A modular, FAIR-compliant MATLAB framework for ODE biochemical pathway modeling, analysis, and parameterization.
ProblemODE-based biological models become hard to build, parameterize, analyze, and share when each lab relies on bespoke scripts.
ContributionArchitected the framework, implemented parameter estimation, sensitivity analysis, and profile likelihood analysis, and connected MATLAB tooling with COPASI and standard formats.
OutcomeValidated the workflow across systems biology and neuroscience models and published the work in Neuroinformatics.
Architected and built a comprehensive scientific software framework following FAIR principles
Implemented algorithms from scientific literature for parameter estimation, sensitivity analysis, and profile likelihood analysis
Engineered interfaces between MATLAB solvers, COPASI, SBML, and SBtab
Created documentation and managed Git/GitHub collaboration across institutions
Reusable ODE modeling pipelineFrom model setup through simulation, parameter estimation, sensitivity analysis, and result validation.
Start
Model setup
Simulation
Parameter estimation
Sensitivity analysis
Profile likelihood
Results
2013-2015 / MSc thesis and research scholarship
Porphyrin Materials Research
Master's-level wet-lab and analytical work on ionic self-assembly of a porphyrin octacation with TPPS-based anions.
ProblemThe study tested whether an unusual porphyrin octacation could form isolable nanomaterials through charge-driven self-assembly.
ContributionSupported synthesis, purification, spectroscopy, concentration analysis, and undergraduate student supervision within a larger collaboration.
OutcomeContributed to a Tetrahedron paper reporting binary, ternary, and variable-composition porphyrin ionic solids.
Worked with the NiTBTAP octacation and TPPS-derived anions to probe how charge balance, pH, and porphyrin speciation affected ionic self-assembly.
Prepared and purified porphyrin assemblies in acidic aqueous media, keeping reaction ratios controlled for downstream characterization.
Used spectroscopy and concentration analysis to compare product compositions against charge-neutral ionic-solid expectations.
Co-supervised two undergraduate interns and contributed publication-ready evidence for binary, ternary, and variable-composition materials.
A modular, FAIR-compliant MATLAB framework for ODE biochemical pathway modeling, analysis, and parameterization.
Problem
ODE-based biological models become hard to build, parameterize, analyze, and share when each lab relies on bespoke scripts.
Contribution
Architected the framework, implemented parameter estimation, sensitivity analysis, and profile likelihood analysis, and connected MATLAB tooling with COPASI and standard formats.
Outcome
Validated the workflow across systems biology and neuroscience models and published the work in Neuroinformatics.
Architected and built a comprehensive scientific software framework following FAIR principles
Implemented algorithms from scientific literature for parameter estimation, sensitivity analysis, and profile likelihood analysis
Engineered interfaces between MATLAB solvers, COPASI, SBML, and SBtab
Created documentation and managed Git/GitHub collaboration across institutions