Team:Imperial College/Software/Background
Background
Background information regarding the technologies that underpin SOAP Lab as well as further information to understand the scope of the project.
BioBricks
Our pipeline encompasses construct design for three different assembly methods: BioBricks, MoClo (or Golden Gate), and BASIC.
We chose to include BioBricks as it is the primary assembly method used by iGEM teams, who
are some of the key users we designed this tool for. We want to make it easier and faster for teams to design parts and contribute to the open source community iGEM has fostered.
We were unable to find any BioBricks script generation tools, and therefore our BioBricks script generation functionality is likely entirely unique.
MoClo (Golden Gate)
MoClo, which also includes the Golden Gate procedure, was chosen due to its popularity, including with iGEM teams, and ability for combinatorial, multi-level constructs.
We based our MoClo script generation off DAMP Lab's Modular Cloning (MoClo) and Transformation in E. coli Workflow. We updated this tool to OT-2 version 2, which has many more features, increased its flexibility and customisability, and optimised it for use in the wet lab based on our wet lab team's feedback.
BASIC
Our third assembly method was BASIC, a method developed by our own Imperial College London. BASIC is capable of combinatorial design, but only requires a single run, and has reusable parts. Parts are connected by linkers,
and many different linkers are available so that constructs are guaranteed to be assembled in the right order. We strongly recommend trying this assembly method, and hope that by including it in our tool we can make
it more accessible to new users.
DNABot, an OT-2 version 1 script generation tool was the basis for our BASIC tool and ultimately an inspiration for the entire project. Like in DAMP Lab's MoClo tool, we updated DNABot to version 2, greatly increased its flexibility and customisability, and optimised it for the wet-lab.
SBOL Data Format
SBOL (Synthetic Biology Open Language) is a democratic and open-source data standard that has grown over the past decade with the needs of synthetic biologists to communicate their designs, allowing it to evolve and keep
pace with the fast-changing needs of the synthetic biology community. SBOL provides both a data format for expressing and sharing genetic designs ('SBOL Data'), as well as a standardised set of symbols to represent
the constituent parts within these genetic designs ('SBOL Visual').
Enriching software tools through data
SBOL Data provides powerful functionalities through its rich data description such as modularity, hierarchy, abstraction, versioning and simplifications of large
design spaces in the context of combinatorial designs. A part can be defined as a component with a plethora of standard fields, including its source, role, and the full sequence of the part. A component may also have
multiple subparts and links to variants of those subparts, making SBOL especially well-suited to high-dimensional experiments. Being able to capture variations on a design within the same file made it an excellent choice
to use as a file format for our pipeline and took the capabilities of our automatic script generation to the next level by allowing us to go directly from design to build.
SBOL as a tool for communication
Such functionalities allow for a more efficient exchange of information and collaboration thanks to its ability to capture the details of entire workflows, networks
of reactions and interactions, and provenance in a way that would be consistent between scientists from different labs and backgrounds. It is a standard that encourages collaboration and as such a harmony between the
silos of disparate fields of expertise within molecular biology, providing a fertile space for development to occur in this field. There is a whole ecosystem springing up around the SBOL standard and we are proud to
have contributed to a part of it.
Opentrons
Opentrons started out as an iGEM project in 2014 and is now experiencing major growth as a provider of lab automation equipment.
We chose to tailor our tool to the Opentrons OT-2 since it spoke to our values of
accessibility. The Opentrons OT-2 machine is an open source liquid handling robot that is currently sold at 5000$. Opentrons is being used more and more in small labs, allowing them to automate their workflows at an
accessible price and without the need for proprietary software. The OT-2 is currently seeing use for the COVID-19 diagnostics:
Walker, K. T., Donora, M., Thomas, A., Phillips, A. J., Ramgoolam, K., Pilch, K. S., …
Meany, T. (2020). CONTAIN: An open-source shipping container laboratory optimised for automated COVID-19 diagnostics. BioRxiv, 2020.05.20.106625. https://doi.org/10.1101/2020.05.20.106625
