Category: Teaching

Publication about Genetic Constructor

While I was working as a research associate in EGF and DI, I have been working with Autodesk Life Sciences on a new software: Genetic Constructor, developed to support synthetic biologists to design DNA, creating a “new visual language that focuses on functional parts abstracted from sequence”. A paper about it was published at the end of last year in ACS synthetic Biology and I am one of the author, making it my second academic publication after Designing with Living Organisms for RTD.

 

Genetic Constructor: An Online DNA Design Platform

Maxwell Bates†, Joe Lachoff†, Duncan Meech†, Valentin Zulkower‡, Anaïs Moisy‡, Yisha Luo‡, Hille Tekotte‡, Cornelia Johanna Franziska Scheitz†, Rupal Khilari†, Florencio Mazzoldi†, Deepak Chandran§, and Eli Groban*†

† Autodesk Life Sciences, San Francisco, California 94111, United States
‡ Edinburgh Genome Foundry, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, U.K.
§ Radiant Genomics, Emeryville, California 94608, United States

ACS Synth. Biol., 2017, 6 (12), pp 2362–2365
DOI: 10.1021/acssynbio.7b00236
Publication Date (Web): October 11, 2017
Copyright © 2017 American Chemical Society

ABSTRACT

Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.

Shanghai, Disneyland , Longxu Mountain, Beijing, Great Wall of China

A selection of pictures from our latest trip in China.
I was still teaching Interior Design in Shanghai SCF – Dongua University. I am proud and would like to congratulate the fourth years students who are currently exhibiting their final year project for the FIRST-EVER SCF Graduate Exhibition 2018.

During the week-ends we had the chance to be there for the Lantern Festival, visited Disneyland Shanghai, went for a hiking trip with Hiking Lovers to the Longxu Mountain (very hard but worth it, it was stunning) and finally went for 3 days in Beijing and hiked on the Great wall (I would recommend anyone who want to do it to contact John – Here is Beijing . He is great and you will experience the wall by your own).

 

Shanghai for the love of Art, Teaching & Food

I am just back from Shanghai, where I had the pleasure and honor to teach Interior Design for 5 weeks at Donghua University representing Edinburgh University. The students have a lot to teach us all over here about passion, hard work and positivity.

It was 5 amazing weeks with my great colleagues and mon amoureux. In our free time we visited lots of galleries (list bellow of some of the best exhibitions I have seen), spend a day walking and riding in Hangzhou around the west Lake and we went for a week end in the mountains. We stayed in xia yan bei village (下岩贝村), hiked 19 peaks (穿岩十九峰), the Hanfei river ( 韩妃江)  and dao tuo xue (倒脱靴). And of course had some amazing food: hot pot, dumplings, wonton soups, noodles, Chinese crepes, vegan dishes…

I am starting to learn basic Chinese to prepare our next trip in March, looking forward to it.
 

 

  • chi K11 .com/.cn
    The work exhibited is digital / conceptual art. What we found most interesting for your practice is the building in itself.
  • MOCA Shanghai – Apple+
    ✸✸✸  The exhibition highlights Japanese designer Ken Miki’s four decades of practice as well as his unique approach to design thinking and education, summarized in what he promotes as “Learning to Design, Designing to Learn”.
  • Rockbund Art Museum – Hugo Boss Asia Art 2017
    High-profile award that honors emerging contemporary artists in the early stages of their artistic creation and exhibition practices.
  • Long Museum West Bund – Antony Gormley
    The first major presentation of Antony Gormley’s work in China. At its core is Critical Mass II (1995) an installation of 60 life-size cast iron body forms.
  • Power station of Art – Shigeru Ban & Li Shan
    ✸✸✸ Shigeru Ban : What is the architectural content to be presented possibly only by exhibitions? The first half of the Exhibition will introduce the disaster relief projects across the world, & the second half of the Exhibition will introduce the projects in progress and the projects in China.
    ✸✸✸ Li Shan : he gave up his decades-long familiarity with painting, and turned his artistic thinking to topics that are related with bio-science. He claimed to be creating on a canvas once reserved only for the God, and created a new artistic discipline: BioArt.
    ✸✸✸ Balkrishna Doshi: Celebrating Habitat-The Real, the Virtual & the Imaginary. The exhibition showcases more than thirty pieces of the Indian architect’s notable works, including personal and public housing, community projects, educational institution, urban planning and furniture design.
  • Modern Art Museum  – Hello, My Name is Paul Smith
    Touring exhibition showcasing the fashion designer’s journey in building his company, as well as his stylistic tastes and eye for design.
  • Dialogue In The Dark
    ✸✸✸ Very exciting life-changing experiences where visitors are guided by blind guides in absolute darkness. You get a chance to experience space and daily environments of life without your sight. Daily routines become exciting and a reversal of role is created where sighted become blind and Blind become sighted. It was a life changing experience. 

 

Dominoes

More informations in the report produced along the process.

The Dominoes have been designed as a concept of a tangible interface for biologists to sketch DNA constructs. The interface consists of a series of pieces representing different DNA parts, using Synthetic Biology Open Language (SBOL).
By manipulating these pieces and snapping them together biologists can sketch DNA sequences. Then, the aim of this project would be to be able be transferred into Genetic Constructor (Autodesk CAD tool for DNA design) to insert the sequences into the sketch blocks and test the validity of their design.
It could then be send to be assembled by Edinburgh Genome Foundry (EGF), a facility at the University of Edinburgh that offers a unique robotic platform to synthesise DNA.
 


