= C1Net Workshop 2 on Metabolic Modelling = == Course Timetable and Resources Index == ||'''Day''' ||'''Time''' ||'''Place''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' || ||'''Monday''' ||13:00 || || || || || ||28/09/15 ||13:30 ||Mary O'Brien Room ||Workshop registration opens. || ||MP, DF, (KA and NM) || || ||14:00 ||" ||Opening and introductions || ||DF || || ||14:30 ||" ||L1. Structure of metabolic networks and their representation ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/L1/Slides.pdf|slides]] ||MP || || ||15:30 ||" ||Tea/coffee || || || || ||16:00 ||" ||L2. Basic Concepts for Modelling Enzyme Kinetics ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L2.pdf|Basic Concepts for Modelling Enzyme Kinetics]] ||DF || || ||17:00 ||" ||P1. Plotting enzyme kinetic functions; graphical solution to a two enzyme system; rough time course calculation for an enzyme-catalysed reaction Plus: Computers: checking internet connectivity, software installati on. ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork2/Practicals/Practical1|Practical_1]] and [[http://mudshark.brookes.ac.uk/Meetings/C1netWork2/Practicals/ScrumPyVM|Installation]] of [[http://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||DF, MP, KA || || ||18:30 ||Lodge ||Room registration for Pipe Partridge block (available from 14:00) || || || || ||19:00 ||Old Library ||Opening reception || || || || ||19:30 ||Deneke Dining Hall ||Dinner || || || || || || || || || || ||'''Tuesday''' ||08:00 ||Deneke Dining Hall ||Breakfast || || || ||29/09/15 ||09:00 ||Mary O'Brien Room ||L3. Further enzyme kinetics for model building, plus ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L3.pdf|Lecture 3 slides]] ||DF || || ||10:00 || ||L3a. Fitting enzyme kinetica ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L3a.pdf|Lecture 3a slides]] [[Meetings/C1netWork2/Plan/Lec3Supp|Supplementary Information on fitting kinetics]] ||DF || || ||10:30 || ||Coffee/Tea || || || || ||11:00 || ||L4. Python and ScrumPy ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/L4/Slides.pdf|Introduction to/Recap of Python]] ||MP || || ||12:30 ||Mary O'Brien Room ||Lunch (buffet) || || || || ||13:30 ||Mary O'Brien Room ||P2. Python and ScrumPy / L4a: Construction and Analysis of Kinetic Models with ScrumPy (Those remembering their Python and ScrumPy can move ahead to P3) ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/L4A/Slides.pdf|Construction and Analysis of Models With ScrumPy]] [[http://mudshark.brookes.ac.uk/Meetings/C1netWork2/Practicals/Practical2|Practical 2 Instructions]] ||MP, DF, (HH , KA,NM) || || ||14:30 || ||P3. Investigating properties of basic model structures ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork2/Practicals/Practical3|Kinetic Modelling]] ||MP, DF, (HH, KA, NM) || || ||15:30 || ||Tea/Coffee || || || || ||16:00 || ||L5. Understanding the control of metabolism - intro to Metabolic Control Analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L5.pdf|Lecture 5 slides]] [[http://mudsharkstatic.brookes.ac.uk/Reprints/ControlofFlux/KBF95BST.pdf|Reprint of The Control of Flux]] ||DF || || ||17:00 || ||P3 continued || ||MP, DF, (HH, KA, NM) || || ||17:30 || ||Close || || || || ||19:00 ||Deneke Dining Hall ||Dinner || || || || || || || || || || ||'''Wednesday''' ||08:00 ||Deneke Dining Hall ||Breakfast || || || ||30/09/15 ||09:00 ||Mary O'Brien Room ||L6. Applications of Metabolic Control Analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L6.pdf|Lecture 6 slides]] ||DF || || ||10:00 ||" ||P3 conclude and P4. Feedback inhibition. ||[[http://mudshark.brookes.ac.uk/Meetings/C1netWork2/Practicals/Practical4|Feedback inhibition modelling]] ||MP, DF, (HH, NM) || || ||10:30 || ||Coffee/Tea || || || || ||11:00 || ||P4 continued. || ||MP, DF, (HH, NM) || || ||12:30 ||Mary O'Brien Room ||Lunch || || || || ||'''13:00 ''' || ||'''Free time. '''Possibility of punting using the [[http://www.lmh.ox.ac.uk/Conferences/What-LMH-offers/Punting.aspx|college punts]] on the river Cherwell, or if unavailable, from [[http://www.cherwellboathouse.co.uk/#section-04|the Cherwell Boathouse]]. || || || || ||16:00 ||Mary O'Brien Room ||Tea/Coffee. || || || || ||16:30''' ''' || ||L7. Examples of metabolic models: threonine synthesis, Entner Duodorff pathway ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L7.pdf|Lecture 7 slides]] [[http://mudsharkstatic.brookes.ac.uk/Reprints/threonine/BJ3560415.pdf|threonine paper 1]] [[http://mudsharkstatic.brookes.ac.uk/Reprints/threonine/BJ3560425.pdf|paper 2]] [[http://mudsharkstatic.brookes.ac.uk/Reprints/threonine/BJ3560433.pdf|paper 3]] [[http://mudsharkstatic.brookes.ac.uk/Reprints/zmobilis/RutkisMicrobiol13.pdf|Entner-Duodoroff paper]] [[http://mudsharkstatic.brookes.ac.uk/Reprints/zmobilis/RutkisMicrobiol13suppmat.pdf|Entner-Duodoroff supp mat]] ||DF || || ||17:30 || ||Prac 4 continued. || ||DF, NM || || ||19:00 ||Deneke Dining Hall ||Dinner || || || || || || || || || || ||'''Thursday''' ||08:00 ||Deneke Dining Hall ||Breakfast || || || ||1/10/15 ||09:00 ||Mary O'Brien Room ||L8. MCA perspective on metabolic engineering from case studies. ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L8.pdf|Lecture 8 slides]] ||DF || || ||10:00 || ||P4. Complete || ||DF, MP, KA, NM || || ||10:30 || ||Coffee/Tea || || || || ||11:00 || ||L9. Calvin cycle model ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/L9/Slides.pdf|Lecture 9 Slides]] ||MP || || ||12:30 ||Mary O'Brien Room ||Lunch || || || || ||13:30 ||Mary O'Brien Room ||P5. Calvin cycle simulation. ||[[Meetings/C1netWork2/Practicals/Practical5|Control Analysis of the Calvin Cycle]] ||DF, KA, NM || || ||15:30 || ||Tea/Coffee || || || || ||16:00 || ||P. 5 continued || ||DF, KA, NM || || ||17:30 || ||Close || || || || ||18:30 ||Monson Room ||Pre-dinner drinks || || || || ||19:00 ||Monson Room ||'''Workshop dinner''' || || || || || || || || || || ||'''Friday''' ||08:00 ||Deneke Dining Hall ||Breakfast and room checkout (Lodge) || || || ||2/10/15 ||09:00 ||Mary O'Brien Room ||P6 Threonine || [[Meetings/C1netWork2/Practicals/Practical6|Threonine practical instructions]]||MP, DF, HH, KA, NM || || ||10:30 || ||Coffee/Tea || || || || ||11:00 || ||Group photo || || || || ||11:15|| ||General Discussion and Conclusions form the week|| ||MP, DF, HH, KA, NM|| || ||12:00 || ||Closing remarks. Presentation of certificates || ||MP, DF, HH, KA, NM || || ||12:30 ||Mary O'Brien Room ||Sandwich lunch (packed) || || || || ||13:30 || ||Departure || || || || || || || || || ||