Team:IISER Mohali/Partnership



Partnership with IISER Bhopal

The Beginning:

On May 25th of this year, team representatives from all Indian teams gathered together to discuss potential dates for AIIM (All India iGEM Meet). It was the first time all of us met each other (albeit virtually!). As we got to know each other, we realized many of us are working on similar tracks - therapeutics and diagnostics.

Since IISER Bhopal was also working on cancer-related diagnostics, they reached out to us towards the end of May proposing a cancer education and awareness program. Initially it was proposed as a collaborative effort and we gladly agreed to host it with them. Simultaneously we were also planning on holding a conference for all teams working on cancer diagnostics together. Both our teams agreed to reach out to other international teams in this regard and we did.

However, life had plans of its own and unfortunately the Second Wave of the SARS_Cov-2 pandemic disrupted our plans. We realized that hosting another conference along with AIIM would be a considerable investment of time and resources. Moreover, since we did not know which of us would be able to access labs, if at all, and how that would impact our projects - it would be wiser to focus on something more central to our projects.

Collaborative Study:

Both of our teams realized we were going to need to conduct surveys at some point in the future. This was critical to both our projects since it gave us an idea of how acute our respective problems are, how aware the general public and other stakeholders of the project are, and how they would respond to diagnostic kits.

Thus, our first effort was in drafting a common survey and having it reviewed by our respective humanities faculty members. Then, we would do a joint analysis of its results and draw important conclusions. Since surveys take long to gather sufficient data, we thought it was best to release it to the public as soon as possible.

The first set of questions were reviewed by Dr. Sandip Kumar Agarwal from IISER Bhopal. They gave us important feedback and asked us to include more objective questions, break our survey into different sections, and use the least amount of scientific jargon. The survey was circulated via social media and received 86 responses. The analysis of the awareness poll can be found here.

Machine Learning Model and Chatbot:

Since we work struggling with a quantitative method to establish a protocol for choosing biomarkers. We approached IISER Bhopal to discuss our problem. They put us in touch with a team member, Harshul who was passionate about solving problems using machine learning. After hearing our problem statement, he got down to building a model with constant feedback from our team. We had two ways to approach the problem, one was purely through molecular level information on proteases, and the other through lifestyle factors. Since it was difficult to obtain information on the latter from reliable databases, we decided to split the problem into two parts.

  1. Build a ML model to choose a panel of biomarkers.
  2. Build a chatbot to take information from the user about their lifestyle

While we would actively use (1) in our project model, we could use (2) as an upgrade to our ML model as soon as we got a reliable data source. The model has been explained in-detail in the software page.

Part Characterization:

Towards the beginning of July, our survey had been finalized. During a subsequent meeting, we helped IISER Bhopal place orders from IDT since we had just placed our own. In August, as we were returning to the lab, the Judging Forms were released. We learnt that IISER Bhopal had not received confirmation to return to campus back then. Since they wished to make a Contribution to fulfil their bronze medal criteria by expanding a Part from the Registry, we planned on waiting until late September in case they needed our help. Meanwhile, IISER Bhopal had prepared a protocol and planned this step of their project.

Finally in October we helped them characterize the part ’’ECFP Coding Device with promoter, RBS, Coding Sequence and Terminator’’. It was part of the ‘Welcome Kit’: Kit Plate 2 - 15 P.

Together, we not only modified the protocol, we also went beyond what was the initial plan. Initially, what seemed like trivial tasks required active involvement from both teams' wet lab departments.
The final protocol can be found on IISER Bhopal’s Parts Page and here.

Key Takeaways and Future Tasks:

  1. Our collaborative survey helped both the teams better understand their own projects. Since both of us were working on diagnostics, it was very important to understand how each stakeholder would perceive such a kit. We received valuable inputs from IISER Bhopal and actively brainstormed on ways to draw out actionable information from the survey responses.
  2. The machine learning model significantly helped us improve our project. We later on got in touch with a NGO, who agreed to help us with the information we needed to scale up our model. This will help us continue our project beyond iGEM 2021 and integrate the chatbot into our app. We look forward to continuing this part of our project.
  3. The Registry Part addition, besides being a medal criteria also helped us extract the best out of iGEM! Our wet lab team helped troubleshoot their protocol, besides being able to provide useful information to IISER Bhopal. Since we have also built a spectrometer for our project, as a next step we can also validate the fluorescent protein and our own hardware in getting readings from it. Unfortunately, since we did not have the laser corresponding to CFP excitation, we could not show the results in iGEM 2021.

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