Working with team members, and under the guidance of two professors, on a Java based Metabolic Optimization and Simulation Tool designed to research organisms and their respective metabolic networks, with the intention of both simulation and discovering ideal gene knock-out combinations for increasing production of target metabolites.

Eclipse, GitHub, Java, JSBML, SBML, SQlite, XML, among other languages and software.

Save Functionality

Worked towards adding SBML (systems biology markup language) save functionality to any optimized or simulated model using the JSBML library.

Settings Factory

Added infrastructure to facilitate for intuitive past session memory access. Used a Factory design pattern which worked by reading and creating an xml settings file, while using get and set methods for easy modifications.

Uses include recently used directories to save user time during browsing as well as the currently installed Gurobi directory as selected by user.


Adding support for acquiring a knowledge of Gurobi's current status on the working computer using various methods.

Gurobi Optimizer is a powerful solver for mathematical programming, featuring support for various programming and modeling languages. It's activation is essential for the working of MOST given its use of Optimization methods.

Phase Separation in a Lipid/Cholesterol System: Comparison of Coarse-Grained and United-Atom Simulations. [PDF]
Residue-Based Coarse Graining using MARTINI Force Field in NAMD [PDF]

VMD - Visual Molecular Dynamics [Link]
GROMACS - Groningen Machine for Chemical Simulations [Link]