Team:Imperial College/Attributions
Our team's formation was quite unique this year in that the recruitment efforts were entirely the result of a student-led initiative started at the beginning of the year, all thanks to the Imperial College synthetic biology
society SynBIC. We came together for the first time in early January and found the selection process had produced a team not only with diverse backgrounds and degree areas, but also with creative talents and cross-disciplinary
interests. In numbers, we were 3 bioengineers, 3 biochemists, 2 physicists and 1 design engineer. Our initial ideas revolved around cutting edge topics such as viral vectors production, modular metabolic engineering, and phase
separation (using intrinsically disordered regions) for compartmentalisation within cells.
After the onset of the pandemic, our focus started shifting more towards a computational project quite organically, as we had always
wanted to incorporate combinatorial testing using Opentrons into our project. Some reshuffling of the team resulted in 3 new recruits with a computational background to drive our nascent design-to-robot program pipeline. During
this stage we outlined the core values and aims that would guide us throughout the project, namely accessibility, communication, and validation.
Accessibility is key in our tool, as there are many budding software tools
that are abstracting away the programming scripts for liquid handlers and emphasise dynamically defining a protocol through an interface, which are however still out of reach or practical use for even leading academic research
labs. The simplicity of our open-source pipeline brings automation directly into the hands of people lacking the technical capabilities or time to run automation equipment in their lab. Our incorporation of SBOL-based designs
as the input is unique to our automation pipeline and encourages the communication of data through SBOL. Being an application of SBOL, we further support the adoption of SBOL as a standard by integrating it into a pipeline.
Lastly, software written for biologists often does not take into consideration the needs of the scientist and cuts short on some crucial details. This is why we validated our web pipeline on our own work, simulated builds of
our real project on Tryptophan optimisation, and partnered up with another iGEM team to run our pipeline and learn from their experiences.
Enough about our project. Meet the team below!
Dr. Geoff Baldwin
Helped us outline the specifications of our software pipeline and to critically evaluate its usability and merit to our end-users. Funded and advised us on BASIC assembly methods and protocols. Helped set up
our lab and introduced us to the guiding overall aims of our project.
Olivia Gallupova
Overseeing and coordinating project. Team lead. Wet lab practical work and validation. Testing of script generation. Pipeline architecture design. Frontend design. Promotional video and graphics.
Benedict Carling
Frontend design and engineering, linking frontend and backend, maintenance of coding practices. Coding of early iteration of backend script generation.
Emma Albertini
Education and mentorship on modelling introduction package. Holding Science Slam and webinars.
Human outreach lead.
Modelling of Tryptophan optimisation.
Treasurer and Wiki master.
Hia Ming
Created the SBOL Parser and reimplemented SBOL Java API features in Python. Sourced and adapted protocols for wet lab validation of software. Practical implementation and planning of validation wet lab work. Integration
between wet and dry lab. Ideation of Tryptophan optimisation project. Communication of SBOL. Human outreach. Promotional video and graphics. Pipeline architecture design. Frontend design.
Gabby Johnston
Reimplementation of DNA-BOT into Opentrons v2. Expansion of DNA-BOT to BioBricks and MoClo assembly protocols and modularisation of script generation. Human outreach interviews and Science Slam public outreach.
Gabriel Swallow
Modelling of Tryptophan optimisation. Creation of and team mentorship in modelling introduction package and tutorials. Human outreach. Promotional video animation, presentation video script writing and videography.
Frontend webpage design and graphics.
Maria Torra
Ideation of Tryptophan optimisation project and specification of genetic pathway engineering and software validation experiments. Wetlab lead. Sourcing and practical planning of wet lab experimental work including protocols,
reagent and parts sourcing. Human outreach and contribution to wetlab wiki.
Raymond Miles
Frontend engineering, SBOL validation, lab space sourcing and wiki design.
Raghav Khanna
Masterminding of frontend implementation, integration of SBOL Designer Java application into browser, overseeing and advising frontend team. Wiki technical implementation.
Scott Stacey
Ideation of Tryptophan project, specification of BASIC backbone library and genetic pathway engineering. Modelling of Tryptophan optimisation. Wet lab protocol sourcing.
James Bayne
Advice and guidance throughout project. Team organisation, screening, and recruitment.
Georg Wachter
Advice and guidance throughout project. Team organisation, screening, and recruitment.
our network
Tom Ellis: advice and opinions on yeast Tryptophan optimisation project in terms of feasibility and merit
Will Shaw: advice and practical lab assistance on BioBricks parts sourcing, amplification and preparation. Point of contact for wet lab reagents. Advice on MoClo protocols. Generated a dCas9 yeast cell line for us, provided general
advice on the Tryptophan optimisation project particularly regarding gRNA part design for gene knockdown.
Liam Hallett: advice and practical lab on BioBricks parts amplification and preparation. Point of contact for wet lab reagents and BASIC assembly help.
Alexis Casas: advice on biodesign automation
Ismael Mullor Rodriguez: advice on iGEM competition running
Rodrigo Ledesma Amaro: advice and opinions on yeast Typtophan optimisation project, especially feasibility
Huadong Peng: point of contact for reagents
our sponsor
Opencell: lab space sponsorship
Wellcome Trust: student bursary and consumables funding
