Differences between revisions 14 and 23 (spanning 9 versions)

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 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	Lecture 6 slides	DF
	10:00	"	P3 conclude and P4. Feedback inhibition.	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 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: threonine synthesis, Entner Duodorff pathway	Lecture 7 slides threonine paper 1 paper 2 paper 3 Entner-Duodoroff paper 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.	Lecture 8 slides	DF
	10:00		P4. Complete		DF, MP, KA, NM
	10:30		Coffee/Tea
	11:00		L9. Calvin cycle model	Lecture 9 Slides	MP
	12:30	Mary O'Brien Room	Lunch
	13:30	Mary O'Brien Room	P5. Calvin cycle simulation.	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	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

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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]] [[http://mudsharkstatic.brookes.ac.uk/Reprints/ControlofFlux/KBF95BST.pdf|Reprint of The Control of Flux]] ||<style="text-align:left;vertical-align:top">DF ||
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-||<height="38px" style="text-align:left;vertical-align:top">30/09/15 ||<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">L6. Applications of Metabolic Control Analysis ||<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">P3 conclude and P4. Feedback inhibition. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP, DF,  (HH, NM) ||
+||<height="38px" style="text-align:left;vertical-align:top">30/09/15 ||<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">L6. Applications of Metabolic Control Analysis ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L6.pdf|Lecture 6 slides]] ||<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">P3 conclude and P4. Feedback inhibition. ||<style="text-align:left;vertical-align:top">[[http://mudshark.brookes.ac.uk/Meetings/C1netWork2/Practicals/Practical4|Feedback inhibition modelling]] ||<style="text-align:left;vertical-align:top">MP, DF,  (HH, NM) ||
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-||<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 ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">17:30 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">S1:  Review of outcomes from practicals 3 and 4. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, NM ||
+||<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:  threonine synthesis, Entner Duodorff pathway ||<style="text-align:left;vertical-align:top">[[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]] ||<style="text-align:left;vertical-align:top">DF ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">17:30 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Prac 4 continued. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, NM ||
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-||<height="18px" style="text-align:left;vertical-align:top">'''Thursday''' ||<style="text-align:left;vertical-align:top">08:00 ||<style="text-align:left;vertical-align:top">Deneke Dining Hall ||<style="text-align:left;vertical-align:top">Breakfast ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">0 ||
||<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 ||
+||<height="18px" style="text-align:left;vertical-align:top">'''Thursday''' ||<style="text-align:left;vertical-align:top">08:00 ||<style="text-align:left;vertical-align:top">Deneke Dining Hall ||<style="text-align:left;vertical-align:top">Breakfast ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<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">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/LecturesDF/C1netW2_L8.pdf|Lecture 8 slides]] ||<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">P4.  Complete ||<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 cont ||<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">L9. Calvin cycle model ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop2/L9/Slides.pdf|Lecture 9 Slides]] ||<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">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 ||
+||<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">P5.  Calvin cycle simulation. ||<style="text-align:left;vertical-align:top">[[Meetings/C1netWork2/Practicals/Practical5|Control Analysis of the Calvin Cycle]] ||<style="text-align:left;vertical-align:top">DF, KA, NM ||
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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">                        ||<style="text-align:left;vertical-align:top">G1:   Intro to group work problems. ||<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">16:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">P. 5 continued ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, KA, NM ||
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-||<height="20px" style="text-align:left;vertical-align:top">2/10/15 ||<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">G1 continued ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP, DF, HH, KA, NM ||
+||<height="20px" style="text-align:left;vertical-align:top">2/10/15 ||<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">P6 Threonine ||<style="text-align:left;vertical-align:top">                        [[Meetings/C1netWork2/Practicals/Practical6|Threonine practical instructions]]||<style="text-align:left;vertical-align:top">MP, DF, HH, KA, NM ||
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-||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:15 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Reports from groups ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">12:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Any questions?  Closing remark.  Presentation of certificates ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP, DF, HH, 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">Group photo ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">11:15||<style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">General Discussion and Conclusions form the week||<style="text-align:left;vertical-align:top"> ||<style="text-align:left;vertical-align:top">MP, DF, HH, KA, NM||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">12:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Closing remarks.  Presentation of certificates ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP, DF, HH, KA, NM ||