| Group |
2024-19 |
Status |
inprogress |
| Title |
Bioinformatics Software Development for DNA Toehold Design Project |
| Supervisor |
N. Kharma |
| Description |
Our project aims to develop a bioinformatics software tool to assist in the design of DNA toehold switches. These switches are synthetic DNA sequences (representing template strands) that allow for mRNA transcription (leading to protein generation) but only when correctly complemented by certain DNA inputs (‘triggers’) at the promoter site. The project will involve designing, building and verifying a bioinformatics software tool that searches a very large space for a diverse set of optimal/near-optimal designs (i.e., sequences), where optimality is a function of a set of (often conflicting) factors that include 2D folding (in both the ON and OFF states), thermodynamic stability, targeting specificity. The deliverables are a user-friendly software platform (together with brief installation, user and maintenance manuals), for the purpose of DNA toehold design in biotech industry/research. The applications for such technology include DNA virus detection and (biological) signal amplification. |
| Student Requirement |
Knowledge in bioinformatics and DNA/RNA structure
Experience in software development
Experience in algorithm implementation
Experience in AI/Machine Learning tools and concepts(recommended)
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| Tools |
Software/Test Equipment: Python/Java/C++/C/MATLAB or similar for data analysis.
Hardware: Computers for development and testing.
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| Number of Students |
6 |
| Students |
Oyeyimika Adeoye, Julian Aloise, Ivan Balkanski, Anthony Fata, Matthew Fellen, Sheng Han Wang |
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