Archive for November, 2009
Open source hardware and software, low-cost and DIY instruments, cloud computing, and the internet of things. Come build the future of scientific labs.
We are putting together a workshop called FutureLabCamp in Boston in early 2010. The focus is building the future of science laboratories with open source hardware and software, low-cost and DIY instruments, cloud computing, and the internet of things. We’re bringing together hardware hackers, HCI wizards, standards builders, and forward-thinking researchers together for an amazingly productive weekend.
It’s not a conference – it is a workshop, with an emphasis on producing useful output.
Find out all about it, and sign up to get on the mailing list, at http://futurelabcamp.org.
We believe every lab instrument should provide a data feed of its measurements and that data aggregation and storage should be effortless, automatic and routine. To that end, our goal during the workshop is to prototype new and existing feed systems for popular lab equipment (Cameron Neylon’s work, Pachube, etc) and to develop a consensus of standards and an ecosystem of projects that lay the foundation for future work. When data aggregation is effortless and routine, a rich new landscape of opportunities emerges for data visualization, micro-attribution, augmented research, better scientific reproducibility, more finely-grained and realtime collaboration, and much more.
In addition to building prototypes, we hope to run several tracks dedicated to the applications of ubiquitous laboratory sensing:
- Hardware: Building open lab instruments and hacking existing lab instruments with an eye toward data logging and automation.
- Software: Automating, augmenting, and aggregating research; from mobile to desktop to cloud.
- Data: Starting, spreading, and refining repositories, journals, micro-attribution, uber-big datasets and standards. Making science machine readable.
- HCI: Natural User interfaces to augment research; visualization techniques for exploring the increasing influx of data
As we’re still in planning stages, we’d love to get your feedback on the event. Is this something you’d find useful? What in particular should we try to build at FutureLabCamp? Let us know in the comments!
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
A bunch of interesting projects ideas were discussed at the DIYbio meetup during the iGEM Jamboree 2 weeks ago – here are my notes:
- 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.
Scientific American Oct 1953 - Evolution in Bacteria
DIYbio aims to be “the institution for the amateur,” developing and providing access to all of the resources a professional might have and an amateur might want, such as equipment, protocols, access to literature, etc. And we are collectively doing so in a distributed fashion right now.
But we are also doing something more, something that will occur slowly, over long time-scales. We are helping lay the foundations for cultural shift. We are laying the foundations for broad, deep, domestic understanding of science and technology.
We are proving that the cultural barriers to practice science in general, and biotechnology in particular, are imaginary. We are proving this by doing it ourselves. We are building a familiarity with the practice and product of science and slowly demonstrating that it can be a cultural activity like musicianship or cooking or solving sudoku puzzles. We are domesticating biotechnology.
As Sophia Roosth recently pointed out, we are proving that “the biological is not something cordoned-off in labs, but something quotidian, personal, and apprehensible,” that we are “intentionally destabilizing what it means to ‘do science’.”
Why is the domestication of biotechnology important? Listen to how W. Brian Arthur begins his recent book, The Nature of Technology:
We are attuned in the deepest parts of our being to nature, to our original surroundings and our original condition as humankind. We have a familiarity with nature, a reliance on it that comes from three million years of at-homeness with it. We trust nature.
When we happen upon a technology such as stemcell regenerative therapy, we experience hope. But we also immediately ask how natural this technology is. And so we are caught between two huge and unconscious forces: Our deepest hope as humans lies in technology; but our deepest trust lies in nature. These forces are like tectonic plates grinding inexorably into each other in one long, slow collision.
The collision is not new, but more than anything else it is defining our era. Technology is steadily creating the dominant issues and upheavals of our time. We are moving from an era where machines enhanced the natural—speeded our movements, saved our sweat, stitched our clothing—to one that brings in technologies that resemble or replace the natural—genetic engineering, artificial intelligence, medical devices implanted in our bodies. As we learn to use these technologies, we are moving from using nature to intervening directly within nature. And so the story of this century will be about the clash between what technology offers and what we feel comfortable with.
By domesticating biotechnology, we are helping society temper its natural mistrust of technology.
DIYbio is just one stone in this cultural foundation, set next to other DIY communities and Citizen Science projects and part of the broader resurgence of DIY culture championed by publications such as MAKE, President Obama, and perhaps the forebears of the internet itself.
Sophia Roosth, a doctoral student at MIT, presented a talk at The Kennedy School of Government STS seminar series on 9 Nov 2009 called “Crafting the Biological: Open-Sourcing Life Science, from Synthetic Biology to Garage Biotech.“
It’s a fantastic talk. Sophia has been engaged in non-institutional biology at least since 2003, when she worked for Natalie Jeremijenko on the singular art / activist Biotech Hobbyist Magazine, and in her talk she presents her anthropological insight into DIYbio, richly contextualizing the social causes and effects of the movement.
Sophia talks about the practice of biology in terms of Knowing and Making. For DIYbiologists, she says:
“Knowing means a personal sort of knowledge, in which quotidian biologies like human bodies or the organisms you might encounter in a produce stand, for example, may be explored and modified. And Making is less about following engineering principles than it is about tinkering and making do, which I claim [DIYbiologists] do to destabilize what counts as legitimate scientific practice.”
“Biology, Knowing, and Making, are all concepts up for grabs at this moment in the life sciences (and in this talk). If what historian Philip Pauly called the ‘engineering ideal for biology‘ unfolded in the 20th century within institutionally-sanctioned spaces, then in the 21st we are witnessing synthetic biologists and self-described biohackers recasting the bioengineering project as malleable and explicitly domestic. Think of the personal computing revolution, but for biology.”
And that’s all in the first 5 minutes! Check it out. It’s great. (mp3)
Imagine this: You’re exploring the salt ponds of San Francisco, and notice the water isn’t clear — it’s red! You dip a piece of plastic into the water to get a sample and notice lots of small little particles in the droplets.
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 37o 50′ 55.5” – W 121o 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.
http://www.viddler.com/player/20829118/
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
2. Digitizing and recording images — getting there
- Standard desktop software for USB webcam
- unknown for pocketscope + iPhone
3. Connecting a USB webcam to an iPhone – ??
4. 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
