Jacob says:

Everyone is welcome and encouraged to vote for the first DIYbio t-shirt until June 6th at midnight when the ballot will close and the winning design will be announced.

The Ballot is located at here.

For those that want to make sure they get in on the first batch pre-orders are available at a discounted $10 at etsy.com.

Here are some of the submitted designs:

p.s. the last is a design that is probably impractical to print by yours truly and was “submitted” on July 2, so it might not officially be in the running.

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!

Grant proposals are being accepted online at http://www.grandchallenges.org/explorations until November 2nd 2009.

“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:

“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:

<

p style=”padding-left: 90px;”>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..

Amyris:

“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.”

Verdezyne:

“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].”

Codexis:

“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 faq at openwetware.org

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 heybryan.org – 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.

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.

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!

Local groups outside the Boston area are sprouting up and folks are getting some quality kitchen table time, as my friend Justin calls it. DIYbio Seattleites had their first meetup, about which Sandy Porter published an excellent article, and Bay Area DIYbiologists met up in San Francisco. If you are looking to start or join a local group, add an entry to the Local Groups page.

There’s been a surge of new interest as several articles and blog posts were published. We’re more than 500 members on the mailing list, which is very exciting! I had an idea that there were hundreds (if not thousands) of enthusiastic amateur biologists out there, and it’s great to see them coming together. I’d love to see a DIYbio conference during 2009, and get to meet all you DIYbioers in person. CodeCon 2009 will be another great chance to do just this, with a new Biohack! track that is currently in open CFP.

Several projects have also sprung up and are progressing in earnest, including building a melamine biosensor, probiotics that produce vitamin C, cheap and open source biology tools, and the seeds of one or more DIYbio iGEM teams. Hardware projects have sprung up as well, with an open-source turbidostat, the Gel Box 2.0 project, and integration/UX research going on with Project SmartLab.

The BioWeatherMap project has enjoyed quite significant progress, and will soon become a PersonalGenomes.org project in collaboration with DIYbio. This is great news, and I hope to see the BioWeatherMap take off over the next few months.

I’m really pumped about this, and look forward to seeing all of the fantastic projects come to fruition!

It’s pretty exciting, because I’ve been talking to the University of Washington about allowing public use of their facilities for DIYbio. That has its own set of hurdles, especially once you get into the realm of IP. So, Dan setting up his lab and needing interested parties, then finding out about DIYbio is perfect timing.

The next Seattle DIYbio meeting will be at Dan’s house in two weeks, and we’re going to advertise it far and wide. I’ll keep you guys posted, and Dan should be sending a message to the list pretty soon. Cool stuff.

IT’S ALL HAPPENING!

-Alec Nielsen