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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

December 12, 2009

Jonathan Cline

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 for this phase)

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:

Read more

diybio graphics

December 11, 2009


Last week I hired Micah & Caroline from to design an extensible diybio logo and related illustrations. I gave them a quick intro to diybio and synthetic biology (see a lot of design notes here) and asked them to create artwork that could be used by and built apon by regional groups + related organizations (diybio-nyc, bosslab, etc.). I stressed extensibility – the final design should support remixing by all interested parties.

Micah & Caroline are about halfway done and I want to show you their work so far and solicit comments and suggestions. Above all the graphics are intended to be a community resource, so they need to be built with community feedback.

They have worked on two things: an extensible diybio logo and diybio themed icons.


Micah & Caroline modified a typeface called “the mix” for the diybio logo to make it look hand-cut. When they are done they will provide the typeface for the community so that any group name can be written with it. As you can see, their current idea has been to cut out illustrations from the “golden days” of amateur science in the pattern of the typeface.

black-filled diybio text & icons

black-filled diybio text & icons

They have garnished this design with a rich wood background which I think goes far in dispelling the typical clinical, clean ethos of science imagery. But it’s also pretty “loud.”

diybio logo cut out of old science diagrams & engravings

diybio logo cut out of old science diagrams & engravings


I also asked the team to design a set of reusable icons and illustrations that represent things common to diybio activities. I wasn’t very specific.

diybio logo and icons grayscale

diybio logo and icons grayscale

What 10 icons should I ask them to design? This is really where feedback would be helpful. For instance, we could ask them to design:

A pipet; dsDNA; a microscope; a waste container; a falcon tube; e. coli; yeast; a petri dish; a generic chemical bottle; DNA sequence.

In this version they incorporated the icons into little bottle-cap pins to emphasize DIY approaches. (note: when they are finished they will provide the source illustrator files to maximize these kinds of reuse.)

diybio logo cutout of science diagrams with bottlecap logos

diybio logo cutout of science diagrams with bottlecap logos

diybio logo variations

diybio logo variations


Please please please mail your feedback to this thread on the diybio google group or in the comments below. In particular, consider these two questions:

  • what 10 icons should be designed?
  • what graphical concepts should comprise the diybio logo?

Go check out my notes for my thoughts. I hope the artwork will be a graphical synthesis of (playfulness + art + DIY) + (science + engineering + biotechnology).

(I’m still thinking about a retro-arcade-game theme…)

Also see these other handy links:

I’ll include my feedback in the comments with everyone else.

All this stuff is licensed CC-BY.

Bryan Bishop presents at and reports from H+ Summit 2009

December 10, 2009


Here I go. Start off with something like “Bryan got to speak at H+ Summit 2009 and spotted some neat numbers.” Maybe this will end up in GBM or H+ magazine as a small blurb?

hplus.eventbriteBryan Bishop presented at the 2009 H+ Summit onopen source hardware and took copious notes. Here he presents some of his favorites:

Patri Friedman. Meeting him in person is like meeting with a living legend. Hell, he wrote the book on seasteading. His talk was short and to the point: let’s make startups for governments and ways of organizing people. You know how everyone says let a thousand flowers bloom? Same thing going on here, except he’s serious about it. The Seasteading Institute is a 501c3 non-profit organization dedicated to living on the high seas and promoting a diversity of ways of living and organizing groups of people. At the end of the talk he gave a shout-out to the DIY scene: 12 miles off the coast, there is no FDA. The talk was recorded and is somewhere here, and here’s the transcript. I didn’t catch the Q&A because I was up next! What a talk to follow.

Todd Huffman also talked (transcript). Todd organized BIL, the simple and free alternative to TEDtalks. Todd spoke about whole brain emulation and his startup, 3Scan. He showed some really amazing videos collected from his team back at TAMU running off of a knife-edge microscope. His plan is to slice and dice brain tissue so as to scan in details all the way down to mitochondrial positions in order to parameterize and seed emulations and simulations of brains.

