Differences between revisions 1 and 27 (spanning 26 versions)

!! Under Construction - Contents Liable to Change !!

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	Lecture: 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		All
Tuesday	AM
	09:00	P2. Pythoncontinued ...	Prac2	All
	10:00	Lecture Intruction to metabolic modelling		DF
	11:00	Lecture: Null space, subsets and elementary modes	Slides	CS
	11:00	Break
	13:00	Lunch
	14:00	P3. LP practical	Prac3	All
	16:00	Lecture: Construction and curation of GSMs	Slides	TD/PV
	PM	Lecture. Biotechnological applications of elementary modes analysis	Slides	DF
		P4. Elementary Modes of the Woods-Ljungdahl Pathway	Prac4	All

Wednesday
	9:00	P3 continued		All
	09:00	Lecture: Linear programming and Flux Balance Analysis	Slides	MP
		Lecture: Validation and construction of models	Slides	TD
	11:00	Break
		Lecture: Determination of minimal media requirements for Campylobacter jejuni	Slides	PV
		P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	All
	13:00	Lunch
	PM	Lecture: Phaeodactylum tricornutm for biofuel synthesis	Slides	DS
		P6. Identifying pathways for TAG synthesis in P. tricornutm	Prac6	All
	16:45

Thursday	AM
	09:00	Lecture. Cupriavadus necator	Slides	NP
		P6 (ctd) P7: KOs for ethylene production in C. necator	Prac7
	13:00	Lunch
	14:00	Practical or Lecture here (LPEMs ?? Reaction CCs ??)

Friday	AM
	09:00	Complete unfinished practicals
	11:00	General discussion. AOB
	13:00	Lunch
	14:00	Go Home !

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

-  ⇤ ← Revision 1 as of 2024-11-19 14:48:02 → 
  Size: 3949
  Editor: mark
  Comment:
+   ← Revision 27 as of 2024-11-29 16:13:02 → ⇥
  Size: 4134
  Editor: trunil
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+= !!           Under Construction - Contents Liable to Change       !! =
-Line 2:
+Line 3:
-== Nottingham 2022 ==
+== Nottingham 2024 ==
-Line 4:
+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]]
-Line 18:
+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 ||Lecture:  Introduction to python and metabolic modelling ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.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 ||
+|| ||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 || ||All ||
||Tuesday ''' ''' ||AM           ''' ''' || || || ||
|| ||09:00 ||P2. Pythoncontinued ... ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
|| ||10:00 ||Lecture Intruction to metabolic modelling || ||DF ||
|| ||11:00 ||Lecture: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||CS ||
-Line 33:
+Line 30:
-|| || ||P3.  Null space, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac3]] ||All ||
-Line 35:
+Line 31:
-|| ||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 ||
+|| ||14:00 ||P3. LP practical ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All ||
|| ||16:00 ||Lecture: Construction and curation of GSMs ||Slides ||TD/PV ||
|| ||PM          ''' ''' ||Lecture. 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 ||
|| || || || || ||
||Wednesday ''' ''' || || || || ||
|| ||9:00||P3 continued|| ||All||
|| ||09:00 ||Lecture: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||MP ||
|| || ||Lecture: Validation and construction of models ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] ||TD ||
 Line 41:
-|| || ||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: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]] ||PV ||
|| || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All ||
 Line 44:
-|| ||PM          ''' ''' ||Lecture 9: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||DS ||
+|| ||PM          ''' ''' ||Lecture: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||DS ||
 Line 46:
-|| ||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]] || ||
+|| ||16:45 || || || ||
|| || || || || ||
||Thursday ''' ''' ||AM          ''' ''' || || || ||
|| ||09:00 ||Lecture. ''Cupriavadus necator''        ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L10.pdf|Slides]] ||NP ||
|| || ||P6 (ctd) P7: KOs for ethylene production in ''C. necator'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P7|Prac7]] || ||
-Line 51:
+Line 52:
-|| ||14:00 ||Concluding remarks, discussion, feedback || || ||
+|| ||14:00 ||Practical or Lecture here (LPEMs ?? Reaction CCs ??) || || ||
-Line 53:
+Line 54:
-|| || || ||
+||Friday ||AM || || || ||
|| ||09:00 ||Complete  unfinished practicals || || ||
|| ||11:00 ||General discussion. AOB || || ||
|| ||13:00 ||Lunch ||
|| ||14:00 ||Go Home ! ||