Date of Award
Master of Science in Computer Science
Computer Science and Statistics
The goal of the work described in this thesis is to improve the software tool used to extract relevant data from an existing larger database, the Protein Data Bank (PDB), in order to populate the newly designed AMPed database that has been developed by Professor Lenore Martin's microbial peptide research group at URI. However, not all data from the PDB site can be automatically loaded into the AMPed database. Thus, this work describes a user-friendly secure web-based tool for manually transferring, editing, and contributing structural and anti-microbial experimental data generated by research labs around the globe into the AMPed.
Once users have uploaded their data into AMPed, it then goes through an evaluation process where it is placed in a 'pending' mode, waiting to be reviewed by Professor Martin or other designated evaluator ('reviewer'). The reviewer gets notified through email when a new entry has been submitted or added to the database.
The designated content reviewer can access the newly uploaded data through a private and secure web-based user interface to evaluate the incoming entries. Within this tool, the reviewer can approve the data, edit it, or simply reject it. The reviewer can then communicate back to the data contributors through email, and inform them about the status of their contributions. If the data has been approved for addition to AMPed, it will rapidly be made available to anyone searching the database.
In addition, we have increased the efficiency of the AMPed website through major improvements in graphical design and usability using the latest techniques available.
Herrera, Abraham, "Web Based Bioinformatics Tool for Contributing Content to the Anti-Microbial Peptide Editable Database" (2016). Open Access Master's Theses. Paper 1133.