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Metabolic Modeling in Bioinformatics: Understanding the Work Cycle

This scenario introduces metabolic modeling in bioinformatics, focusing on the work cycle and the calculation of metabolite concentration changes. Learn how to initialize concentrations, constants, and calculate rates of change to simulate biological processes effectively.

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Metabolic Modeling in Bioinformatics: Understanding the Work Cycle

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  1. Welcome toIntegrated BioinformaticsWednesday, 27 October • Scenario 5: Metabolic modeling (Introduction)

  2. You

  3. 40 20 60 0 AAAR!! 60 ft/sec * 60 sec = 3600 ft ???

  4. 40 20 60 0 AAAR!! 60 ft/sec * 60 sec = 3600 ft ???

  5. New position 40 20 60 0 AAAR!! speed * 0.1 sec = small change in position + original position

  6. New position 40 20 60 0 AAAR!! speed * 0.1 sec = small change in position + original position

  7. 40 20 60 0 AAAR!! Modeling: The Work Cycle

  8. 40 20 60 0 AAAR!! x0 Position (x) Modeling: The Work Cycle • Initialize concentrations for each metabolite

  9. 40 20 60 0 AAAR!! x0 Position (x) [G6P] VMax[G6P] + Km d[F6P] / dt = dP / dt = Modeling: The Work Cycle • Initialize concentrations for each metabolite 2. Initialize constants for each reaction

  10. 40 20 60 0 AAAR!! x0 Position (x) Modeling: The Work Cycle • Initialize concentrations for each metabolite 2. Initialize constants for each reaction 3. Calculate the rate of change of each metabolite, given the current concentrations dx/dt

  11. 40 20 60 0 AAAR!! x0 Position (x) . dt = x Modeling: The Work Cycle • Initialize concentrations for each metabolite 2. Initialize constants for each reaction 3. Calculate the rate of change of each metabolite, given the current concentrations 4. Multiply each rate of change by a time increment, giving an increment for each metabolite dx/dt

  12. 40 20 60 0 AAAR!! x0 Position (x) = x x0 + x => new x Modeling: The Work Cycle • Initialize concentrations for each metabolite 2. Initialize constants for each reaction 3. Calculate the rate of change of each metabolite, given the current concentrations 4. Multiply each rate of change by a time increment, giving an increment for each metabolite . dx/dt dt 5. Add the increment to the original concentration to a new concentration

  13. 40 20 60 0 AAAR!! x0 Position (x) = x x0 + x => new x Modeling: The Work Cycle • Initialize concentrations for each metabolite 2. Initialize constants for each reaction 3. Calculate the rate of change of each metabolite, given the current concentrations 4. Multiply each rate of change by a time increment, giving an increment for each metabolite . dx/dt dt 5. Add the increment to the original concentration to a new concentration

  14. V+ S1 S2 V- S1 S2 Ks1 Ks2 Kp1 Kp2 - S1 P1Ks1 Kp1 S2 P2Ks2 Kp2 1 + + 1 + + S1 + S2P1 + P2 Modeling GlycolysisUsing data of Eisenthal & Cornish-Bowdin Equation 2 V =

  15. V+ S1 S2 V- S1 S2 Ks1 Ks2 Kp1 Kp2 - V = S1 P1Ks1 Kp1 S2 P2Ks2 Kp2 1 + + 1 + + S1 + S2P1 + P2 Modeling GlycolysisUsing data of Eisenthal & Cornish-Bowdin

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