IDEAS CITY 2015: The Collective NYC Biome Map


Petri-plates with bacteria modified with fluorescent protein under UV light, show parts of NYC grid map.
(Photo credit Marta Molina Gomez and Ali Schachtschneider)


Genspace citizen science biotech lab and scientist Christine Marizzi from Cold Spring Harbor Laboratory’s DNA Learning Center worked together to create a map of NYCs collective microbiome, as part of the New Museum’s IDEAS CITY Festival 2015.

Screen Shot 2015-06-04 at 12.56.51 AM
               Painting with bacteria on site at IDEAS CITY. (Photo credit Bella Cohen)

The theme of IDEAS CITY Festival 2015 was The Invisible City, an homage to Italo Calvino’s literary masterpiece. This theme is rooted in civic action, with each of the Festival’s platforms serving as an invitation to explore questions of transparency and surveillance, citizenship and representation, expression and suppression, participation and dissent, and the enduring quest for visibility in the city.
During three days of conferences, debates, workshops, performances, and architectural and artistic interventions, IDEAS CITY explored many of these questions.

Genspace approached this year’s theme of The Invisible City by making the invisible visible through offering the public access to NYCs collective microbiome! We set up a tent at IDEAS CITY Festival where people painted with harmless genetically engineered bacteria on petri plates prepared with stencils of a grid of NYC.
In addition the PathoMap “Swab Squad” team joined our tent, explained their project to the public and shared the “SwabKit”, which allows anyone to explore NYC microbiome and help crowd source microbial samples from around the city.

PathoMAP SwabKit

PathoMAP, SwabKIT. You too could become an explorer and help collect microbial samples of your CITY! PathoMap is a project led by Dr. Christopher Mason at Weill Cornell Medical College that began in 2013, to explore the microbiome and metagenome of New York City, and sequenced DNA from surfaces across the entire NYC subway system, the Gowanus Canal, and public parks.


In the second part of the event, people joined Genspace and Christine to participate in a hands-on Bacteria Printing Workshop. The painted petri dishes holding the now grown- and visible!- bacteria were printed onto paper and then reassembled into the map of NYCblending the microbial prints into a collective artwork, making the  microbial community of NYC visibleThe artistic hands-on experience was enriched with a lively discussion and background teachings about the perception of Genetic Engineering and microbes in our society. Participants also learned how the scientific community is mapping microbial ecosystems in urban environments and how citizen scientists can get involved.

So what is the microbiome? The microbiome is the ecological community of all microorganisms that share our body space. The human body contains over ten times more microbial cells than human cells, although the entire microbiome weighs only about three pounds. The total number of genes associated with the human microbiome exceeds the total number of human genes by a factor of 100-to-one. We are outnumbered indeed!

Microbes reside everywhere – on land, in water, and in the air – yet they are too small to be seen with the human eye. New York City is a melting pot of cultures, both human and microbial, and every citizen has a personalized microbiome. Collectively we shape New York City’s urban-biome by our lifestyle choices and this unseen microbial world significantly impacts us.

This project succeeded to engage the public to learn about NYC’s microbiome and to collectively create an assemblage of New York City – a microbial-map! The map will be featured on our website which will go live soon.

Stay tuned for more about The Collective NYC Biome Map with upcoming workshops, talks and hands-on activities at Genspace and beyond!

Bacterial Printing workshop III
Bacteria Printing Workshop. (Photo credit: Christine Marizzi)
Bacterial Printing workshop V

The painted plates before printing. (Photo credit: Christine Marizzi)


The event was made possible thanks to:

Genspace at IDEAS CITY 
Ali Schachtschneider
Marta Molina Gomez
Annelie Koller
IDEAS CITY Festival 2015
The New Museum
Genspace NYC  
Project Coordinator & Organizer: Nurit Bar-Shai
Scientific Director at Genspace: Oliver Medvedik
Production & Design Coordinator: Ali Schachtschneider, Marta Molina Gomez
Christine Marizzi, DNA Learning Center
Project Scientific Coordinator
Instructor, NYC Microbiome Map Printing Workshop
OMTA (Tal & Omer Golan)
NYC Biome Map Design
PathoMAP team
Project Leader:  Christopher Mason at Weill Cornell Medical College
Project Coordinator: Ebrahim Afshinnekoo
Post-doc Associate and Visualization Guru: Elizabeth Henaff
Artist in Residence: Dave Rife
Artist in Residence: Gabe Liberti
Sylvia Saborio, VEEVO
Tansgenic Bacteria Printing




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Biofabricate: Genspace Pop Up Lab

Genspace_Biofabricate_imgGenspace set up a pop-up DIYBio LAB at ‘BIOFABRICATE’,  The world’s first summit dedicated to biofabrication for future industrial and consumer products, organized by Suzanne Lee of Biocouture in partnership with Synbiobeta.

The event featured a full day of speakers and keynote talks from pioneering biomaterial, biotech and biofabrication start-ups along with key researchers, designers, thought leaders and academics, as well as multiple workshops, a design lab and the pop up lab.

The pop up lab was a space for people to come and ‘Grow Your Own Scoby’ and make necklaces filled with culture to take home, interact with the material in a living, grown, and dried state, check out slime mold and mycelium under the microscope, or learn how to pipette, while chatting with members about Genspace and biofabrication! People could come and interact with some of the materials discussed throughout the day, and learn how a DIY lab could support them in their projects. A few Genspace members projects were displayed along with the pop up lab as well as in the design lab, and multiple members spoke throughout the day.