 
I have conducted a series of interview with biologist to determine what are the needs: how do they currently design DNA, how they would use them, where, when, what symbols or shape they are using most, do they need different kit depending the organism they are working with (yeast, mammalian cells, plants…) …
It also allowed me to discuss their projects to determine what could be potential future needs. I am currently in the process of designing the fist set of prototype to be tested in different labs at the University of Edinburgh.
 

 
In addition, during these interviews, we discussed how they would communicate the DNA design process to the general public: how to keep the process simple but accurate and what could be an interesting interaction to understand the principles of synthetic biology. It resulted in another project ‘Tales of Synthetic Biology’ presented Here.

From these interviews I have designed a kit of general blocs and 3 different options for the EMMA kit.

Design – general blocs
  • Use of 5 different colours for the coding sequence (promoter – CDS – terminator) to visualise 1 transcription unit. It will be useful when one transcription unit is will be to be express in the bacteria for the duplication (antibiotic resistance for example) and others will be expressed in the plant/yeast…
  • Blank pieces with directional arrow for projects where the direction is crucial at the early design stage.
  • Larger pieces for Transcription Unit (containing promoter – CDS – terminator) for high level sketch.
  • Small pieces for localisation signal, tag… to annotate some aspect inside a block
  • Two different proposals to visualise the strength of a promoter.
  • Two special set to design sequences for Golden Gate of Gibson assembly, in-order to determine the ending and connecting sequence of the blocks.
  • Each type of block is done with a speci c colour + a symbol to give the maximum visual markers, helping to design a sequence.
Design – EMMA kit

One kit where the colours correspond to type of the blocks, one where they correspond to position of the blocks and finally to the type of the blocks and they are numbered for the position.
 

Winogradsky Columns

I am thinking to develop a political art installation using a series of Winogradsky columns.

They illustrates how different microorganisms perform their interdependent roles: the activities of one organism enable another to grow, and vice-versa. These columns are complete, self-contained recycling systems, driven only by energy from light.

Invented in the 1880s by Sergei Winogradsky, the device is a column of pond mud and water mixed with a carbon source such as newspaper (containing cellulose), blackened marshmallows or egg-shells (containing calcium carbonate), and a sulphur source such as gypsum (calcium sulphate) or egg yolk. Incubating the column in sunlight for months results in an aerobic/anaerobic gradient as well as a sulphide gradient. These two gradients promote the growth of different microorganisms such as Clostridium, Desulfovibrio, Chlorobium, Chromatium, Rhodomicrobium, and Beggiatoa, as well as many other species of bacteria, cyanobacteria, and algae.

 

 

Useful links

https://en.wikipedia.org/wiki/Winogradsky_column
http://www.sumanasinc.com/webcontent/animations/content/winogradsky.html
http://archive.bio.ed.ac.uk/jdeacon/microbes/winograd.htm
https://www.scientificamerican.com/article/bring-science-home-soil-column/
http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/winogradsky.html

Biodesign Challenge

The Biodesign Challenge offers art and design students the opportunity to envision future applications of biotechnology.

This semester I am part of the teaching team of the Biodesign Challenge course at the School of Design – University of Edinburgh. We are part of this international competition, were master and undergrad students are going to develop projects involving biology concepts in group of 3/4 around the theme ‘Communication’. The course is lead by Larissa Pschetz and Bettina Nissen, Naomi Nakayama & Eric Thorand.

The Biodesign Challenge offers art and design students the opportunity to envision future applications of biotechnology in a competition that highlights student work. Our organizers connect classrooms with a team of biologists and experts to guide the students as they develop their ideas.

At the end of the semester, the winning teams are invited to New York City to showcase their designs in front of members the academic, industrial, and design communities at the Biodesign Summit in June 2016.

from Biodesign Challenge Website

Teaching Interior Design in Shanghai

I had the huge honour to go in Shanghai to be a Senior Teaching Fellow Interior Design responsible for representing the work of Edinburgh University in interior design within the context of Donghua University – Shanghai International College of Fashion and Innovation (and the wider MoE of China).
I taught Interior Design from year 1 to 4 the key skills associated with the discipline, giving tutorials, supervised activities and presentations, organised visits and assessed the work of the students, providing feedback at the end of the 5 weeks projects.

 

 
I had the pleasure to work with amazing colleagues: Sam Booth, Designer and Founder of Echo Living was my direct colleague in Interior Design (thank You Sam for these two amazing weeks, I feel very lucky of being able to work with you and mostly meeting you and your beautiful values), Emily Ford-Halliday and  Elena Tsyplakova from Fashion (thank you too for your kindness and energy) and the all team in Shanghai: Linn, MingJu and Steve (thank you for let us feel welcome and your support).

 

 
I was blown away with the standard of the work the students produced, amazed by their determinations, passion and hard work. Thank you all, I am missing working with you, it was a truly exceptional experience.

 

 

You can watch and read this short interview of Rachel Simmonds, the teacher I was replacing, to get some insights of what I experienced there.