Gregory Benford (transcript) also showed up and talked about personal genomics, or what he calls “nutrigenomics”. It turns out that he bought the original Methuselah flies. The Methuselah flies were super-longevity flies living well beyond average lifespans. With these flies he sequenced their genome and found particular up-promoted and down-regulated genes that might be causing the flies to live longer. The idea is to then synthesize custom pharmaceuticals that enable and disable gene regulation for different (but targeted) genes in the human body. Greg is really amazing in person, although maybe that’s just me being a fanboy for his scifi after all these years? At some point you go “wtf, I’m having a one-on-one with Gregory Benford!” (He was also at the Singularity Summit earlier this year.)

You should also check out Anselm Levskaya‘s talk on brain input/output projects, Dylan Morris, and Christine Peterson had some good suggestions for not dying.

And one final plug- there’s no transcript for me because I was presenting (!) on open source hardware (1, 2, 3).

h+ magazine: diybio movement takes on aging

December 9, 2009


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

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 (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.

diybio-boston meetup at Sprout 22 Nov 09

December 2, 2009


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

Introducing FutureLabCamp 2010

November 21, 2009

Jason Bobe

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

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

November 19, 2009


BOSSLab logo

The Boston Open Source Science Lab (

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 at

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 ( 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:

You can get directions to Sprout here:

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


iGEM 09 Jamboree DIYbio meetup recap

November 18, 2009


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 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 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 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.

The Bigger Picture: Domesticating Biotechnology

November 17, 2009


Scientific American Oct 1953 - Evolution in Bacteria

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.

Crafting the Biological

November 11, 2009



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)

An iPhone Microscope

November 8, 2009


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.

A close up look at my tshirt

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

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

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

The new DIYbio Forums!

October 5, 2009


Want to chat with other members of the DIYbio community? Come check out the DIYbio Forums!


Come talk about your latest project!

Come talk about your latest project!

  • Getting Started – What is DIYbio? What should be my first experiment?
  • General – News, speeches, and other talk!
  • Ongoing Projects – Let’s hear about your projects and results
  • Safety – Where to get and give advice for responsible and safe practice
  • Regional Groups – DIYbio SF, Boston, Seattle, New York!

To get started, just register, upload a smiling picture, and introduce yourself!

For those of you who tweet, link your Twitter feed to your profile under “Account/Personal Information

And, for you RSS junkies out there, the DIYbio Forums have an RSS feed here

As always, if you have any questions the DIYbio team is just a click away:

DIYbio New York: DNA Extraction Party

September 24, 2009


The DIYbio New York group had a “DNA Extraction Party” at ConfluxCity 2009. What’s that?

Check it out at the DIYbio NYC blog

A perfect day for making DNA in NYC


Bill & Melinda Gates Foundation Grand Challenges Explorations Round 4

September 4, 2009

Jonathan Cline

The Bill & Melinda Gates Foundation is now accepting grant proposals for Round 4 of Grand Challenges Explorations, a US$100 million initiative to encourage unconventional global health solutions. Anyone can apply, regardless of education or experience level.

Grant proposals are being accepted online at until November 2nd 2009.

A Quick Guide to Teaching R Programming to Computational Biology Students

September 4, 2009

Jonathan Cline

A great article in the recent PLoS Computational Biology – freely accessible to all!  Additionally, check out: OpenWetWare’s topic on “R”.

A Quick Guide to Teaching R Programming to Computational Biology Students

by Stephen J. Eglen*, Cambridge Computational Biology Institute, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom

The name “R” refers to the computational environment initially created by Robert Gentleman and 1 Robert Ihaka, similar in nature to the “S” statistical environment developed at Bell Laboratories ( [1]. It has since been developed and maintained by a strong team of core developers (R-core), who are renowned researchers in computational disciplines. R has gained wide acceptance as a reliable and powerful modern computational environment for statistical computing and visualisation, and is now used in many areas of scientific computation. R is free software, released under the GNU General Public License; this means anyone can see all its source code, and there are no restrictive, costly licensing arrangements. One of the main reasons that computational biologists use R is the Bioconductor project (, which is a set of packages for R to analyse genomic data. These packages have, in many cases, been provided by researchers to complement descriptions of algorithms in journal articles. Many computational biologists regard R and Bioconductor as fundamental tools for their research. R is a modern, functional programming language that allows for rapid development of ideas, together with object-oriented features for rigorous software development. The rich set of inbuilt functions makes it ideal for high-volume analysis or statistical simulations, and the packaging system means that code provided by others can easily be shared. Finally, it generates high-quality graphical output so that all stages of a study, from modelling/analysis to publication, can be undertaken within R. For detailed discussion of the merits of R in computational biology, see [2].

