Selected Software Projects

• Given a set of nucleotide sequences, sequence analysis approach is used to identify the presence of any Category A bacterial pathogen proteins and identify the bacterial species of the host DNA
• Perl, Bash, BLASTp, BLASTx, tBLASTn, BASH, HTML

• A stable and unbiased set of proteomes ideal for functional annotation and protein classification efforts
• Perl, BASH, HTML

• Web based UniRule automated protein annotation
• Oracle, Hibernate, Java, JSP, JSF, Woodstock, Tomcat

• Scalable and efficient management framework for large-scale OWL ontologies
• Java, MySQL, OWLAPI, Pellet

• A change metrics evaluation suite for evaluating the changes and their semantic implications in evolving OWL ontologies
• Class oriented metrics
• Class definition oriented metrics
• Class subsumption hierarchy oriented metrics
• Axiom oriented metrics
• Java, OWLAPI, Pellet

• Web site for the Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina
• PHP, HTML, CSS, MySQL

• Developing parallel Bayesian probabilistic component analysis algorithm on some fMRI deception data. The goal of experiment is to see if there is any cooperative regions of brain activate together and such activity correlates to the deception activity
• Matlab, MPI, Parallel Programming, Linux Cluster

• Web interface to access OMSSA MS/MS search engine
• Runs on a Linux cluster using Portable Batch System (PBS) and Maui cluster scheduler
• Search is always done on the best available compute node
• Email notification of search events
• Upload spectra now, but run later
• Re-run previously uploaded dta batch files without uploading again
• Results are archived on the system, and can be downloaded by their owners at any time
• Results include the XML output of OMSSA, a csv file with the peptides, a file with the OMSSA command used and a log file
• CGI, Perl, Linux Cluster

• Web frontend for parallel blast search
• Runs on a Linux cluster with mpiBLAST, Portable Batch System (PBS) and Maui cluster scheduler
• Search is done in parallel on the best available compute nodes
• Support both LDAP and local authentication for security and search results management
• Email notification of search events
• Search results are archived on the system, and can be downloaded by their owners at any time
• View search event information, i.e. search parameters, wall time used etc
• CGI, Perl, Linux Cluster

• Initial development with a working version released in 2005
• PHP, HTML, CSS, JavaScript, MySQL, PostgreSQL

• Developed a XML parser for Melanie two-dimensional electrophoresis (2-DE) gel analysis platform data (PHP)
• Developed a tool for visualizing 2D gel electrophoresis data (Java, Applet)
• PHP, Matlab, Java, PostgreSQL

• Developed an online gradebook for CSE class assignments dropbox system, 2000+ students used to submit course works and securely view grades each semester
• Tomcat, JSP, MySQL

• Open source web interface designed for Nessus network security scanner
• Support SSL communication
• User authentication and user access control
• Online user and system management
• Multiple sessions and reusing of scan settings
• Centralized management of scan settings and scan reports
• Network security analysis
• Automatic email notification
• Scan report and scan settings in HTML format
• Nessus, Tomcat, JSP, MySQL, JSSE

• Designed and developed an order entry and inventory management system for Choice Apparel wholesale dealer in Columbia, SC
• VB.NET, ASP.NET, ADO.NET, SQL server 2000

• Designed and developed the multi-channel non-destructive integrity evaluation program
• LabView