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	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	Prac3 Slides	All / MP
	16:00	L4: Construction and Curation of GSMs	Slides	TD/PV

Wednesday
	09:00	P3: (continued)		All
	10:00	L6: Biotechnological applications of elementary modes analysis	Slides	DF
	11:00	P4. Elementary Modes of the Woods-Ljungdahl Pathway	Prac4	All
	13:00	Lunch
	14:00	L6: Linear programming and flux balance analysis	Slides	MP
	15:00	L7: Phaeodactylum tricornutm	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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 Line 21:
-|| ||14:00 ||L1:  Introduction to python and metabolic modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L1.pdf|Slides]] ||MP ||
+|| ||14:00 ||'''L1''':  Introduction to python and metabolic modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/L1.pdf|Slides]] ||MP ||
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-|| ||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 ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||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 ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
 Line 26:
-|| ||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/Nottingham2022/L4.pdf|Slides]] ||CS ||
+|| ||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/Nottingham2022/L4.pdf|Slides]] ||CS ||
 Line 30:
-|| ||14:00 ||P3: Basic Model Properties ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]]  [[http://mudsharkstatic.brookes.ac.uk/Nottingham2024/ScrumPySlides.pdf|Slides]] ||All / MP ||
|| ||16:00 ||Lecture: Construction and curation of GSMs ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] ||TD/PV ||
+|| ||14:00 ||'''P3:''' Basic Model Properties ||[[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/Nottingham2022/L7.pdf|Slides]] ||TD/PV ||
 Line 34:
-|| ||09:00 ||P3 continued || ||All ||
|| ||10:00 ||Lecture. Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DF ||
|| ||11:00 ||P4. Elementary Modes of the Woods-Ljungdahl Pathway ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
+|| ||09:00 ||'''P3:''' ''(continued)'' || ||All ||
|| ||10:00 ||'''L6:''' Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DF ||
|| ||11:00 ||'''P4.''' Elementary Modes of the Woods-Ljungdahl Pathway ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
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-|| ||14:00 ||Lecture: Linear programming and flux balance analysis ||Slides ||MP ||
|| ||15:00 ||Lecture:  ''Phaeodactylum tricornutm'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||PV ||
|| || ||P5:  ''Phaeodactylum tricornutm'' ||Prac5 ||All ||
+|| ||14:00 ||'''L6:''' Linear programming and flux balance analysis ||Slides ||MP ||
|| ||15:00 ||'''L7: ''' ''Phaeodactylum tricornutm'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||PV ||
|| || ||'''P5: ''' ''Phaeodactylum tricornutm'' ||Prac5 ||All ||
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-|| ||09:00 ||P5 continued ||- ||- ||
|| ||10:00 ||Lecture: Correlation coefficients and LPEMs ||Slides ||CS ||
+|| ||09:00 ||'''P5:''''' (continued) '' ||- ||- ||
|| ||10:00 ||'''L8:''' Reaction Correlation Coefficients and LPEMs ||Slides ||CS ||