A Mention of DIYBio in the Commercial Development of Synthetic Biology

July 20, 2009

Jonathan Cline

The following is a cross-post from the 88 Proof Synth Bio Blog.

BIO hosted a round-table discussion with leading-edge companies on technical and commercial advances in applications of synthetic biology. Speakers in the session represent leading firms in the field, Amyris, BioBricks Foundation, Verdezyne and Codexis.”

This industry-centric conference call prominently mentioned “hobbyists doing Synthetic Biology in their garages.” The Progress in Commercial Development of Synthetic Biology Applications podcast can be listened to at this link.

BIO is a biotechnology advocacy, business development and communications service organization for research and development companies in the health care, agricultural, industrial and environmental industries, including state and regional biotech associations.

Below are my notes and summary from the conference call. (Disclaimer: all quotes should be taken as terse paraphrases and see the official transcript, if any, for direct quotes.)


“BIO sees synthetic biology as natural progression of what we’ve been doing all along [previous biology and biotech commercial research]. […] Industrial biotechnology gives us tools to selectively add genes to microbes, to allow us to engineer those microbes for the purposes of [biofuels] or production of other useful products. Synthetic biology is another tool which allows us to do this, and is an evolutionary technology, not a revolutionary technology. It grows out of what our companies have always been doing with metabolic shuffling or gene shuffling, etc. [Synthetic biology] has become so efficient that new ways of thinking about this field are necessary. We are beginning to build custom genomes from the ground up, a logical extension of the technologies [biotech companies] have developed. […] “

Industrial biotechnology’s phases:

1. Agriculture (previous phase)
2. Heathcare (previous phase)
3. and today’s phase: biofuel production, food [enrichment], environmental cleanup

Challenges in today’s world are: energy and environment (greenhouse gases, manufacturing processes, … how to also develop these in the developing world); Synthetic biology can help to address these problems.

“Every year the development times [of modifying organisms for specific tasks] are shortened [due to availability of more genomic information].”

“There is unpredictability in synthetic biology [however] this is still very manageable.”

This comment was a response to a ‘fluffy’ question about the ‘risks/dangers’ of the technology.

“[This technology is accessible because as we have heard in the news] there are now home hobbyists experimenting with this in their garage laboratories.”

Hmm; I wonder who they are talking about..


“We have been moving genes around for quite a while. [The difference today which yields Synthetic Biology is that] we can do things easily, rapidly and at small [measurement] scale.” Synthetic biology allows scientists to integrate all the useful [genomic, bioinformatics] data into a usable product [much more rapidly than before]. Previously it would take months to modify a microorganism, now we are down to 2-3 weeks [which is] limited only by the time required for yeast to grow [and we aren’t looking to speed that part up]; this is a rapid increase in the ability to test ideas and [measure] outputs. We view synthetic biology as very predictable [in the sense that un-intended consequences are inherently reduced]. We engineer microorganisms to grow in a [synthetic environment for fermination in a ] steel tank which reduces it’s ability to grow in a natural environment [thus] the organism loses out against environmental yeast [so modified organisms won’t cause problems in the environment since they will die]. We need more people who can understand complete pathways, complete metabolisms.”


“Synthetic Biology is a toolset to create renewable fuels and chemicals. […] The benefits of Synthetic biology are, 1. profitability, as sugar is a lower cost of carbon; 2. efficiency, from use of [standard high efficiency] fermentation processes; 3. from efficiency improvements, this improves margin, 4. decreased capital costs; 5. Use of bio-economy, using local crops [for biomass] or local photosynthetic energy to yield [chemicals for local use]. Now we can explore entire pathways in microorganisms [compared to previously when we could only look at single genes]. Traditionally, chemical engineering is the addition of chemicals to create a functionality [whereas in microbial engineering the microorganism directly creates the outputs desired]. We retooled for synthetic biology very easily [from originally building chemical engineering systems].”


