Differences between revisions 2 and 59 (spanning 57 versions)

Metabolic Modelling: Tools, Techniques, and Applications in Research

Nepal 2024

Tutors

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

Guest Speaker

Dr Anu Raghunathan (AR: National Chemistry Laboratory, Pune)

Course Timetable and Resources

Day	Time	Activity	Links	Tutor
Day 1 - Mon(23/09)
PM	09:30	Arrival, Admin & Registration etc
	10:00	Welcome and introduction to the course - why do modelling?		DS/MP
		Lecture 1: Introduction to metabolic modelling.	Slides	PV/TD
		Lecture 2: Python and computational representation of metabolic networks.	Slides	TD
		P1. Computers: checking internet connectivity, software installation.	Prac1	All
AM	12:00	Lunch
	13:00	P1 Continue
	14:00	P2. Python and ScrumPy	Prac2	All
	15:00	Tea/Coffee Break
	15:30	P2 Continue
		Close
Day 2 - Tues(24/09)
AM	10:00	Lecture 3: Genome to Pathway using Pathway Tools	Demo	DS
	11:00	Lecture 4. Linear programming, Flux Balance Analysis and Applications		AR
PM	12:00	Lunch
	13:00	P4: Linear programming and Flux Balance Analysis	Prac4
	15:00	Tea/Coffee Break
	15:30	P4. Continue
	16:00	Lecture 5: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
		Close
Day 3 Wed (25/09)
	10:00	P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	All
PM	12:00	Lunch
	13:00	Lecture 6: Antimicrobial target identification by GSMM	Slides	PV/MP
AM	14:00	P6: Antimicrobial target identification by GSMM	Prac6 Materials	All
	15:00	Tea/Coffee Break
	15:30	Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied.
		Close
Day 4 - Thurs (26/09)
AM	10:00	Participants to present the outcome of the group discussion
PM	12:00	Lunch
	13:00	P6. Continue
	15:00	Finish Practicals/General Discussion		All
		Go Home!

