Differences between revisions 20 and 42 (spanning 22 versions)

Workshop on Metabolic Modelling

Nottingham 2022

Tutors

Mark Poolman (MP: Oxford Brookes University)
David Fell (DF: Oxford Brookes University)
Yanica Said (YS: Oxford Brookes University)
Dipali Singh (DS: Quadram Institute, Norwich)
Nicole Pearcy (NP: University of Nottingham)

Guest Speaker

Prof. John Wain (JW: Quadram Institute, Norwich)

Reading List

A reading list for topics covered in the course is provided here (updated).

Course Timetable and Resources

Day	Time	Activity	Links	Lecturer
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	Slides	JW
		Lecture 2: Introduction to metabolic modelling. Mathematical representation of metabolic networks.	Slides	DF
		Tea/coffee
		Lecture 3: 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 4: Null space, subsets and elementary modes	Slides	MP
	11:00	Break
		P3. Null space, subsets and elementary modes	Prac3	All
	13:00	Lunch
	PM	Lecture 5. Biotechnological applications of elementary modes analysis	Slides	DF
		P4. Elementary Modes of the Woods-Ljungdahl Pathway	Prac4	All
Thursday
	09:00	Lecture 6: Linear programming and Flux Balance Analysis	Slides	MP
		Lecture 7 : Validation and construction of models	Slides	DS
	11:00	Break
		Lecture 8: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
		P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	DS
	13:00	Lunch
	PM	Lecture 9: Phaeodactylum tricornutm for biofuel synthesis	Slides	DS
		P6. Identifying pathways for TAG synthesis in P. tricornutm	Prac6	All
	16:45	close
Friday	AM
	09:00	Lecture 10. Cupriavadus necator	Slides	NP
		P6 (ctd) P7: KOs for ethelene production in C. necator	Prac7
	13:00	Lunch
	14:00	Concluding remarks, discussion, feedback

None: Meetings/Nottingham2022/Timetable (last edited 2024-11-20 15:33:18 by mark)

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= Overview =
[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/DraftTT.pdf|Timetable overview]] (Subject to change)
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- . A reading list for topics covered in the course is provided [[Meetings/Nottingham2022/Reading|here]].
+ . A reading list for topics covered in the course is provided [[Meetings/Nottingham2022/Reading|here]] (updated).
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-|| ||13:00 ||Welcome and introduction to the course.    Outline of the week. ||'''' ''' ||MP et al ||
|| || ||Lecture 1: Title TBC || ||JW ||
|| || ||Lecture 2:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||DF ||
+|| ||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 ||
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-|| || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software                  installation. ||[[Meetings/Nottingham2022/ScrumPyInstall|Installation]]                   of !ScrumPy. ||All ||
+|| || ||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. ||[[Meetings/Nottingham2022/ScrumPyInstall|Installation]]  of !ScrumPy. ||All ||
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-|| ||09:00 ||L3. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||NP ||
|| || ||Demo for Prac 2. || ||MP ||
|| || ||P2. Python and !ScrumPy (Part 1) ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
+|| ||09:00 ||P2. Python and !ScrumPy ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
|| || ||Lecture 4: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||MP ||
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-|| || ||P2. Python and !ScrumPy  (Part 2) ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
+|| || ||P3.  Null space, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac3]] ||All ||
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-|| ||PM          ''' ''' ||L3b.  Examples of Elementary Modes Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3b.pdf|Slides]] ||DF ||
|| || ||L4. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||DF ||
|| || ||Demo for Prac 3 || ||TBC ||
|| || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac 3]] ||All ||
|| || ||Break || || ||
|| || ||P3. Models, kernels, subsets and elementary modes (continued) || ||All ||
|| ||16:45 ||Close || || ||
+|| ||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 ||[[Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
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-|| ||09:30 ||Demo for Prac4 || ||MP ||
|| || ||P4. Structural analysis of the Calvin Cycle. ||[[Meetings/Nottingham2022/Prac4|Prac 4]] ***instructions ||ALL ||
+|| ||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 ||
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-|| || ||L5. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||NM ||
|| || ||L6.  Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||DF ||
+|| || ||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 ||
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-|| ||PM          ''' ''' ||L7.  The unique metabolism of ''Acetobacterium woodii'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] [[Meetings/Nottingham2022/ScrumPy_demo|ScrumPy_demo]] ||NM ||
|| || ||P5. Flux Balance Analysis of alkane biosynthesis in ''E                      coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] ||All ||
+|| ||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 ||
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-|| ||09:30 ||L8. a: Summary of Null-space and linear programming approaches   b: Practical applications of LP        ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]]; [[http://mudsharkstatic.brookes.ac.uk/Nepal2018/L4b.pdf|Slides]] ||MP, DF ||
|| || ||P5  Flux Balance Analysis of alkane biosynthesis in ''E                      coli''. ||[[Meetings/Nepal2018/Prac5|Prac 5]] || ||
|| ||11:00 ||Break || || ||
|| || ||Practical 5 continues || || ||
+|| ||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]] || ||
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-|| || ||Conclusions || || ||
+|| ||14:00 ||Concluding remarks, discussion, feedback || || ||