“Biocatalysts [are] enzymes or microbes with novel properties [for commercial use]. Green alternatives to classic manufacturing routes. Biocatalysts require fewer steps and fewer harmful chemicals. Synthetic biology is one tool towards this [to] quickly create genes and pathways [using the massive amounts of genomic information now available]. [Use of] Public [genome] databases [allow us to] chop months off the [R&D] timeline. [One desire] of scientists in synthetic biology is making the microorganisms [predictable, as in in engineering] however in commercial environments we can make variants very quickly [so we can deal with variants]. There are many companies which focus on commodification of biological synthesis and we use a variety of suppliers. The analysis [the R&D] required for designing new pathways is [what is lacking in skillsets of today’s biologists].”

Drew Endy:

Patents costs are drastically more than the cost of the technology itself. The technology of the iGEM competition costs $3-4 million per year for all international teams, whereas the costs of patenting all submitted Biobricks every year would be 25k per part for 1,500 parts for a total of over $37 million dollars; thus, the patent costs are much more expensive than the technology, so this is an area which is being worked on. The next generation of biotech is hoped to “run” on an open “operating system” made from an open foundation [where new researchers can use existing genetic parts as open technology rather than having to build everything from scratch].

(For my further editorial, go to the full post at 88 Proof Synth Bio Blog.)

There you have it. Synthetic biology is the leaner, meaner biotech for the future.

DIYbio at Maker Faire this weekend in San Mateo, CA

May 28, 2009


Want to see a gel box in action or extract DNA from your saliva? Come by the DIYbio booth at Maker Faire this weekend. DIYbio SF is in the main Expo Hall on Saturday and Sunday, ready to spark your imagination!300x250
I’ll also be giving a talk on  gasoline made from sugar cane, houses grown from trees, and chairs made of ivory — from 3:00 pm to 4:00 pm on Saturday, Stage B at the Maker Faire. Interested? Come on by!
DIYbio In Action!
Saturday + Sunday (May 30 and 31)
San Mateo County Expo Center

DIYbio Presentation
Tito Jankowski
3:00 – 4:00 pm Saturday
Stage B, Maker Faire

If you’ve seen our booth at Maker Faire — sign up for our mailing list at Google Groups – DIYbio SF
Also check out another Maker Faire group — they build remote control replicas of WWII submarines, arm them with BB gun cannons powered by CO2, and battle until only one floats the winner!

DIYbio Salon at Noisebridge

May 3, 2009


We held the first DIYbio Salon this past Saturday at Noisebridge in San Francisco.


Glofish fluoresce -- green, red, and orange!

Among other topics, we chatted a lot about Glofish — the genetically modified zebrafish that fluoresce under blue light. Some of us are aquarium-lovers and others are molecular biology-lovers, so we wondered out loud about everything from how to best display glofish to the low level molecular biology that goes into creating modified zebrafish.

We also got into other cool topics about interfacing computers and biology. Rachel from the Cyborg group at Noisebridge described “eyes on the back of your head” — a motion sensing jacket she’s working on. Here’s a great article from Wired about “adding senses”.

I’ve uploaded the slides from the “Intro to DIYbio segment” to scribd. The focus was on the software, wetware, and hardware in DIYbio — and how projects like Arduino allow computers to interact with the real world: DIYbio Salon  (Powerpoint)

If you have any questions, or would like to attend the next DIYbio Salon, let me know. Thanks to everyone at Noisebridge for providing space for the DIYbio Salon to get started!


DIYbio Boston at Cambridge Science Festival this Saturday

April 21, 2009

Jason Bobe

Doing the infamous dna extraction

Doing the infamous dna extraction

If you’re in the Boston area, drop by the Cambridge Science Festival between noon and 4:00pm this Saturday, April 25, to visit the DIYbio table! We’ll be in the tent at the opening Science Carnival – see the Cambridge Science Festival’s schedule for details.

DIYbio interview on Food Chain Weekly Radio

April 18, 2009

Jason Bobe

Mac Cowell, Sandra Porter, and Meredith Patterson (who wrote her thoughts on the show) were in a fascinating discussion about DIYbio on the Food Chain weekly radio program with Michael Olson this morning. The audio will be available to download soon.

iGEM Closes Doors to Amateurs

April 10, 2009


How can amateurs participate in iGEM? -

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 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.


