Team:Imperial College/Description
Project OVERVIEW
Introducing SOAP Lab: a comprehensive computer-aided pipeline that infers genetic circuit designs from SBOL data files, and produces custom DNA assembly scripts based on a user’s specifications. SOAP Lab enables the the design of DNA parts in the SBOL Data format and the production of scripts for the use of liquid handling machines for said parts.
Application of the project
We produced a tool that has great potential to improve outcomes in labs around the world.
Our project allows biologists with lacking dry lab skills to improve the operation of their workflows by accessing powerful tools
of automation that would be outside their reach otherwise.
Our Goals
We planned to make a user friendly workflow that would allow for an incresed throughput of genetic designs through automation. We met the goal of user fiendliness by using an intuitive UI that would produce constructs in
a widely used data format in synthetic biology SBOL. The next step was to incorporate the information contained in the SBOL genetic design into a ready to run script for a liquid handler. We validated our instrument
through a collaboration with the iGEM Hamburg team that managed to implement our entire workflow in just an afternoon with no prior experience.
Our Inspiration
Covid-19 was an inspiration, in a way. Due to the worldwide breakout of Covid we were forced out of the labs of our university and our teammates were working together from around the world. This really made lab time a
scarce resource for us so we looked into ways of improving the speed and quality of our work when finally a lab would become available. Around that time our university had recently aquired a large number of OT-2 opentrons
machines for lab automation and we were seeing the many applications of them, for example, in the fight against Covid at OpenCell, where they were used to speed
up diagnostics. To test out our pipeline ourselves we reached out to OpenCell, who kindly sponsored us and allowed us to use their OT-2.
Our Product
In the early days of our project, we realised that there is a significant gap between biologists and the vast array of tools designed to make their life easier. For instance while lab automation provides streamlined workflows, increased
scalability, and increased reproducibility, there is a barrier to entry constituted by the coding and debugging expertise required for lab automation as well as the costs linked to aquiring the necessary equiptment.
Our task was to bridge the gap and improve the accessibility of automation tools for biologists, especially with lab automation costs falling quickly. We began to look into reducing the learning curve for the use of automation workflows,
ways of using existing standards to enable the interoperability of existing tools. To produce value by meeting the requirements of biology labs and provide a tool for the customization and automated implementation of protocols.
SOAP Lab
Our chosen acronym: SOAP stands for SBOL to Opentrons Automated Pipeline.
SBOL stands for Synthetic Biology Open Language, an open source, standardised language for encoding synthetic biology constructs and
parts. Opentrons is the liquid handler we chose for its exceptional affordability and modularity. Automated: we are aiming to bring synthetic biology automation to new users, and improve automation for more experienced users.
Finally our product is a comprehensive pipeline that seamlessly takes users from designing their constructs to producing them in the lab, all through an intuitive website. This fits in with our ethos of accessibility
and communication: creating a direct line that connects the latest synthetic biology software innovations to the wet lab, in only a few clicks.
Impact
Our software’s main goal was to enable the design of DNA parts and the production of scripts in the python programming language for the liquid handling robot Opentrons OT-2. These scripts would then be used by the OT-2 to
implement an automated DNA assembly workflow for MoClo, BASIC, and BioBricks assembly methods. The software solves an issue in extant software by addressing different areas of the automation pipeline that seldom interact,
often because of the use of different data formats. To address this problem we have created an online tool that facilitates the design of DNA parts produces a ready to run script for part assembly. To make our work easily
adoptable in existing workflows we chose the widely used and shareable standard SBOL. SBOL is well maintained and updated regularly to meet the needs of the synthetic biology community and contains a large amount
of data enabling us to introduce combinatorial design handling in our software.
We communicated with Professor Chris Myers from the university of Utah and Professor Baldwin from Imperial College London who was also our supervisor for the project. Our discussions inspired us to incorporate and adapt software from their labs (such as SBOL Designer, SBOL Validator, and DNAbot) into our pipeline.
Future Progress
In future, we hope to integrate our project into a larger pipeline such as Galaxy SynBioCAD, which incorporates the entire design-build-test-learn cycle, and are in
discussions with the creators at the moment. This would allow our product to reach many more users, and greatly increase its usefulness.
With this possibility in mind, we aim to continue to improve and expand our
tool based on user feedback:
- Add real-time error tracking and prediction to Opentrons protocols
- Expand assembly methods:
- MoClo - add CIDAR MoClo, allow multi-level constructs in a single run
- BioBricks - allow multi-level constructs in a single run
- BASIC - include DNA methylation
- MoClo - add CIDAR MoClo, allow multi-level constructs in a single run
- Integrate Plateo, a tool by the Edinburgh Genome Foundry that allows tracking of plates and wells
- Interface SBOL Designer directly with the front end