IMG_8687the Pop Up Lab
IMG_8691the lab and some members projects
IMG_8683GYOS: grow your own scoby!IMG_8669scoby: living, wet and dry culturesIMG_8680the pipetting stationIMG_8689Some members projects featured in the Pop Up lab

Featuring members projects:

Heather Dewey-Hagborg, Stranger Visions, exploring the traces of the DNA you leave behind; Ali Schachtschneider, Fungal Shoes, Bacterial Textiles and Garmentobject exploring the bodies interaction with biomaterial technology through the growth of cellulose, mycelium and bacterial materials; Fabiola Einhorn, 174 Magazine, exploring how Synthetic Biology and bio-tech fabrications will integrate into our everyday life and citizens access to its making; And at the Design Lab: Genspace 2012 iGEM team collaboration with Terreform One, Gen2Seat, a biodegradable Genetic Generation sitting Module; Sylvia Saborio, Vee Vo, creating wall papers tiles using traditional print making techniques and engineered bacteria; and Genspace co-founder Nurit Bar-Shai, Objectivity [tentative], exploring how bacteria communication and network systems might inform smarter design.
IMG_8724 Projects in the Design LabIMG_8725


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Genspace wins gold medal at 2014 iGEM competition!


igem goldAh, success! After working our butts off for months, we participated in the iGEM Giant Jamboree and won a gold medal (the second time Genspace has done so, but this time we could compete under our own name in the new Community Lab Track!).

20141101_092048Jonathan Badal at the podium during our presentation.

20141102_191358Explaining our project to the iGEM judges…

20141102_194449…and to other participants.

20141101_202150The team relaxes after the presentation is over at a local bar…

20141102_001505…and meets some old friends.

20141103_140754At the awards ceremony, seeing out name on the list of gold medal winners!

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Genspace co-founder Dr. Ellen Jorgensen gives keynote speech at Maker Faire Rome event.

Watch Make Cells Dance- Ellen’s Maker Faire presentation

UntitledMaker Faire Rome is even bigger than World Make Faire in New York! It was held at the beautiful Auditorium Parco della Musica and it took days to see it all. There were makers from all over the world exhibiting their creations. Everything from 3D food printing to giant robot musicians. It was fabulous, as befits the incredible city of Rome. There was an exhibit spotlighting the history Italian innovation that included an Olivetti Programma 101, the first ‘portable’ computer and one that Ellen has fond memories of from high school. She had a great time hanging out with friends too.





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#ScienceHack: Violacien Factory Design Automation with OpenTrons


Yesterday Genspace hosted the second #ScienceHack. It was awesome to participate in a new type of peer-to-peer syn-bio research and design event. And, there was a robot!!!

The format of a #ScienceHack, designed by the awesome team at Synbiota, brings labs across the world together to work on optimizing a genetic circuit. We are focused on the circuit to produce violacein, an anti-cancer and anti-parasite drug that currently costs more than $360K per gram. The #sciencehack uses the Genomikon system to re-design genetic circuits with the hope of bringing this cost down significantly. Genomikon is a biological prototyping platform that modularizes DNA building blocks so that snapping together a novel genetic design is easier than ever.

G_rulesbA diagram broadly describing the Genomikon plasmid assembly process.

While the six gene pathway to produce violacein is known, it remains mysterious. For example, it is unclear where the promotor sequence that initiates the pathway’s expression is located. In order to optimize design, then, we need to use the old trial and error strategy, producing and testing as many different designs as possible. That is why the distributed nature of a #ScienceHack is so great — with people across the world collaborating, it is possible to make a design that drastically lowers the cost of this violacein without millions of dollars to pay lab fees.

Vio-1This is the chemical process to make Violacein and the genes associated with each step.

Synbiota provides an amazing platform for sharing data and protocols, making it the basic collaboration tool for open science projects. And we were lucky to have Connor Dickie, CEO of Synbiota and one of the main developers of the open source genetic design software GENtle, at the event to show us how to design DNA in silico. Check out everyone’s genetic designs here at the event’s Synbiota project page. And this PDF provides information on the different strategies teams used to optimize violacein production.

Affordable lab robotics is another way to pump out violacein factory designs to test and accelerate the pace of optimization. Actually designing the pathway is the crucial part, but it takes hours of lab work to produce an e. coli strain in order to test a design and see how good it is. If a robot can do the time consuming genetic assemblies, individuals can spend more time problem solving and designing and less time pipetting and waiting. Is am a part of the team, also including Chiu Chau and Nick Wagner, developing OpenTrons, an affordable open automation platform well on its way to doing synthetic biology.

The OpenTron BETA

The whole OpenTrons team came to the #sciencehack to show off the assembly for automating the magnetic bead wash step — the most time consuming part of the Genomikon protocol — that Chiu and Nick designed over the weekend. It uses a custom 3D printed holder for the vial, and a magnetic tip that the pipette can use repeatedly to move the wash magnet back and forth. You can see it in action in the video above.

magnetBeadHolderA 3D printed magnet stand Chiu made for Genspace classes that use the Genomikon kit.

I teamed up with Christal Gordon to design the simplest deoxyviolacein pathway on GENtle and begin the process of automating the DNA assembly. But once the protocol is complete, we will share it so that other OpenTrons users can download and repeat it to assemble their own violacein factory designs.

toolboxAlpha1The prototype lab suitcase, my pipette, and the Genomikon violacein factory kit.

The OpenTrons team was also excited to show off our new Android controlled, modular, portable synthetic biology kit prototype. Its a lab in a box! Heating, cooling, and centrifuge all included, with a vortex soon to be added. Next, it will be re-designed to work with the automation platform.

The #sciencehack is a great format, and it was a pleasure to experiment with such cool and capable tools as Synbiota, Genomikon, and OpenTrons. I have a feeling these three have quite a future together! Watch this space for updates on how our violacein factory designs preform, and please be in touch with any questions or to be involved (opentronsinfo |at| gmail |dot| com).

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