April 8, 2009


diybio faq at

diybio faq at

Bryan Bishop has herioically created a DIYbio FAQ (three cheers!).  In the interest of neutrality, I copied his latest version to OpenWetWare/wiki/DIYbio/FAQ today and I encourage everyone to edit that version mercilessly.  Otherwise Bryan will become the official keeper of the holy DIYbio FAQ flame and the canonical version will reside at – this may be a fine solution for now.

The FAQ contains information on Getting Started with DIYbio, local DIYbio groups, Synthetic Biology, iGEM, videos, Keiki gels, and MiniFAQs on DNA synthesis and microfluidics.  Obvious content to expand are the sections on social and legal issues, basic wetlab equipment, lab services available to amateur biologists, and current projects in the community.

DIYbio San Francisco – Glow in the Dark 1

April 2, 2009



Step 1. Planning our experiment

The pressure cooker shot out steam, like an enormous teapot. At over 200˚F, steam had just sterilized our liquid agar, the favorite food of growing cells.

We’re on our way to make glowing cells with the Carolina Sciences “Green Gene Colony Transformation Kit” (aka E. Coli K-12 + a GFP plasmid). This first step for DIYbio SF was a long time in the making!


Step 2: Josh measures and mixes LB agar

At the beginning of March, Praveen and Marnia began working with Noisebridge, a local hackerspace, to put together a Lab Safety and Ethics page. Tim ordered the Carolina kit and stored it at his apartment. Micah offered to donate a fridge, Meredith volunteered her pressure cooker , and Marnia brought a digital scale.

This past weekend, 5 DIYbiologists met at Noisebridge in the Mission district: Marnia, Josh, Tim, Micah, and myself, Tito.


Step 3: Marnia turns on the pressure cooker

We started the session by cleaning out a fridge donated by Micah and talking through the safety aspects of our tools and materials. We agreed that any broken glassware would need to be cleaned up immediately and Marnia showed us how the pressure cooker worked.

To the right, you can see the 4 steps that we took in order to make our plates. Marnia will be seeding the E. Coli K-12 on these plates and we will be adding our GFP DNA plasmid to these cells during our next session.

We will be completing this kit over 3 “Glow in the Dark” sessions:


Step 4: Pour and refrigerate agar plates

1. Making Agar Plates
2. Growing glowing GFP cells
3. Visualizing DNA with Electrophoresis

Kit: Carolina Green Gene Colony Transformation ($49)

Materials used:
Petri dishes
LB Agar

Equipment used:
Pressure Cooker

DIYbio is a new and exciting topic — as a community we focus on making science safe and approachable by understanding our materials, following safe practices, and tackling tough issues like public perception. As well, remember these important areas outside of the science itself, especially when working in someone else’s space: schedule space with the owner, get everything approved, and say many “thanks” afterwards!

Thank you to Noisebridge for hosting us as we boot-up DIYbio SF!

Our project was accepted for the MAKE Magazine “Maker Faire — we’ll be showing off our cells from May 29-May 31st in San Jose, California!

This week in DIYbio!

March 26, 2009


Microfluidics, a competition for free sequencing, an abundance of ideas for cheap lab equipment both second-hand and DIY, and thoughtful discussions on the current state of public perception and the future of regulation have made for quite an interesting week in DIYbio.


Bryan Bishop and others experiment with Sharpies and glass slides for making DIY microfluidics.

Why not sequence a genome? Sandra Porter suggests the idea and and Jason Bobe shares a writeup on a likely partner for this, Cofactor Genomics. No sooner does Jason suggest raising funds, and pledges $100 to kick-start the idea, than Tito Jankowski mentions the fact that Cofactor is running a contest for a free ~700Mb sequencing project for education. Follow along on the “Why not sequence a genome?” thread.


Lots of people ask about the best way to get started with a DIY lab setup for doing amateur biology. It turns out that now is a great time to shop for your lab on eBay! Aaron Hicks shares his experience on in the “DIY Lab Setup” discussion thread.

Dan Heidel posts a review of a nice (and affordable) $100 pipetter set.

Cheap CCDs might enable building spectrophotometers and using dynamic light-scattering to probe the sizes of molecules in a solution in the “DIY biophysical setups?” thread.

