Differences between revisions 13 and 14

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	slides	MP
	15:30	"	Tea/coffee
	16:00	"	L2. Basic Concepts for Modelling Enzyme Kinetics	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.	Practical_1 and Installation of 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	Lecture 3 slides	DF
	10:00		L3a. Fitting enzyme kinetica	Lecture 3a slides Supplementary Information on fitting kinetics	DF
	10:30		Coffee/Tea
	11:00		L4. Python and ScrumPy	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)	Construction and Analysis of Models With ScrumPy Practical 2 Instructions	MP, DF, (HH , KA,NM)
	14:30		P3. Investigating properties of basic model structures	Kinetic Modelling	MP, DF, (HH, KA, NM)
	15:30		Tea/Coffee
	16:00		L5. Understanding the control of metabolism - intro to Metabolic Control Analysis	Lecture 5 slides	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		DF
	10:00	"	P3 conclude and P4. Feedback inhibition.		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 college punts on the river Cherwell, or if unavailable, from the Cherwell Boathouse.
	16:00	Mary O'Brien Room	Tea/Coffee.
	16:30		L7. Examples of metabolic models: Calvin cycle, threonine synthesis, Entner Duodorff pathway		MP + DF
	17:30		S1: Review of outcomes from practicals 3 and 4.		DF, NM
	19:00	Deneke Dining Hall	Dinner

Thursday	08:00	Deneke Dining Hall	Breakfast		0
1/10/15	09:00	Mary O'Brien Room	L8. MCA perspective on metabolic engineering from case studies.		DF
	10:00		P5. Calvin cycle simulation.		DF, MP, KA, NM
	10:30		Coffee/Tea
	11:00		P5 cont		DF, MP, KA, NM
	12:30	Mary O'Brien Room	Lunch
	13:30	Mary O'Brien Room	P6. Engineering threonine production.		DF, KA, NM
	14:30		P6 cont		MP, DF
	15:30		Tea/Coffee
	16:00		G1: Intro to group work problems.		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	G1 continued		MP, DF, HH, KA, NM
	10:30		Coffee/Tea
	11:15		Reports from groups
	12:00		Any questions? Closing remark. Presentation of certificates		MP, DF, HH, KA, NM
	12:30	Mary O'Brien Room	Sandwich lunch (packed)
	13:30		Departure

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-||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">L4.  Python and ScrumPy ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/L4/Slides.pdf|Introduction to/Recap of Python]]||<style="text-align:left;vertical-align:top">MP ||
+||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">L4.  Python and ScrumPy ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/L4/Slides.pdf|Introduction to/Recap of Python]] ||<style="text-align:left;vertical-align:top">MP ||
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-||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">L5. Understanding the control of metabolism - intro to Metabolic Control Analysis ||<style="text-align:left;vertical-align:top">                        [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L5.pdf|Lecture 5 slides]]||<style="text-align:left;vertical-align:top">DF ||
+||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">L5. Understanding the control of metabolism - intro to Metabolic Control Analysis ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L5.pdf|Lecture 5 slides]] ||<style="text-align:left;vertical-align:top">DF ||
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-||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:00 ||<style="text-align:left;vertical-align:top">Mary O'Brien Room ||<style="text-align:left;vertical-align:top">Tea/Coffee ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="56px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:30''' ''' ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Examples of metabolic models L8.  MCA perspective on metabolic engineering from case studies. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF ||
+||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:00 ||<style="text-align:left;vertical-align:top">Mary O'Brien Room ||<style="text-align:left;vertical-align:top">Tea/Coffee. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="56px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:30''' ''' ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">L7. Examples of metabolic models: Calvin cycle, threonine synthesis, Entner Duodorff pathway ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP + DF ||
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-||<height="20px" style="text-align:left;vertical-align:top">1/10/15 ||<style="text-align:left;vertical-align:top">09:00 ||<style="text-align:left;vertical-align:top">Mary O'Brien Room ||<style="text-align:left;vertical-align:top">L9:  Entner-Duodoroff simulation in more detail ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">10:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">P5.   Intro to P5 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, MP, KA, NM ||
+||<height="20px" style="text-align:left;vertical-align:top">1/10/15 ||<style="text-align:left;vertical-align:top">09:00 ||<style="text-align:left;vertical-align:top">Mary O'Brien Room ||<style="text-align:left;vertical-align:top">L8.  MCA perspective on metabolic engineering from case studies. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">10:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">P5.  Calvin cycle simulation. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, MP, KA, NM ||
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-||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">P5. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, MP, KA, NM ||
+||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">P5 cont ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, MP, KA, NM ||
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-||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">13:30 ||<style="text-align:left;vertical-align:top">Mary O'Brien Room ||<style="text-align:left;vertical-align:top">L10:  A kinetic model of the Calvin Cycle ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">P6 :  Calvin cycle simulation ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP, DF ||
+||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">13:30 ||<style="text-align:left;vertical-align:top">Mary O'Brien Room ||<style="text-align:left;vertical-align:top">P6.  Engineering threonine production. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, KA, NM ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">P6 cont ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP, DF ||