Differences between revisions 3 and 47 (spanning 44 versions)

Metabolic Modelling: Tools, Techniques, and Applications in Research

India 2024

Tutors

Dr Mark Poolman (MP: Oxford Brookes University)
Dr Anu Raghunathan (AR: NCL, Pune)
Dr Dipali Singh (DS: Quadram Institute, Norwich)
Pareena Verma (PV: Oxford Brookes University)
Dr Trunil Desai (TD: Oxford Brookes University)

Guest Speaker

Prof. Sundip Kundu (SK: University of Calcutta)

Course Timetable and Resources

Day	Time	Activity	Links	Tutor
Day 1 - Tues(17/09)
PM	12:00	Arrival, Admin & Registration etc
	12:30	Lunch
	14:30	Welcome and introduction to the course - why do modelling?		MP/ AR
	14:30	Lecture 1: Introduction to metabolic modelling.	Slides	PV/TD
	15:00	Lecture 2: Python and computational representation of metabolic networks.	Slides	TD
	15:30	Tea/Coffee Break
	15:45	P1. Computers: checking internet connectivity, software installation.	Prac1	All
		P2. Python and ScrumPy	Prac2	All
		Close

Day 2 - Wed (18/09)
AM	09:00	Lecture 3: Null space, elementary modes and conserved cycles	Slides	TD
	10:00	Lecture 4. Linear programming, Flux Balance Analysis and Applications	Slides	AR
	11:00	P3. Null space, subsets and elementary modes	Prac3	All
PM	12:30	Lunch
	14:30	Constraint-based modelling of C3, C4 and CAM		SK
	15:30	Tea/Coffee Break
	15:45	P4: Linear programming and Flux Balance Analysis	Prac4

Day 3 Thurs (19/09)
AM	9:00	P4: Continued
	10:00	Lecture 5: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
	11:00	P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	All
PM	12:30	Lunch
	14:30	Lecture 6: Antimicrobial target identification by GSMM - INNOTARGETS	Slides	PV/MP
	15:30	Tea/Coffee Break
	15:45	P6: Antimicrobial target identification by GSMM - INNOTARGETS	Prac6 Materials	All
Day 4 - Fri (20/09)
AM	09:00	Finish Practicals/General Discussion		All
		Go Home!

-  ⇤ ← Revision 3 as of 2024-09-05 13:42:46 → 
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+   ← Revision 47 as of 2024-09-19 04:04:14 → ⇥
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-Deletions are marked like this.
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-= Innotargets: Introduction to Metabolic Modelling =
== Barcelona 2023 ==
+= Metabolic Modelling: Tools, Techniques, and Applications in Research =
== India 2024 ==
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- * Dr Anu Raghunathan
 * Dr Dipali Singh
 * Pareena Verma
+ * Dr Anu Raghunathan (AR: NCL, Pune)
 * Dr Dipali Singh (DS: Quadram Institute, Norwich)
 * Pareena Verma  (PV: Oxford Brookes University)
 Line 10:
- * 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)
-Line 16:
+Line 11:
- * Dr. Rodriguez-Caso (University of Malaga)
+ * Prof. Sundip Kundu (SK: University of Calcutta)
-Line 19:
+Line 14:
-||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' ||
||30/05/23 Tuesday || || || || ||
||AM ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
|| ||13:00 ||Lunch || || ||
+||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Tutor''' ||
||Day 1 - Tues(17/09) || || || || ||
||PM ||12:00 ||Arrival, Admin & Registration etc || || ||
|| ||12:30 ||Lunch || || ||
|| ||14:30 ||Welcome and introduction to the course - why do modelling? || ||MP/ AR ||
|| ||14:30 ||Lecture 1:  Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L1.pdf|Slides]] ||PV/TD ||
|| ||15:00 ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L2.pdf|Slides]] ||TD ||
|| ||15:30 ||Tea/Coffee Break || || ||
|| ||15:45 ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/ScrumPyInstall|Prac1]] ||All ||
|| || ||P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac2|Prac2]] ||All ||
|| || ||Close || || ||
-Line 24:
+Line 26:
-||PM ||14:00 ||Welcome and introduction to the course - why do modelling? || ||MP ||
|| || ||Lecture 1:  Introduction to metabolic modelling.   Mathematical  representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||YS ||
|| ||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|Prac1]] ||All ||
|| || ||P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
|| ||1800 ||Close || || ||
+||Day 2 - Wed (18/09) || || || || ||
||AM ||09:00 ||Lecture 3: Null space, elementary modes and conserved cycles ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||TD ||
|| ||10:00 ||Lecture 4. Linear programming, Flux Balance Analysis and Applications ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L4.pdf|Slides]] ||AR ||
|| ||11:00 ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac3|Prac3]] ||All ||
||PM ||12:30 ||Lunch || || ||
|| ||14:30 ||Constraint-based modelling of C3, C4 and CAM || ||SK ||
|| ||15:30 ||Tea/Coffee Break || || ||
|| ||15:45 ||P4: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] || ||
-Line 32:
+Line 35:
-||Wednesday || || || || ||
||AM ||09:00 ||Lecture 3: Null space, elementary modes and conserved cycles ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||OE ||
|| || ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona/Prac3|Prac3]] ||All ||
|| ||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 || || || || ||
||AM ||09:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||OE ||
|| || ||Lecture 5: Response to varying ATP demand in a metabolic model of '' Salmonella typhimurium'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L5.pdf|Slides]] ||MP ||
|| ||10:30 ||Break || || ||
|| || ||P4 Central metabolism of ''S. epidermidis'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] ||YS/DS ||
|| || || || || ||
|| ||13:00 ||Lunch || || ||
|| || ||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 ||
|| || || || || ||
||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 ||[[https://mudshark.brookes.ac.uk/Meetings/C1NetWork1/Prac7|Prac6]] ||(Optional if time allows) ||
|| ||13:00 ||Lunch || || ||
|| || ||Go home! || || ||
+||Day 3 Thurs (19/09) || || || || ||
||AM ||9:00 ||P4: Continued || || ||
|| ||10:00 ||Lecture 5: Determination of minimal media requirements for Campylobacter jejuni ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L8.pdf|Slides]] ||DS ||
|| ||11:00 ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All ||
||PM ||12:30 ||Lunch || || ||
|| ||14:30 ||Lecture 6: Antimicrobial target identification by GSMM - INNOTARGETS ||[[http://mudsharkstatic.brookes.ac.uk/India2024/L7.pdf|Slides]] ||PV/MP ||
|| ||15:30 ||Tea/Coffee Break || || ||
|| ||15:45 ||P6: Antimicrobial target identification by GSMM - INNOTARGETS ||[[http://mudsharkstatic.brookes.ac.uk/India2024/P5_instructions.pdf|Prac6]]  [[http://mudsharkstatic.brookes.ac.uk/India2024/P5_tar.tar|Materials]] ||All ||
||Day 4 - Fri (20/09) || || || || ||
||AM ||09:00 ||Finish Practicals/General Discussion || ||All ||
|| || ||Go Home! || || ||