Ginkgo in Geekville

Just a quick pointer to an op-ed in the Globe. Apparently Mayor Menino is interested in transforming Boston’s Seaport District, which Ginkgo calls home, into an innovation zone where young scientists and engineers can live and work, on the cheap.

But Menino may be on to something by promoting the waterfront to young scientists and programmers who are more invested in the construction of DNA strands than in water views and high ceilings.

Mayor Menino, you got my vote! 🙂

Biotech Lab on the Cheap

A few weeks ago, the Globe ran a story on High Tech’s Hand Me Downs. At Ginkgo, we’ve been pretty creative about putting together our lab. Ebay, labs closing up, labs moving, companies shutting down, Dovebid … we’ve tried it all for lab equipment & supplies. So here’s a few tips for those who might come after us.

Tip #1: The best deals are direct. When a company shuts down, it may elect to sell all its equipment to a lab equipment reseller but some choose to auction the equipment off themselves. Most biotech companies aren’t that old and they bought their equipment new, so most of the equipment works and is in good shape. These purchases tend to be a win-win. The company can often sell to you for more than they could a reseller, and you can often get the equipment for less than you would at a reseller.

Tip #2: BE NICE. Companies usually keep one or two employees on to handle the equipment sales after the company has gone under. This person, and all their colleagues, just lost their jobs and now he/she has to work long hours to sell off the lab in an orderly fashion. Being obnoxious just makes their lives harder and isn’t going to make them any more willing to give you a great deal.

Tip #3: You win some, you lose some. Be prepared to buy a few duds. Buying used equipment is always a bit of a gamble. That robot may not work perfectly right. Or something might break in the move. But overall you’ll generally come out ahead: buying three PCR machines for $800 each when only one of them works is still better than buying one new.

Tip #4: Some stuff you just can’t get used. Some equipment has really high resale value or has only been on the market for a short time, so used ones are scarce. The Nanodrop is an great example. It can be pretty hard to find a Nanodrop used, and if you do … it will usually go for a pretty high price. In these cases, it is often worth pricing out a new one. Some manufacturers offer startup/academic discounts which can make new equipment competitive with hard-to-find used items.

Tip #5: Always get the software and dongle! Many pieces of lab equipment require proprietary software or a dongle for operation. If the equipment doesn’t come with the software or dongle, think twice before buying. Oftentimes manufacturers don’t even sell software for older models anymore, and if they do, it can easily run you $2-5k. So that great deal stops looking so great when you factor in these added costs.

That’s it for now. Happy hunting!

Mayor Menino visits Ginkgo


Mayor Menino visited Ginkgo today to formally announce our move to Boston and present us with a $150,000 check from the Lifetech Boston loan program for early stage startups. Barry gave him a tour around our new digs and even showed him a demo of one of our Ginkgo-bots.

You can check out coverage by the Boston Herald and the Mass High Tech.

We’d like to give a shout-out to all those who made our move to Boston possible – in particular Martina Toponarski from Lifetech Boston, Bill Nickerson from the BLDC, Mayor Menino, and Ginkgo’s landlord Paul Mustone from Reflex Lighting.

Update: See also Emily Singer’s Technology Review article and Mayor Menino’s Wicked Local column.

Pearl Biotech Open Gel (Un)Box(ing)


Just received our gel box in the mail today.  Pearl has added a great tweak to the standard gel box with an illuminator that fits snuggly under the box.  The illuminator apparently does a good job of exciting SYBR Safe DNA stain so you can watch your DNA running in real time.  The design is open sourced and it would be great to see someone design a camera mount for the gel box to make a cheap gel imager.   All in all, the box looks solidly built and it’s exciting to see people innovating on tools for biological engineering.  Looking forward to seeing more from Pearl in the future.

From the Archives: Root Bridges

Some Synthetic Biologists aspire to live in a house grown from a reprogrammed tree. We’re not there yet but our ability to train trees to form useful structures certainly gives cause for optimism. Take for example the living root bridges of the War-Khasis tribe in Northeastern India. Strong, flexible roots are trained to grow across rivers and take root on the far side. While a bridge can take 10 years to grow some may be more than 500 years old and still getting stronger. Much like good whiskey, these root bridges take a long time to make, but once made, they get better and better.

Image source – Vanlal.

Bacterial Edge Detector

One of Ginkgo’s favorite biological engineers – Jeff Tabor, has just published his latest engineered biological system, a bacterial edge detector, in Cell Magazine.


The edge detector is a great example of combining different biological parts (light sensors, cell-to-cell signaling molecules, reporters, and logic gates) to make a complicated engineered biological system.  In the final system, the engineered E.coli are spread in a lawn on a petri dish and light is shown on the dish in a particular shape.  The bacteria at the edge of the shape detect that they are at the interface between light and dark (this is the really amazing bit that requires communication between neighboring cells and some genetically-encoded logic) and express a reporter protein creating an outline of the shape.

This project was actually begun by Jeff and the UT Austin iGEM team in the 1st iGEM competition in 2004.  During the 4 months of the competition they didn’t manage to get the edge detector working, but they did build the first bacterial photography system (“Coliroid“) which was later published in Nature.

Hopefully Jefff’s success with the edge detector will be an inspiration for this year’s iGEM teams to go after ambitious projects!

Design Your BioBrick Systems On-the-Go

Just a quick post to let you know that Cesar from Drew’s lab has released the first version of his BioBrick Studio app for the iPhone on the iTunes Store. It lets you do some basic browsing of BioBrick parts from the Registry of Standard Biological Parts.

It’s pretty cool that Cesar is experimenting with design environments for biological systems on different platforms. Next time you’re in the lab and can’t remember which part to pull out of the freezer, grab your iPhone and use BioBrick Studio to double check. 😉

Changes coming to the Registry of Standard Biological Parts

If you haven’t visited the Registry of Standard Biological Parts lately, you should stop by and take a look. We’ve been helping out in the re-design and re-organization of the parts collection available there. Randy and Meagan are constantly looking to improve the Registry so that it is more useful to iGEM teams and academic labs. After a fair bit of consideration, this year we’ve deliberately tried to make the Registry easier to browse for newcomers. The basic idea was to try to make the Registry look more like a catalog. Thus, if you visit the Registry catalog of parts, you can browse parts and devices by type, by assembly standard, by function, by contributor, or by chassis.

For each group of parts, we’ve added text and pictures to better explain why and how you’d want to use those parts in larger systems. For example, there have long been a number of plasmid backbones available from the Registry. Depending on whether you want to assemble parts together, operate a multi-component synthetic system, express a protein or measure the behavior of a part, you might choose to use a different plasmid backbone. By visiting the plasmid backbones page, you can find all of these backbones organized and linked from one place.

The Registry is always a work in progress, so stay tuned for even more changes coming soon. And of course, we’d welcome your feedback. So take a look and let us know what you think!