Introducing legacy program scripting to molecular biology toolkit (MBT)
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| Title: | Introducing legacy program scripting to molecular biology toolkit (MBT) |
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| Authors: | Newell, Todd |
| Source: | Theses |
| Publisher Information: | RIT Digital Institutional Repository |
| Publication Year: | 2008 |
| Collection: | Rochester Institute of Technology: RIT Scholar Works |
| Subject Terms: | JavaCC, Molecular biology toolkit, Molecular visualization, Script |
| Description: | 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. |
| Document Type: | text |
| File Description: | application/pdf |
| Language: | unknown |
| Relation: | https://repository.rit.edu/theses/6936; https://repository.rit.edu/context/theses/article/7941/viewcontent/TNewellMastersProjectPPt.pdf; https://repository.rit.edu/context/theses/article/7941/filename/0/type/additional/viewcontent/TNewellMastersProjectReport.pdf |
| Availability: | https://repository.rit.edu/theses/6936 https://repository.rit.edu/context/theses/article/7941/viewcontent/TNewellMastersProjectPPt.pdf https://repository.rit.edu/context/theses/article/7941/filename/0/type/additional/viewcontent/TNewellMastersProjectReport.pdf |
| Accession Number: | edsbas.A2F6D7C1 |
| Database: | BASE |
Nájsť tento článok vo Web of Science | Abstract: | 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. |
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