ICT Mumbai and IISER Berhampur have been very supportive of each other’s projects since teaming up for Event Organisation in the All India iGEM Meet in IISc Bangalore. There have been several informative discussions regarding the Values and Risks involved in the projects. In addition, IISER Berhampur has helped ICT mumbai smoothen out the errors while uploading the Promotional Video and in the Subtitle File generation. Meanwhile, ICT Mumbai has helped in clearing out doubts regarding Visa Procedures. These teams have also collaborated extensively on the modelling aspect of the projects. The details are as follows:
07/06/2022:
IISER Berhampur was facing issues regarding the choice between the whole-cell and ligand-based SELEX due to difficulties in screening for suitable aptamers that can bind to the uropathogenic E.coli. In addition, there were several web servers that they had tried and tested, like MAWS, that could not provide the desired results with appreciable accuracy. Meanwhile, ICT Mumbai could not decide if they should order sequences reported in the literature directly or order sequences suggested by a computational model like RBS Library Calculator. We were both trying to figure out ways on how to design the first set of sequences. With different opinions from Human Practices with different experts and the literature having different methods, we both were just confused. We presented each other our problem in a meet and came towards conclusive thoughts. It was very important for us to hear from each other on what could be pragmatically achieved with the time frame of the competition and what aspects could be further built upon as well.
15/06/22-20/06/22
Both the teams collaborated to learn about the RNAFold web-server and how to analyse the implications of the DNA secondary structure on the translationational efficiency or half-life.
28/06/22-27/07/22
We brainstormed every week together regarding our AIIM presentations. When the All India iGEM Meet responsibilities were getting distributed we took the same set of responsibilities and worked on them together till the end of AIIM.
Discussions between the team regarding their projects continued throughout the timeframe. Continuous update on every deadline and results. ICT-Mumbai completely missed adding vtt file to their promo video. Thankfully in their conversation with IISER Behrampur they realised about this. IISER Behrampur very generously helped us adding the English subtitles last minute!!
14/09/2022
IISER-BPR tried using a Neural Network based model called AptaNet during their initial screening phase to predict the binding efficiency of their aptamers. It did not give desirable results but they shared their ideas and learnings with us and we then thought of using Neural Networks to try and predict protein expression levels. However, we discovered that there exists no such open-source Neural Network for predicting the expression using a sequence string. So, we developed and trained a model of our own using data from already existing literature and it showed promising results in the initial trials.
IISER Berhampur was facing issues regarding choosing the right web-server to perform folding of the aptamers. ICT Mumbai was very helpful in clarifying some of these doubts by suggesting the Molecular Operating Environment (MOE) to perform our protocols. Upon discussion with ICT Mumbai, IISER Berhampur was able to come to the conclusion that RNA Composer would be the best candidate for such tasks and so the two teams decided to join forces to reduce the burden of brute-forcing nearly 500 aptamers.
30/09/2022
ICT Mumbai very graciously offered to connect IISER Berhampur with Dr. Reshamwala, who is a professor in ICT Mumbai, with an expertise in Intellectual Property rights. He advised us regarding the future plans of our prototype and how we must proceed with applying for IPRs for our project.
We wish to continue our partnership and camaraderie beyond the iGEM Time Frame. IISER Behrampur is a greatly talented team. Absolutely glad to have interacted with the team.
