Differences between revisions 1 and 22 (spanning 21 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 ??

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
AM	09:00	Lecture 4. Linear programming and Flux Balance Analysis	Slides	OE
		Lecture 5: S. typhim model	Slides	MP
	10:30	Break
		S.typhim prac	Prac4	All (Styphim ? to big a jump from P3?)

	13:00	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
AM	09:00	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)

-  ⇤ ← Revision 1 as of 2023-05-02 11:56:33 → 
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+   ← Revision 22 as of 2023-05-18 13:08:16 → ⇥
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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)
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+Line 9:
- * Nicole Pearcy  (NP: University of Nottingham)
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+Line 10:
-== Guest Speaker ==
 * Prof. John Wain  (JW: Quadram Institute, Norwich)
+Guest Speaker ??
-Line 17:
+Line 12:
-== Reading List ==
 . A reading list for topics covered in the course is provided [[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Reading|here]] (updated).
+ * TBA ??
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+Line 16:
-||Tuesday ||AM           ''' ''' || || || ||
||03/04/22 ||09:00 ||Arrival, Admin & Registration || || ||
|| ||PM || || || ||
|| ||12:00 ||Lunch || || ||
|| ||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 ||
|| || ||Tea/coffee || || ||
|| || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||MP ||
|| || ||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 4: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||MP ||
|| ||11:00 ||Break || || ||
|| || ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All ||
+||30/05/23 Tuesday || || || || ||
||AM ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
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+Line 19:
-|| ||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 ||
||Thursday          ''' ''' || || || || ||
|| ||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 ||
|| ||11:00 ||Break || || ||
|| || ||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 ||
+|| || || || || ||
||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 || || ||
|| || ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L2.pdf|Slides]] ||MP ||
|| || ||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 48:
+Line 34:
-|| ||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]] || ||
+|| || || || || ||
||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]] || ||
||AM||09:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||OE ||
|| || ||Lecture 5: S. typhim model ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L5.pdf|Slides]] ||MP ||
|| ||10:30 ||Break || || ||
|| || ||S.typhim prac ||[[http://mudshark.brookes.ac.uk/Barcelona2023/PracStyphim|Prac4]] ||All (Styphim ?  to big a jump from P3?) ||
|| || || || || ||
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-|| ||14:00 ||Concluding remarks, discussion, feedback || || ||
+|| || ||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 ||
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+Line 48:
-|| || || || || ||
|| || || || || ||
+||Friday || || || || ||
||AM ||09:00 ||Lecture 7: construction and validation ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.pdf|Slides]] ||DS ||
|| || ||Finish practicals/General discussion/Something else || || ||
|| ||13:00 ||Lunch || || ||
|| || ||Go home! || || ||