1. Krebs Cycle Analyzer Christopher Clement Ryan Miller BMES 546

2. Problem Need to develop a tool to simulate the change in the chemical state of a system as the Krebs Cycle produces energy. Want a general-use tool to analyze/simulate any system of chemical reactions.

3. Krebs Cycle Process that takes glucose and converts it to energy through a series of chemical reactions. Image from https://wikispaces.psu.edu/pages/viewpage.action?pageId=97552144https://wikispaces.psu.edu/pages/viewpage.action?pageId=97552144

4. Demo

5. Data Flow User Loads Excel Template Cycle Generated (GraphViz) Graphs / GUI Initialized User Presses Start Click Node Click Arrow Export Sim Data

6. Data Flow – Press Start User Presses Start System applies chemical reactions to update state Charts and cycle updated Until Stop is pressed

7. Data Flow – Node Clicked Click Node Popup prompts user to update chemical amount System state updated with new amount

8. Data Flow – Arrow Clicked Click Arrow Popup prompts user to update chemical reaction coefficients Chemical reaction coefficients updated with new numbers

9. Data Flow – Export Sim Data Export Sim Data User selects output file Simulation data written to Excel file

10. Input Data Format Excel template – Worksheet containing an adjacency matrix – Worksheet containing chemical reactions – Worksheet containing start state

11. Data Structures Adjacency matrix stored as a numerical matrix State and labels stored as cell arrays Arrow data stored as cell array Struct containing key methods passed to GUI Timer used to iterate simulation

12. Challenges Difficult to keep user input file simple – Associate node links with chemical reactions Backend-frontend integration – Elegant solution was not obvious Node coloring

13. Future Work Improve graph layout algorithm Additional chart functionality Reduce number of windows Improve node coloring Additional housekeeping

14. References http://www.mathworks.com/matlabcentral/fileexchange/4518 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651525/ http://www.graphviz.org

15. Questions?