Differences between revisions 15 and 18 (spanning 3 versions)

Innotargets: Introduction to Metabolic Modelling

DRAFT/UNDER CONSTRUCTION - STUDENTS PLEASE IGNORE

Barcelona 2023

Tutors

Mark Poolman (MP: Oxford Brookes University)
Oliver Ebenhoeh (OE: Heinrich Heine University, Dusseldorf)
Yanica Said (YS: Oxford Brookes University)
Dipali Singh (DS: Quadram Institute, Norwich)

Guest Speaker ??

TBA ??

Reading List ??

Suggestions ?

Course Timetable and Resources

Day	Time	Activity	Links	Lecturer

30/05/23 Tuesday
AM

|| || || ||

	09:00	Arrival, Admin & Registration Hotel check-in etc
	13:00	Lunch

PM	14:00	Welcome and introduction to the course - why do modelling?	Slides	MP (Not Yet Created)
		Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks.	Slides	YS (Cut down and align w/ L3)
	15:30	Tea/coffee
		Lecture 2: Python and computational representation of metabolic networks.	Slides	MP
		P1. Computers: checking internet connectivity, software installation.	Installing ScrumPy	All (Not Yet Created)
		P2. Python and ScrumPy	Prac2	All (Review)
	1800	Close

Wednesday

|| || || ||

AM

	09:00	Lecture 3: Null space and elementary modes and conserved cycles (? keep the latter ? something else ?)	Slides	OE (review - ensure alligned w/ L2 and P3)
		P3. Null space, subsets and elementary modes	Prac3	All (review - do we need more?)
	10:30	tea/coffee
		P3 continues
	13:00	Lunch
PM	14:00	Guest lecture - Synthetic Biology: Uncovering principles of biological design applying math and experiments.		Dr. Rodriguez-Caso
	15:00	Depart social activity		All

Thursday			Prac4
	09:00	Lecture 4. Linear programming and Flux Balance Analysis	Slides	OE
		Lecture 5: S. typhim model	Slides	MP
		Break
		S.typhim prac	Prac4	All (Styphim ? to big a jump from P3?)
		Lunch
		Lecture 6: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
		P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	All
Friday		Lecture 7: construction and validation	Slides	DS
		Finish practicals/General discussion/Something else
	13:00	Lunch
		Go home!

None: Meetings/Barcelona2023/Timetable (last edited 2023-05-29 12:34:39 by mark)

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-||Tuesday ||AM           ''' ''' || || || ||
||30/05/23 ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
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-|| ||PM || || || ||
+||30/05/23 Tuesday || || || || ||
||AM ||
''' ''' || || || ||
|| ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
-Line 24:
+Line 25:
-|| ||14:00 ||Welcome and introduction to the course - why do modelling? ||[[https://mudsharkstatic.brookes.ac.uk/Barcelona2023/L0.pdf|Slides]] ||MP ||
|| || ||Lecture 1:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||YS ||
|| || ||Tea/coffee || || ||
+|| || || || || ||
||PM||14:00 ||Welcome and introduction to the course - why do modelling? ||[[https://mudsharkstatic.brookes.ac.uk/Barcelona2023/L0.pdf|Slides]] ||MP  ('''Not Yet Created''') ||
|| || ||Lecture 1:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||YS (Cut down and align w/ L3) ||
|| ||15:30||Tea/coffee || || ||
-Line 28:
+Line 30:
-|| || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/ScrumPyInstall|Installation]]  of ScrumPy. ||All ||
|| || ||Close || || ||
||Wednesday           ''' ''' ||AM           ''' ''' || || || ||
|| ||09:00 ||P2. Python and ScrumPy ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
|| || ||Lecture 3: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||OE ||
|| ||11:00 ||Break || || ||
|| || ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All ||
+|| || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona2023/ScrumPyInstall|Installing ScrumPy]] ||All ('''Not Yet Created''') ||
|| || ||P2. Python and ScrumPy||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]]||All (Review)||
|| ||1800||Close || || ||
|| || || || || ||
||Wednesday           ''' ''' ||
''' ''' || || || ||
||AM|| || || || ||
|| || || || || ||
|| ||09:00||Lecture 3: Null space and elementary modes and conserved cycles (? keep the latter ? something else ?) ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||OE (review - ensure alligned w/ L2 and P3) ||
|| || ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All (review - do we need more?) ||
|| ||10:30||tea/coffee|| || ||
|| || ||P3 continues|| || ||
-Line 36:
+Line 43:
-||PM||14:00||Guest lecture - Synthetic Biology: Uncovering principles of biological design applying math and experiments.|| ||Dr. Rodriguez-Caso||
|| ||15:00 ||Depart social activity ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
||Thursday          ''' ''' || || || || ||
|| || ||Lecture 4. Linear programming and Flux Balance Analysis||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]]||YS||
+||PM ||14:00 ||Guest lecture - Synthetic Biology: Uncovering principles of biological design applying math and experiments. || ||Dr. Rodriguez-Caso ||
|| ||15:00 ||Depart social activity || ||All ||
|| || || || || ||
||Thursday|| || ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]]|| ||
|| ||09:00||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||OE||
-Line 41:
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-|| || ||Break|| || ||
|| || ||S.typhim prac ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/PracStyphim|PracTyphim]] ||All ||
|| || ||Lunch|| || ||
+|| || ||Break || || ||
|| || ||S.typhim prac ||[[http://mudshark.brookes.ac.uk/Barcelona2023/PracStyphim|Prac4]] ||All (Styphim ?  to big a jump from P3?) ||
|| || ||Lunch || || ||
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-|| || || || || ||
||Friday||
''' ''' ||?? Lecture 7: construction and validation ?? ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.pdf|Slides]] ||DS ||
||Friday || || || || ||
+||Friday || ||Lecture 7: construction and validation ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.pdf|Slides]] ||DS ||
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-|| || ||Go Home || || ||
+|| ||13:00 ||Lunch || || ||
|| || ||Go home! || || ||


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