I needed to mount the microscope to something flat.

Using the packaging, a whole bunch of tape, and a butter knife for stability, I mounted the microscope to the cardboard. Then I got the microscope to line up with my iPhone’s camera – and snagged this picture of a quarter. It’s pretty tedious to get the scope aligned with the camera, so I called it a night after nabbing a cool picture of the threads from the green Foo Camp shirt I was wearing.

My t-shirt through the Radioshack pocket scope + iPhone

Day 2 – When I returned home after work, I was inspired to make a more permanent mount that wouldn’t go out of alignment as easy. I had a package of moldable plastic beads lying around from Maker Fair. The beads melt in boiling water, forming a big malleable blob. You mold the blob to whatever shape you desire and when it cools, it’s hard plastic. This stuff was great, and you can re-heat and reform it too. After my first attempt at molding a mount, I discovered the problem wasn’t just the mounting. The precise alignment needed between the scope and the phone was too much, I estimate about 1/16″ difference would cause the image on the microscope to move outside of the iPhone’s sight.

Stabilizing the pocket scope

Over the next few days, I attempted to enlarge  the image using eyeglasses from a Dollar store, and other types of magnifying lenses, none of which helped. At this point, I had a good understanding for the challenges ahead. I wrote Amy back to see what a copy of the Cellscope would cost, but the parts she suggested were about $300. I decided to let the project settle and moved on to something else. Then I met the Hackteria team…

Turning a $20 webcam into a 200x USB microscope

At the DIYbio + iGEM meeting last week at MIT, a team from Hackteria (Bangalore) showed us how it’s done. Mac brought a $20 USB webcam to the meeting for us to hack. Basically just unscrew the case, flip the little lens around, and there you have it, a 200x USB microscope. Of course, focusing is still a manual process and somewhat tricky.

Above: A video from Hackteria’s USB webcam project

Summary: Overall, I went through a lot of crummy ideas to get to some ok ones. Many of my best “discoveries” were simply stumbling upon the great work of others, like the Cellscope and Hackteria! Turning a USB webcam into a microscope is great for innovation in low cost labs. The next step is mobility – hooking one of these up to an iPhone, either through the USB port or just relying on the built in camera. Check out the Hackteria blogpost, here.

Challenges: A portable iPhone microscope

1. Low cost magnification  – solved

• USB webcam or Manual pocket scope

1. Digitizing and recording images — getting there

• Standard desktop software for USB webcam
• unknown for pocketscope + iPhone

1. Connecting a USB webcam to an iPhone  – ??

2. Obtaining and positioning the sample — ??

• This is the most challenging part of the project. How would you use an iPhone microscope? Do you want to keep it in your pocket? If you want to look at a leaf, how do you hold the scope + sample so that they stay in focus? Do you need to keep slides with you as well, in order to quickly mount your sample?

After reading this, you might get the initiative to try building something of your own. Go for it! Fail fast. Fail frequently!

I’ve started a discussion in the DIYbio Forums, and would love to hear about your thoughts, ideas, and progress!

– Tito Jankowski is a founder of Pearl Biotech. His interests include building better hardware for biology.

Sources – Hackteria: DIY USB microscope Instructables: 30 minute USB microscope Critter Salon CellScope

How can amateurs participate in iGEM? -

Several weeks ago the Director of iGEM (my old boss) asked me to drop by to chat. He basically told me iGEM wasn’t going to allow amateur teams for 2009, despite earlier statements to the contrary, for two reasons:

1. iGEM depends on the academic institution of each team to provide a safety framework for that team. Because there is no formal safety framework or guidelines or precedent for amateur teams working outside of traditional labs, iGEM is afraid of the potential safety liability and doesn’t want amateur teams to participate until there is some kind of framework (2010!).

2. Most of iGEM’s funding comes from grants to support undergraduate education. A host of amateurs who are not undergraduates would be supported by grants for undergraduate education, which could be a situation the grantors wouldn’t like. Randy didn’t want to take that risk.

Randy also said iGEM would clarify the situation by making a press release regarding these changes, or at least describe them in an organizational email to the iGEM-interest email list. That didn’t happen. So in the meantime, I’ve been verbally explaining the situation to groups of people I think may be starting iGEM teams.

There is some good news: if you want to participate in iGEM in an amateur capacity, you can still do so by collaborating with a local iGEM team. This could help a lot with the fundraising for both the local diybio group and the iGEM team. DIYbio-Boston and DIYbio-NYC are both exploring collaborations with local teams.

As a community we need to start addressing the safety concerns society and the larger scientific establishment has with garage and coworking space wetlab work. I’m sure there are a multitude of opinions on how and what to do, and even what not to do. But I believe we need to organize some kind of formal statement anticipating and addressing these safety concerns, preferably with the help of objective experts. If you are interested in helping figure out how to do this, email safety@diybio.org. I’m thinking we should establish a DIYbio safety working group to be responsible for taking a leadership role on this developing real solutions.

I spoke with Randy about organizing a 1-day DIYbio symposium at the same time and place as iGEM this year (which is at MIT on the weekend of October 31). He was receptive to this idea. I think it would be very valuable to bring as much of the community together as possible to meet and discuss these issues and to present a collective snapshot of their work and projects to the world. There would be cross-pollination with many of the iGEM participants, and lastly, I’d like to use the symposium as a deadline by which some group or groups of people could formally present thoughts and work on our safety strategy to the community and to the rest of the world.

The International Genetically Engineered Machine competition (iGEM) is about 5 years old now and bigger than ever.

iGEM 2008 at the Jamboree

More than 1000 students are expected to participate in 2009 by applying the principles of synthetic biology and using a kit of standard biological parts to try and design novel biological systems.  The Registry of Standard Biological Parts (hosted by MIT) maintains a collection of the components and full systems each team creates for the competition.  After the summer, all the teams gather at the iGEM Jamboree to present their work for awards and prizes.

All in all, it’s an amazing competition generating tons of new innovation in synthetic biology.  The fixed deadline and possibility of winning prizes motivates fast, concrete results and helps teams get funding (there is a psychological shift: donors are funding a team with the prospect to win instead of basic research).

So, who wants to start an iGEM team?  Because iGEM is opening its doors to the wider community of biohackers for the first time this year with a non-institutional teams division.  I spoke with Randy Rettberg on Friday about the specifics:

• Team registration will be $500, due March 31.
• There will be an additional per-person Jamboree fee later
• All teams will have access to iGEM Partner deals ($0.20/bp synthesis from GeneArt; MatLab + simbiology toolkit)
• All teams can request parts from the Registry.  Requests will have to be approved by a Safety Committee.
• Each team will get to present their work with a 5-minute talk and a poster at the Jamboree
• The Jamboree will be Oct 31 – Nov 2.

For more information about iGEM, visit: http://igem.org

This is the first post in a series about iGEM, the Registry of Standard Biological Parts, and Synthetic Biology.