Workshop on Metabolic Modelling

Nottingham 2024

Tutors

Mark Poolman (MP: Oxford Brookes University)
Trunil Desai (DS: Oxford Brookes University)
Pareena Verma (PV: Oxford Brookes University)
Cristiana Sebu (CS: University of Malta)
Prof. David Fell (DF: Oxford Brookes University ) - Online

Reading List

A reading list for topics covered in the course is provided here

Course Timetable and Resources

Day	Time	Activity	Links	Lecturer
Monday	AM
09/12/2024	09:00	Arrival, Admin & Registration
	PM
	12:00	Lunch
	13:00	Welcome and introduction to the course. Outline of the week.		MP et al
	14:00	L1: Introduction to python and metabolic modelling	Slides	MP
		Tea/coffee
	15:00	P1: Computers: checking internet connectivity, software installation.-> P2	Installation of ScrumPy.	All
	16:00	P2: Introduction to Python 22	Prac2	All
Tuesday	AM
	09:00	P2: Introduction to Python (continued)	Prac2-(ctd)	All
	10:00	L2: Introduction to metabolic modelling	Slides	DF
	11:00	L3: Null space, subsets and elementary modes	Slides	CS
	13:00	Lunch
	14:00	P3: Basic Model Properties 22	Prac3 Slides	All / MP
	16:00	L4: Construction and Curation of GSMs	Slides	TD/PV

Wednesday
	09:00	P3: (continued)		All
	10:00	L5: Biotechnological applications of elementary modes analysis	Slides	DF
	11:00	P4. Elementary Modes of the Woods-Ljungdahl Pathway 22	Prac4	All
	13:00	Lunch
	14:00	L6: Linear programming and flux balance analysis	Slides	MP
	15:00	L7: Phaeodactylum tricornutm 22/L9	Slides	PV
		P5: Phaeodactylum tricornutm	Prac5	All

Thursday	AM
	09:00	P5: (continued)	-	-
	10:00	L8: Reaction Correlation Coefficients and LPEMs	Slides	CS
	13:00	Lunch
	14:00	P7. LPEM?		All

Friday	AM
	09:00	Discussion		All
	12:00	Lunch
	14:00	Go Home !

None: Meetings/Nottingham2024/Timetable (last edited 2024-12-06 14:46:49 by mark)

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-Deletions are marked like this.
+Additions are marked like this.
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+=== (Under Construction - Contents Liable to Change) ===
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+Line 3:
-== Nottingham 2022 ==
+== Nottingham 2024 ==
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+Line 5:
- * 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)
+ * Mark Poolman   (MP: Oxford Brookes University)
 * Trunil Desai       (DS:  Oxford Brookes University)
 * Pareena Verma (PV:  Oxford Brookes University)
 * Cristiana Sebu  (CS: University of Malta)
 * Prof. David Fell (DF:  Oxford Brookes University ) - Online
-Line 14:
+Line 12:
- . A reading list for topics covered in the course is provided [[Meetings/Nottingham2022/Reading|here]] (updated).
+ . A reading list for topics covered in the course is provided [[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Reading|here]]
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+Line 16:
-||Tuesday ||AM           ''' ''' || || || ||
||03/04/22 ||09:00 ||Arrival, Admin & Registration || || ||
+||Monday ||AM           ''' ''' || || || ||
||09/12/2024 ||09:00 ||Arrival, Admin & Registration || || ||
-Line 23:
+Line 21:
-|| || ||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 ||
+|| ||14:00 ||'''L1''':  Introduction to python and metabolic modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L1.pdf|Slides]] ||MP ||
-Line 26:
+Line 23:
-|| || ||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 ||
|| || ||Close || || ||
||Wednesday           ''' ''' ||AM           ''' ''' || || || ||
|| ||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 ||
|| ||11:00 ||Break || || ||
|| || ||P3.  Null space, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac3]] ||All ||
+|| ||15:00 ||'''P1''': Computers: checking internet connectivity, software installation.-> P2 ||[[https://gitlab.com/MarkPoolman/scrumpy/-/wikis/Manual/Install|Installation]]  of [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]]. ||All ||
|| ||16:00 ||'''P2''': Introduction to Python    **22** ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
||Tuesday ''' ''' ||AM           ''' ''' || || || ||
|| ||09:00 ||'''P2''': Introduction to Python ''(continued) '' ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2-(ctd)]] ||All ||
|| ||10:00 ||'''L2:''' Introduction to metabolic modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L2.pdf|Slides]] ||DF ||
|| ||11:00 ||'''L3:''' Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L3.pdf|Slides]] ||CS ||
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-|| ||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 ||
||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 ||
+|| ||14:00 ||'''P3:''' Basic Model Properties **22** ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]]  [[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/ScrumPySlides.pdf|Slides]] ||All / MP ||
|| ||16:00 ||'''L4: '''Construction and Curation of GSMs ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L4.pdf|Slides]] ||TD/PV ||
|| || || || || ||
||Wednesday ''' ''' || || || || ||
|| ||09:00 ||'''P3:''' ''(continued)'' || ||All ||
|| ||10:00 ||'''L5:''' Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L5.pdf|Slides]] ||DF ||
|| ||11:00 ||'''P4.''' Elementary Modes of the Woods-Ljungdahl Pathway **22** ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
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-|| ||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]] || ||
+|| ||14:00 ||'''L6:''' Linear programming and flux balance analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L6.pdf|Slides]] ||MP ||
|| ||15:00 ||'''L7: ''' ''Phaeodactylum tricornutm   **22/L9**'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L7.pdf|Slides]] ||PV ||
|| || ||'''P5: ''' ''Phaeodactylum tricornutm'' ||Prac5 ||All ||
|| || || || || ||
||Thursday ''' ''' ||AM          ''' ''' || || || ||
|| ||09:00 ||'''P5:''''' (continued) '' ||- ||- ||
|| ||10:00 ||'''L8:''' Reaction Correlation Coefficients and LPEMs ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L8.pdf|Slides]] ||CS ||
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-|| ||14:00 ||Concluding remarks, discussion, feedback || || ||
+|| ||14:00 ||P7. LPEM? || ||All ||
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-|| || || ||
+||Friday ||AM || || || ||
|| ||09:00 ||Discussion || ||All ||
|| ||12:00 ||Lunch ||
|| ||14:00 ||Go Home ! ||