Developing bioinformatics algorithms tools for handling multiple different quantitative mass spectrometry data and large peptide repositories.

Key Achievements:

* Integral to the development of TagGraph (written in Python/SQLite), a powerful computational tool that addresses two principle challenges of searching very large sequence spaces using mass spectrometry data. TagGraph accurately assigns peptides bearing multiple unspecified post-translational modifications (PTMs) or amino acid substitutions and thereby expands our ability to survey the full landscape of PTM function and regulation.

* Developing “AntigeMS” (written in PHP/Python/MySQL), a large collaborative repository of immunoprecipitation-captured antigenic peptides. In addition to data aggregation, AntigeMS implements multiple analysis and visualization tools to help its users compare various aspects of the data. Streamlined data uploads, stringent data quality checks, and general maintenance. Thus far, AntigeMS has enabled the simplification and deconvolution of the complex and ambiguous antigen presentation peptides in various contexts including cancer and viral infections.

* Created virtual machines with Hyper-V in order to have multiple OS flavors for working and testing environments. This has served as the platform for porting lab software/tools to AWS (Amazon Web Services) and other commonly used operating systems.

* Collaborated with members of the bench science team in order to design and build customized scripts and software solutions that accelerate the analysis of mass spectrometry (MS) data thus facilitating biological discovery.

* Serving as the general lab coding and computational consultant.

* Automated MS data-archiving pipeline, integrating both local and cloud-based redundancies.

Directed all aspects of software development and systems integration projects for a variety of applications.

Key Achievements:

* Facilitated the design and development of internal use web UI for the QA lab using PHP/MySQL to allow easy data entry, inventory tracking, and machine listing test case management.

* Spearheaded the automation of in-house testing tools by creating PHP/Python/MySQL scripts.

* Streamlined information presentation by incorporating the automated test cases into the QA portal and display test results back to web pages in the form of tables and charts.

* Improved testing efficiency and saved resources by maintaining and enhancing the in-house data integrity test tool (written in Python).

Directed all aspects of maintaining and enhancing monthly finance tools including the updating of UI per user request, billing rules, billing, and payment calculations. Designed database tables to store billing rules for hospitals, doctors’ contracts, and other required information for billing purposes. Developed SQL queries and stored procedures to generate reports for use by the finance department.

Key Achievements:

* Improved the process of invoicing such as web pages and enabled finance users to input the billing rules and incorporate them along with other required billing information into stored procedures used to create invoices to hospitals.

* Developed web pages to enable finance users to input doctors’ contracts.

* Created SQL stored procedures to compute doctors’ compensations and to generate pay stubs thereby allowing the finance department to conduct query via web pages.

Responsible for the deployment process of the company’s in-house developed software called Satmetrix Composer Lite and MarketStat Phase II.

Key Achievements:

* Developed search tools and web survey translations to enhance production systems and created Perl scripts to export and modify data for projects.

* Developed user-friendly web interfaces using ASP and Perl for managing database and wrote SQL queries to ensure table integrity.