Our iGEM journey has been an exciting blend of ideation, problem-solving, and consistent progress. From the initial stages in June to our current strides in September, we've worked hard to bring our vision of IMPROViSeD to life. Below is a detailed reflection on the key moments from March through September, where we highlight the pivotal tasks, decisions, and milestones that shaped our project.
March — June
Ideation and Exploration. The early months were all about brainstorming and exploring different directions. From March to June, we rigorously debated potential projects, experimenting with ideas like predicting metal-binding proteins and genome-wide miRNA prediction. These discussions gave us critical insight into various possibilities, but it wasn't until late June that we began to narrow our focus toward protein complexes and integrated modelling platforms, an area that would soon give rise to IMPROViSeD.
July
Settling on IMPROViSeD and Laying the Groundwork. With July, came a burst of momentum. Our team finalized the IMPROViSeD platform, which centered on using experimental cross-linking data for modelling protein complexes. We now had a solid direction, and the task ahead was to bring this platform to life.
Week of 14th July
The first week after our decision was focused on ensuring the responsiveness of our web page to make it user-friendly and accessible, and this is where we started laying the foundations of our wiki. Meanwhile, we also worked on the team logo design, a crucial part of our identity, and made strides in planning an educational app for computational biology to engage with younger audiences. While the designs were still being refined, the core framework of the project was coming together, and our registration code for modelling went through its initial phase of implementation.
Week of 21st July
Alongside technical progress, we were actively engaging in outreach. Our school visits were postponed this week, but we kept busy with presentations on GPCRs (we were yet to finalize the wet lab aspects of the project), adding to our educational efforts and refining our storytelling abilities for future workshops. These talks were intended to help us present our scientific ideas in a more accessible format.
Week of 28th July
The final week of July saw us diving into full-scale workshops. We also participated in the AIIM judging session (we presented our project to a panel of judges comprising field experts and iGEM ambassadors and also a poster to the congregation) while mapping out a detailed plan for our upcoming experimental procedures. Additionally, we began a literature review focused on AI-based functional prediction of proteins and expanded our documentation efforts for future use. This was also the week when our coding team refined EDMC (Eucledian Distance Matrix Completion) methods and focused on geometric refinement for the protein models.
August
Refining the Platform and Expanding Our Reach. August was a month of refining our technical workflows and enhancing outreach efforts.
Week of 4th August
We began the creation of our Project Promotion Video, a crucial step in communicating our vision to the broader iGEM audience. This week also included a visit to NPS Rajajinagar School, where we connected with students, sparking interest in synthetic biology. On the technical front, the team continued refining the EDMC methods, overcoming some initial challenges and progressing with geometric refinement, ensuring the stability of our model.
Week of 11th August
The middle of August was marked by the organization of a hackathon, where we brainstormed contact lists, platforms, and problem statements. This gave our project a fresh burst of energy. Concurrently, we focused on completing important forms, like the safety forms and team page updates. In terms of coding, we made strides with refinement II for our modelling methods, making the system more robust.
Week of 18th August
By the third week of August, we had successfully completed the second round of CLI refinement (the BEPT tool). Meanwhile, we tackled the final stages of the hackathon, making sure everything was in place for a smooth experience. Documentation was also underway, with updates on the safety and attribution forms.
Week of 25th August
The last week of August was a productive one. We integrated a SDP (Semi-Definite Program) Solver into the platform, further enhancing its functionality. This week also involved refining our safety form submission, ensuring that all necessary precautions were meticulously documented and in line with iGEM requirements. This is also where we had finalized on our wet lab aspects and discussed with Dr. Manjula Das regarding protein availability.
September
The Final Push. September marked the final stretch, where everything started coming together.
Week of 1st September
The first week of the month was marked by the submission of our final safety form and the Project Promotion Video. This was a significant milestone, as it marked the completion of key deliverables for the competition. We focused heavily on getting the video ready, making sure that it visually captured our journey and the core ideas behind IMPROViSeD.
Week of 8th September
With the video submitted, we turned our attention toward the team roster and polishing the final theme design. The homepage design was crafted with care, bringing to life the essence of our project. Simultaneously, the attribution and documentation process began, making sure that every contribution was properly acknowledged and recorded for the final submission. We received the LCN2 Protein this week and began standardizing the in-gel digestion protocol. The software team was focusing on post-processing steps.
Week of 15th September
Mid-September was all about field visits and visual presentation. We organized an industry and clinic visit, aimed at bridging the gap between our theoretical work and real-world applications. A team photo was also taken, which would be used on our website.
Week of 22nd September
As the month drew to a close, we entered the final phase of preparations. Attribution forms, judging forms, and software submissions were all tackled with care and precision, ensuring that nothing was left incomplete. The documentation effort also intensified, with every element being thoroughly reviewed and refined. The post-processing steps for the software were nearing completion. The mass spectrometry data for the in-gel digested peptide was available from the mass spectrometry facility at IISc. We also received MMP9 this week and began standardizing the cross-linking experiments.
Week of 29th September
The final week was all about polishing and validating our work. We focused on optimising the results, making sure that our platform was ready for the judges. The last push toward submission involved wrapping up documentation, preparing final validation results, and ensuring that all loose ends were tied up.
October
Conclusion. From ideation to execution, each phase of our project has been crucial in shaping IMPROViSeD into a powerful tool for understanding protein complexes. Our journey through these months reflects the hard work, collaboration, and dedication of each team member. As we enter the final stages of the competition, we're excited to present our work and demonstrate the impact of our platform.
