Contribution

Throughout the 2024 project cycle, iGEM Toronto has developed many designs, software tools, parts, and protocols that will serve future iGEM teams and the broader iGEM community. Additionally, our pursuits in entrepreneurship, human practices, outreach, and finance have taught us many important lessons that can aid future iGEM teams’ work. We present our key insights below.

We have made our software and validation scripts open-source and available on our iGEM GitLab, as well as in a Python package. Our software includes our data manipulation scripts and our custom tokenizer, which allows fitting plasmid sequences up to 4x longer in the same context length. It also includes key features such as our callbacks, optimizers and training pipeline

Full details can be found on our Software page.

We have also publicized our database of key oriV motifs from across literature used in our own motif discovery: motif database. This database was largely beneficial to us, as we could not find any similar open source resources that had compiled motifs and the most conserved and widely observed iterons from across literature.

Full details of training and validation can be found on our Model page.

We have developed a high-throughput system for rapidly testing the functionality of a wide range of oriV sequences. By optimizing both the cloning and testing protocols, we streamlined the entire workflow, enabling us to produce reliable results in less than two days from start to finish. This system dramatically accelerates the characterization of new oriV variants, offering high efficiency for projects requiring large-scale validation.

We applied our workflow to test oriV sequences generated by their machine learning model. This integrated approach allowed us to experimentally validate computationally designed oriVs for the first time, revealing functional sequences that include key elements such as a promoter, RNAII, and a replication start site. The ML-generated sequences contained combinations of these components that were proven to be functional, which has never been done before. Future iGEM teams can make use of our workflow, as well as key learnings from our Lab Notes.

We have developed frameworks for increasing throughput in wet lab operations, including:

• Use of machine learning tools to expedite assays
• Use of internet-of-things to minimise human error and strengthen data storage
• Use of industrial process engineering techniques in laboratory floor settings

To an extent, we also have demonstrated functionality of these frameworks, and worked towards developing prototypes for each. All of these frameworks are usable and applicable to labs and other iGEM teams regardless of objective, ensuring modularity and transferability.

View our Hardware page for full details.

We analysed the foundational models developed by our team, and through extensive research, analysis, mentorship, we crafted a specific use-case of our foundational models with appropriate product-market fit.

Through this process, we:

1. Took part in a 4-month rigorous incubator program at the University of Toronto’s flagship incubator the Hatchery.
2. Took part in iGEM Startups’ very own Venture Creation Labs, where we made it through all stages of the program, and got selected to showcase at the BioInnovation fair in Paris.
3. We’ve deployed the use of business frameworks, including Skills Gap Analysis, Lean Business Model Canvas, SWOT, gantt charts, and more. These are compiled into a comprehensive business plan crafted using the FEEL methodology of venture creation.
4. We created a 3-minute investor ready pitch through VCL, and a 6-minute investor ready pitch through NEST.
5. We’ve outlined a 2-year cash flow projection for company-wide operations.
6. We crafted a comprehensive 10-year funding timeline, from pre-seed to Series B.
7. To validate the feasibility of each of our steps, we relied heavily on the feedback from industry and academic mentors that have worked at NVIDIA, AMD, Apple, BDC Capital, and more.
8. We secured an industry project with a first customer, pending the development of our technology.
9. We’ve received the approval of our university’s flagship incubator to the “Go-To-Market” stage.

Future iGEM teams can benefit from each of the company deliverables our team has created when engaging in creating their own ventures, whether through their iGEM team or even iGEM Startups. Please refer to our iGEM Toronto Entrepreneurship wiki page for more details.

Future iGEM teams can draw lessons from our human practices and outreach initiatives for the best practices regarding engaging with stakeholders, assessing the impact of their project on various communities, and promoting their team through social media channels. Other iGEM teams can utilize and adapt these resources to support their own human practices campaigns and outreach efforts.

Please see our Human Practices and Outreach pages for more information.

We played a pivotal role in ensuring the financial health and sustainability of our team. Through careful budget management, we allocated resources efficiently, ensuring that all divisions (wet lab, dry lab, etc.) had the necessary funds to operate while maintaining a balanced budget. Additionally, we actively sought potential sponsorships. To make a contribution to future iGEM teams, we share our sponsorship package, which was essential in highlighting the value of our projects and initiatives. This package was an essential tool for attracting sponsors, helping to secure critical funding for ongoing and future team endeavors, and we believe that this can be a useful reference for future iGEM teams.