Computational Team

The Optimus Primer GUI offers an interface for independent and desktop centered design. IMPLEMENTATION DETAILS FOR GUI OPTIMUSPRIMER NEEDED

The surface application is written in C# for the Microsoft Surface. The system is accessible from the G-Nome Surfer interface. Users create designs by sliding the highlight on the gene's ends and selecting the primers. Users then can BLAST designs and run tests based on alignment and Gibb's free energy. Alignment results are generated using a .jar and BLAST results are generated using the NCBI BLAST software. Both are accessed from the command line, with BLAST results being written to file and parsed out for display and alignment results being pulled from common output for further calculation for hetero-dimer and self-dimer tests. The surface application provides a streamlined, intuitive interface for learning and collaborative design.

The surface application and the desktop GUI use the same algorithms.

Ethical User Study practices:

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Overview: Optimus Primer

Optimus Primer is an environment for designing primers and saving genes as BioBricks. We have built two interfaces-a desktop GUI for independent research and design and the surface application for collaborative learning and design. Both allow users to run a number of tests on designs to determine their feasibility before saving as BioBricks.

Demo Video

Wetlab

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Results:

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Safety practices: