| Group |
2017-11 |
Status |
completed |
| Title |
Ribosoft |
| Supervisor |
Dr. N. Kharma |
| Description |
A stable web-service which would automatically provide ranked designs of independent ribozymes. From a black-box perspective, the user enters a target RNA sequence, and provides environment parameters. The output provides a list of ranked ribozymes with sequence information and their characteristics.
The web-service is used to return correct information on the ribozymes, used to target a specific RNA sequence, and silences the gene via RNA cleavage. The web-service will interface with various independent web-services to provide results that are then ranked using multi-objective optimization.
Web-service UI should be user-friendly, and provide all design specifications for the target RNA sequence to cleave, and the ribozymes to use.
Optimization and generalization of existing algorithms to facilitate the use of the web-service is necessary to process the large data samples (big data), and assess all the permutations of the ribozyme designs. Real-life validation of the results will be determined by an outside source, determining if the algorithms are correctly generating ribozyme designs to cleave the target RNA sequence.
Software documentation is necessary to allow for maintenance of the service in the future by developers.
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| Student Requirement |
A stable web-service which would automatically provide ranked designs of independent ribozymes. From a black-box perspective, the user enters a target RNA sequence, and provides environment parameters. The output provides a list of ranked ribozymes with sequence information and their characteristics.
The web-service is used to return correct information on the ribozymes, used to target a specific RNA sequence, and silences the gene via RNA cleavage. The web-service will interface with various independent web-services to provide results that are then ranked using multi-objective optimization.
Web-service UI should be user-friendly, and provide all design specifications for the target RNA sequence to cleave, and the ribozymes to use.
Optimization and generalization of existing algorithms to facilitate the use of the web-service is necessary to process the large data samples (big data), and assess all the permutations of the ribozyme designs. Real-life validation of the results will be determined by an outside source, determining if the algorithms are correctly generating ribozyme designs to cleave the target RNA sequence.
Software documentation is necessary to allow for maintenance of the service in the future by developers.
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| Tools |
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| Number of Students |
5 |
| Students |
Thomas Vaudry-Read (ECE), Anita Haurie (ECE), Daniel Adams (ECE), Steve Ferriera (CSE), Christopher Paslawski (CSE) |
| Comments: |
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| Links: |
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