Regulation and perception

An article from GenomeWeb gets us thinking about the perception by the public and the larger scientific establishment. A prolific discussion ensues.

Bryan Bishop brings up a new report out of U. Virginia “New Life, Old Bottles: Regulating First Generation Products of Synthetic Biology“, with video.

Extract DNA from Strawberries

March 20, 2009


Yummy strawberries

Yummy strawberries have lots of DNA

Syndicated from “Do-it-yourself Strawberry DNA”

Strawberries, bacteria, humans—all living things have genes, and all of these genes are made of DNA. That’s why scientists can take a gene from one living thing and put it into another. For example, they can put human genes into bacteria to make new medicines.

How do scientists take DNA out of a living thing? It’s not that hard—there are lots of ways to do it! You can follow the directions in the video below to get DNA out of a strawberry. Or you can follow the steps after that. Either way you’ll have strawberry DNA at the end!

What you need:

  • measuring cup
  • measuring spoons
  • rubbing alcohol
  • 1/2 teaspoon salt
  • 1/3 cup water
  • 1 tablespoon Dawn dishwashing detergent
  • glass or small bowl
  • cheesecloth
  • funnel
  • tall drinking glass
  • 3 strawberries (green tops removed)
  • reclosable plastic sandwich bags
  • test tube or small glass jar (like the kind spices come in)
  • bamboo skewer or kabob sticks  (find them at the grocery store)

What to do:

  1. Chill the rubbing alcohol in the freezer. (You’ll need it later.)
  2. Mix the salt, water, and Dawn detergent in a glass or small bowl. Set the mixture aside. This is your extraction liquid.
  3. Line the funnel with the cheesecloth, and put the funnel’s tube into the glass.
  4. Put the strawberries in the plastic bag and push out all the extra air. Seal it tightly.
  5. With your fingers, squeeze and smash the strawberry mixture for 2 minutes.
  6. Add 3 tablespoons of the extraction liquid you made in Step 2 to the strawberries in the bag. Push out all the extra air and reseal the bag.
  7. Squeeze the strawberry mixture with your fingers for 1 minute.
  8. Pour the strawberry mixture from the bag into the funnel. Let it drip into the glass until there is no liquid left in the funnel.
  9. Throw away the cheesecloth and the strawberry pulp inside. Pour the contents of the glass into the test tube or small glass jar so it is 1/4 full.
  10. Tilt the test tube or jar and very slowly pour the cold rubbing alcohol down the side. The alcohol should form a layer on top of the strawberry liquid. (Don’t let the alcohol and strawberry liquid mix. The DNA collects between the two layers!)
  11. Dip the bamboo skewer into the test tube where the alcohol and strawberry layers meet. Pull up the skewer. The whitish, stringy stuff is DNA containing strawberry genes!

You can try these steps to purify DNA from lots of other living things. Grab some oatmeal or kiwis from the kitchen and try it again! Which foods give you the most DNA?

Here is a link to troubleshooting tips and FAQ list from the “Extract DNA from Anything Living” experiment: 20 Most Frequently Asked Questions

This Week in DIYbio – Match 15, 2009 Edition

March 15, 2009

Jason Bobe

Howdy DIYbioers! Thanks for stopping by. Here are a few highlights from the past week:

Discussions and happenings this week

DIYbio in the Big Apple – The NYC DIYbio group had a meetup on March 9th, and has started a blog and YouTube channel.

Basics of gel electrophoresis – Dan Heidel gives an excellent and readable rundown of the basics of gel electrophoresis.

Biology forums – Ellen Jorgensen and Bryan Bishop shared a set of forums where anyone can ask technical questions about their work. Ellen recommended the (very active) forums from Biotechniques magazine, and Bryan shared a comprehensive list of other related forums.

Citizen science for climate and plants – Cory Tobin shared a call for citizen scientists from the Nature Climate Feedback blog, which may be of interest to some DIYbio scientists, along with a podcast from the US Geological Survey about the program.

Do your biology in space – Jonathan Cline mentioned CubeSat, a platform for 10 cm^3, 1 kg satellite projects, and included links to design specifications as well as information about a developer meetup in April.

