Tag: ui

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.

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.