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-= This web page under is under construction. =
= Innotargets: Introduction to Metabolic Modelling =
== India 2024 ==
+= Metabolic Modelling: Tools, Techniques, and Applications in Research =
== Nepal 2024 ==
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-TBD
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">'''Day''' ||<style="text-align:left;vertical-align:bottom">'''Time''' ||<style="text-align:left;vertical-align:bottom">'''Activity''' ||<style="text-align:left;vertical-align:bottom">'''Links''' ||<style="text-align:left;vertical-align:bottom">'''Tutor''' ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">Day 1 – Monday ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">AM ||<style="text-align:right;vertical-align:bottom">09:30:00 ||<style="text-align:left;vertical-align:bottom">Arrival, Admin etc ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot"> ||<style="text-align:right">10:00:00 ||<style="text-align:left">Welcome and introduction to the course - why do modelling? ||<style="text-align:left"> ||<style="text-align:left">MP ||
||<height="&quot" style="text-align:left;17px&quot"> ||<style="text-align:right">10:30:00 ||<style="text-align:left;vertical-align:bottom">Lecture 1: Introduction to metabolic modelling. ||<style="text-align:left"> ||<style="text-align:left">TBD ||
||<height="&quot" style="text-align:left;17px&quot"> ||<style="text-align:left"> ||<style="text-align:left;vertical-align:bottom">Lecture 2: Python and computational representation of metabolic networks. ||<style="text-align:left"> ||<style="text-align:left">TBD ||
||<height="&quot" style="text-align:left;17px&quot"> ||<style="text-align:left"> ||<style="text-align:left;vertical-align:bottom">P1. Computers: checking internet connectivity, software installation. ||<style="text-align:left"> ||<style="text-align:left">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">12:00:00 ||<style="text-align:left;vertical-align:bottom">Lunch ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">PM ||<style="text-align:right;vertical-align:bottom">13:00:00 ||<style="text-align:left;vertical-align:bottom">P1. Contd. ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">13:30:00 ||<style="text-align:left">P2. Python and ScrumPy ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">17:00:00 ||<style="text-align:left;vertical-align:bottom">Close ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot"> ||<style="text-align:left"> ||<style="text-align:left"> ||<style="text-align:left"> ||<style="text-align:left"> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">Day 2 – Tuesday ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">AM ||<style="text-align:right;vertical-align:bottom">10:00:00 ||<style="text-align:left;vertical-align:bottom">Lecture 3: Null space, elementary modes and conserved cycles ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">TBD ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">P3. Null space, subsets and elementary modes ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">12:00:00 ||<style="text-align:left;vertical-align:bottom">Lunch ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">PM ||<style="text-align:right;vertical-align:bottom">13:00:00 ||<style="text-align:left;vertical-align:bottom">Lecture 4: Linear programming and Flux Balance Analysis ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">TBD ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">P4. LP – Central metabolism of Staphylococcus epidermidis ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">17:00:00 ||<style="text-align:left;vertical-align:bottom">Close ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot"> ||<style="text-align:left"> ||<style="text-align:left"> ||<style="text-align:left"> ||<style="text-align:left"> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">Day 3 – Wednesday ||<style="text-align:left"> ||<style="text-align:left"> ||<style="text-align:left"> ||<style="text-align:left"> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">AM ||<style="text-align:right;vertical-align:bottom">10:00:00 ||<style="text-align:left;vertical-align:bottom">Lecture 5: Construction, Validation and Applications of GSMs ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">DS ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">11:00:00 ||<style="text-align:left;vertical-align:bottom">Lecture 6: Antimicrobial resistance mechanism in E.coli ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">PV ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">Lunch ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot">PM ||<style="text-align:right;vertical-align:bottom">13:00:00 ||<style="text-align:left;vertical-align:bottom">P5: LP – Antimicrobial resistance ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">15:00:00 ||<style="text-align:left;vertical-align:bottom">Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied. ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">17:00:00 ||<style="text-align:left;vertical-align:bottom">Close ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:left"> ||<style="text-align:left"> ||<style="text-align:left"> ||<style="text-align:left"> ||
||<height="&quot" style="text-align:left;17px&quot"> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">Day 4 – Thursday ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">AM ||<style="text-align:right;vertical-align:bottom">10:00:00 ||<style="text-align:left;vertical-align:bottom">Participants to present the outcome of the group discussion ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">Lunch ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom">PM ||<style="text-align:right;vertical-align:bottom">13:00:00 ||<style="text-align:left;vertical-align:bottom">Lecture 7: Determination of minimal media requirements for Campylobacter jejuni ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">DS ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">14:00:00 ||<style="text-align:left;vertical-align:bottom">P6: Determination of minimal media requirements for Campylobacter jejuni ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom">All ||
||<height="&quot" style="text-align:left;17px&quot;;vertical-align:bottom"><<BR>> ||<style="text-align:right;vertical-align:bottom">17:00:00 ||<style="text-align:left;vertical-align:bottom">Close ||<style="text-align:left;vertical-align:bottom"><<BR>> ||<style="text-align:left;vertical-align:bottom"><<BR>> ||
+ * Dr Anu Raghunathan (AR: National Chemistry Laboratory, Pune)
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+== Course Timetable and Resources ==
||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Tutor''' ||
||Day 1 - Mon(23/09) || || || || ||
||PM ||09:30 ||Arrival, Admin & Registration etc || || ||
|| ||10:00 ||Welcome and introduction to the course - why do modelling? || ||DS/MP ||
|| || ||Lecture 1:  Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L1.pdf|Slides]] ||PV/TD ||
|| || ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L2.pdf|Slides]] ||TD ||
|| || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/ScrumPyInstall|Prac1]] ||All ||
||AM ||12:00 ||Lunch || || ||
|| ||13:00 ||P1 Continue || || ||
|| ||14:00 ||P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac2|Prac2]] ||All ||
|| ||15:00 ||Tea/Coffee Break || || ||
|| ||15:30 ||P2 Continue || || ||
|| || ||Close || || ||
||Day 2 - Tues(24/09) || || || || ||
||AM ||10:00 ||Lecture 3: Genome to Pathway using Pathway Tools ||Demo ||DS ||
|| ||11:00 ||Lecture 4. Linear programming, Flux Balance Analysis and Applications || ||AR ||
||PM ||12:00 ||Lunch || || ||
|| ||13:00 ||P4: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] || ||
|| ||15:00 ||Tea/Coffee Break || || ||
|| ||15:30 ||P4. Continue || || ||
|| ||16:00 ||Lecture 5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L7.pdf|Slides]] ||DS ||
|| || ||Close || || ||
||Day 3 Wed (25/09) || || || || ||
|| ||10:00 ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All ||
||PM ||12:00 ||Lunch || || ||
|| ||13:00 ||Lecture 6: Antimicrobial target identification by GSMM ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L5.pdf|Slides]] ||PV/MP ||
||AM ||14:00 ||P6: Antimicrobial target identification by GSMM ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/P5_instructions.pdf|Prac6]]  [[http://mudsharkstatic.brookes.ac.uk/Nepal2024/P5_tar.tar|Materials]] ||All ||
|| ||15:00 ||Tea/Coffee Break || || ||
|| ||15:30 ||Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied. || || ||
|| || ||Close || || ||
||Day 4 - Thurs (26/09) || || || || ||
||AM ||10:00 ||Participants to present the outcome of the group discussion || || ||
||PM ||12:00 ||Lunch || || ||
|| ||13:00 ||P6. Continue || || ||
|| ||15:00 ||Finish Practicals/General Discussion || ||All ||
|| || ||Go Home! || || ||