Projects for the Amateur Scientist – Jason Morrison shared a link to a PDF of C.L. Stong’s Projects for the Amateur Scientist (1960), which contains several very approachable amateur biology protocols.

Get your DIYbio any way you like it!

The DIYbio mailing list is a great resource and full of vibrant discussion, but sometimes it’s a bit much to handle. Luckily, you can edit your subscription settings and elect to receive only daily digests, or turn off email entirely and catch up on discussion at your own pace by reading the DIYbio mailing list online.

As an alternative, you can subscribe to the very low-traffic DIYbio Announce list, which has less than five messages per week.

Lastly, for those of you on Twitter, come follow DIYbio on Twitter! We’ll tweet interesting information, letting you know about big DIYbio publications, news, and events.

So, until next week, keep experimenting, keep safe, and keep sharing your science!
— Jason M.

DIYbio in 4 minutes – O’Reilly Ignite Boston 5

March 5, 2009


I gave another lightning talk about DIYbio at Ignite Boston 5 in February 09.
The DIYbio Community – Presented at Ignite Boston 5 (2009) from mac cowell on Vimeo.

We founded, a community for amateur scientists, last year in May, just in time to present at ignite boston 2008. Since then, the community has grown. In this talk, I spend 5 minutes giving a lighting overview of the community and the current hot projects members are working on: new, cheap, diy-hardware, distributed science experiments (think flashmobs for science), a biohacking coworking space, and some molecular biology experiments (including making genetically engineered fluorescent yogurt, a melamine biosensor, and a biological counter).

Two Weeks in DIYbio

February 27, 2009

Jason Bobe

Howdy, DIYbio! Here are some great threads that have sprung up in the last two weeks. Do discuss!

SageBase – Sean Zuzu mentioned that Merck just pledged a ton of high-resolution, very expensive data to the public domain, along with some software and other resources to make it work.

Legislation – Daniel Crookston posited that DIYbio is eventually going to face government regulation, and that we should consider the shape of self-regulation. Drew Souza, who “is involved in the federal government’s current efforts to address the risks posed by synthetic biology,” weighs in.

DIY competent cells – Sgt. York proposes DIY protocols for making competent cells, and many folks join in. There’s also a discussion of winning cheap electroporators on eBay.

What are Minipreps, anyway? Cory Tobin and Dan Heidel discourse on a variety of methods for purifying plasmid dna, including “salting out” with ethanol precipitation, chloroform precipitation, and CsCl ultracentrifugation.

DIYbio and Syn Bio software – Jason Morrison asks what kinds of software people would like to see or are currently working on. An open-source alternative to VectorNTI seems to be a popular want. Clotho is a great start, and a project that people should contribute to. Clotho has been described as A Plasmid Editor” for BioBricks.

Lego tube shaker – Douglas Ridgway shares a Lego tube shaker that his son built, and Andrew Hessel and Bryan Bishop chip in with suggestions for furthering the prototype and a DIYbio Kids group and Saturday morning show.

Well, that’s it for DIYbio – if you’re up for cooking up a batch of Ultimate Breakfast Sausage or Chocolate Enchiladas, you should check out this week’s MAKE Blog “Weekend Builder” email in my inbox. But if you’re up for cooking up a batch of RFP or gel boxes, let us DIYbioers know!

This week in DIYbio

February 17, 2009


This week: Gel electrophoresis in a straw

This week: Gel electrophoresis in a straw


Hi everyone — Thoughts and discussions took a backseat to projects and results. This week we had everything from starting DIY iGEM Teams to sharing results of straw electrophoresis. Check it out!


Links and Discussion:

  • Defining and shaping DIYbio culture (Security, Safety, and Responsibility) is discussed by Roger Brent and others (thread)
  • Do-it-yourself PCR by Scientific American is brought to attention by Reshma Shetty (thread)
  • Can ‘open peer review’ work for biologists? Jason Morrison and others discuss an article from Nature (thread)
  • Flu biology: Lora wonders if we can sequence different strains of flu (thread)

iGEM opens registration to DIYbio and more

February 9, 2009


UPDATE 10 April 2009: iGEM Closes Doors to Amateurs

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

iGEM 2008 at the Jamboree

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:

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

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