Todd Newell


Successful navigating of the ever-changing landscape of molecular visualization programs requires a common thread that can offer users an oasis from the maelstrom of new languages, proprietary applications, and miniscule software life-cycles. Crossapplication scripting remains the benchmark, allowing scientists and researchers to speak a common tongue. The introduction of a new, powerful visualization language, Molecular Biology Toolkit (MBT), has tempted many users to abandon previous methodologies and adopt a new mode of research. MBT, however, is not without drawbacks. Its lack of scripting capabilities creates unmanageable complexity for unsophisticated end-users, namely those without the ability to program. MBT, thus, lacks the basic handholds for its widespread acceptance in the molecular visualization community. As a toolkit package without its own mode of execution, its design challenges users to develop their own customized features and applications. However, able to contribute as a text based virtual molecular collection or a fully rendered 3D molecular representation, MBT has the tools researchers want in a new visualization program. Using JavaCC to parse legacy commands and in turn executing MBT methods all from a single, simple command, I have reintroduced scripting to the modern molecular visualization landscape. Combining these two programs, this project takes steps to encourage the exciting molecular manipulations capable in MBT while bridging to a friendly, user-centric scripting patterns required by end-users not entrenched in software development.

Publication Date


Document Type

Master's Project

Student Type


Department, Program, or Center

Computer Science (GCCIS)


Geigel, Joseph

Advisor/Committee Member

Craig, Paul

Advisor/Committee Member

Bischof, Hans-Peter


Note: imported from RIT’s Digital Media Library running on DSpace to RIT Scholar Works in February 2013.


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