Differences between revisions 1 and 10 (spanning 9 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)
Hester Chapman (HC: University of Nottingham)

Guest Speaker ??

TBA ??

Reading List ??

Suggestions ?

Course Timetable and Resources

Day	Time	Activity	Links	Lecturer
Tuesday	AM
30/05/23	09:00	Arrival, Admin & Registration Hotel check-in etc

	PM
	12:00	Lunch

13:00

Welcome and introduction to the course - why do modelling?

Slides

		Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks.	Slides	YS
		Tea/coffee
		Lecture 2: Python and computational representation of metabolic networks.	Slides	MP
		P1. Computers: checking internet connectivity, software installation.	Installation of ScrumPy.	All
		Close
Wednesday	AM
	09:00	P2. Python and ScrumPy	Prac2	All
		Lecture 3: Null space, subsets and elementary modes	Slides	OE
	11:00	Break
		P3. Null space, subsets and elementary modes	Prac3	All
	13:00	Lunch

	PM	Lecture 4. Linear programming and Flux Balance Analysis	Slides	YS
	15:00	Depart social activity	Prac4	All
Thursday
	09:00	Lecture 5: S. typhim model	Slides	MP
		S.typhim prac	PracTyphim	All
	11:00	Break
		Lecture 6: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
		P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	All
	13:00	Lunch
	PM	Lecture 7: staph epi	Slides	DS

	P6. Using the staph epi model	Prac6	All
Friday
	Guest Lecture
	Finnish practicals/General discussion/Something else
	Lunch
	Go Home

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

-  ⇤ ← Revision 1 as of 2023-05-02 11:56:33 → 
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+   ← Revision 10 as of 2023-05-10 17:12:43 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
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-DRAFT/UNDER CONSTRUCTION STUDENTS PLEASE IGNORE
+== DRAFT/UNDER CONSTRUCTION - STUDENTS PLEASE IGNORE ==
-Line 9:
+Line 6:
- * David Fell        (DF: Oxford Brookes University)
+ * Oliver Ebenhoeh (OE: Heinrich Heine University, Dusseldorf)
-Line 12:
+Line 9:
- * Nicole Pearcy  (NP: University of Nottingham)
+ * Hester Chapman (HC: University of Nottingham)
-Line 14:
+Line 11:
-== Guest Speaker ==
 * Prof. John Wain  (JW: Quadram Institute, Norwich)
+== Guest Speaker ?? ==
 * TBA ??
-Line 17:
+Line 14:
-== Reading List ==
 . A reading list for topics covered in the course is provided [[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Reading|here]] (updated).
+== Reading List ?? ==
 . Suggestions ?
-Line 23:
+Line 20:
-||03/04/22 ||09:00 ||Arrival, Admin & Registration || || ||
+||30/05/23 ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
|| || || || || ||
-Line 26:
+Line 24:
-|| ||13:00 ||Welcome and introduction to the course.    Outline of the week. || ||MP et al ||
|| || ||Lecture 1: Young microbiologists need models not critics ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||JW ||
|| || ||Lecture 2:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DF ||
+|| ||13:00 ||Welcome and introduction to the course - why do modelling? ||[[https://mudsharkstatic.brookes.ac.uk/Meetings/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 ||
-Line 30:
+Line 36:
-|| || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||MP ||
+|| || ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L2.pdf|Slides]] ||MP ||
-Line 35:
+Line 41:
-|| || ||Lecture 4: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||MP ||
+|| || ||Lecture 3: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||OE ||
-Line 39:
+Line 45:
-|| ||PM          ''' ''' ||Lecture 5. Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DF ||
|| || ||P4.   Elementary Modes of the Woods-Ljungdahl Pathway ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
+|| ||PM          ''' ''' ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||YS ||
|| ||15:00 ||Depart social activity ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
-Line 42:
+Line 50:
-|| ||09:00 ||Lecture 6: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||MP ||
|| || ||Lecture 7 : Validation and construction of models ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] ||DS ||
+|| ||09:00 ||Lecture 5: S. typhim model ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L5.pdf|Slides]] ||MP ||
|| || ||S.typhim prac ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/PracStyphim|PracTyphim]] ||All ||
-Line 45:
+Line 53:
-|| || ||Lecture 8: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]] ||DS ||
|| || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||DS ||
+|| || ||Lecture 6: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L6.pdf|Slides]] ||DS ||
|| || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All ||
-Line 48:
+Line 56:
-|| ||PM          ''' ''' ||Lecture 9: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||DS ||
|| || ||P6. Identifying pathways for TAG  synthesis in ''P. tricornutm'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P6|Prac6]] ||All ||
|| ||16:45 ||close || || ||
||Friday          ''' ''' ||AM          ''' ''' || || || ||
|| ||09:00 ||Lecture 10. ''Cupriavadus necator''        ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L10.pdf|Slides]] ||NP ||
|| || ||P6 (ctd) P7: KOs for ethelene production in ''C. necator'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P7|Prac7]] || ||
|| ||13:00 ||Lunch || || ||
|| ||14:00 ||Concluding remarks, discussion, feedback || || ||
|| || || || || ||
|| || || || || ||
|| || || || || ||
+|| ||PM          ''' ''' ||Lecture 7:  staph epi ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.pdf|Slides]] ||DS ||




|| || ||P6. Using the staph epi model ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P6|Prac6]] ||All ||
||Friday || || || || ||
|| || ||Guest Lecture || || ||
|| || ||Finnish practicals/General discussion/Something else || || ||
|| || ||Lunch || || ||
|| || ||Go Home || || ||