Differences between revisions 3 and 66 (spanning 63 versions)

Metabolic Modelling: Tools, Techniques, and Applications in Research

Nepal 2024

Tutors

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

Guest Speaker

Dr Anu Raghunathan (AR: National Chemical Laboratory, Pune - online)

Course Timetable and Resources

Day	Time	Activity	Links	Tutor
Day 1 - Mon(23/09)
AM	09:30	Arrival, Admin & Registration etc
	10:00	Welcome and introduction to the course		DS
		From genome to pathway using Pathway Tools	Demo	DS
		Lecture 1: Introduction to metabolic modelling.	Slides	TD/MP
		P1. Computers: checking internet connectivity, software installation.	Prac1	All
PM	12:00	Lunch
		P1: Continue
	14:00	Lecture 2: Python and computational representation of metabolic networks.	Slides	TD/MP
		Lecture 3: Why do metabolic modelling?		MP
	15:00	Tea/Coffee Break
	15:30	P2: Python and ScrumPy	Prac2	All
	17:00	Close
Day 2 - Tues(24/09)
AM	10:00	Lecture 4: Linear programming, Flux Balance Analysis and Applications	Guest Lecture	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)
AM	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
	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		All
	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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+Line 4:
- * Dr Mark Poolman (MP: Oxford Brookes University)
+ * Dr Mark Poolman (MP: Oxford Brookes University - online)
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+Line 6:
- * Pareena Verma  (PV: Oxford Brookes University)
+ * Pareena Verma  (PV: Oxford Brookes University - online)
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+Line 10:
-TBD
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">'''Day''' ||<style="&quot;text-align:left;vertical-align:bottom&quot;">'''Time''' ||<style="&quot;text-align:left;vertical-align:bottom&quot;">'''Activity''' ||<style="&quot;text-align:left;vertical-align:bottom&quot;">'''Links''' ||<style="&quot;text-align:left;vertical-align:bottom&quot;">'''Tutor''' ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">Day 1 – Monday ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">AM ||<style="&quot;text-align:right;vertical-align:bottom&quot;">09:30:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Arrival, Admin etc ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot&quot; ;&amp;quot&quot"> ||<style="&quot;text-align:right&quot;">10:00:00 ||<style="&quot;text-align:left&quot;">Welcome and introduction to the course - why do modelling? ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;">MP ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot&quot; ;&amp;quot&quot"> ||<style="&quot;text-align:right&quot;">10:30:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lecture 1: Introduction to metabolic modelling. ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;">TBD ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot&quot; ;&amp;quot&quot"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lecture 2: Python and computational representation of metabolic networks. ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;">TBD ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot&quot; ;&amp;quot&quot"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">P1. Computers: checking internet connectivity, software installation. ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">12:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lunch ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">PM ||<style="&quot;text-align:right;vertical-align:bottom&quot;">13:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">P1. Contd. ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">13:30:00 ||<style="&quot;text-align:left&quot;">P2. Python and ScrumPy ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">17:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Close ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot&quot; ;&amp;quot&quot"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">Day 2 – Tuesday ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">AM ||<style="&quot;text-align:right;vertical-align:bottom&quot;">10:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lecture 3: Null space, elementary modes and conserved cycles ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">TBD ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">P3. Null space, subsets and elementary modes ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">12:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lunch ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">PM ||<style="&quot;text-align:right;vertical-align:bottom&quot;">13:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lecture 4: Linear programming and Flux Balance Analysis ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">TBD ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">P4. LP – Central metabolism of Staphylococcus epidermidis ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">17:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Close ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot&quot; ;&amp;quot&quot"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">Day 3 – Wednesday ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">AM ||<style="&quot;text-align:right;vertical-align:bottom&quot;">10:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lecture 5: Construction, Validation and Applications of GSMs ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">DS ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">11:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lecture 6: Antimicrobial target identification by GSMM - INNOTARGETS ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">PV ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lunch ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot&quot; ;&amp;quot&quot">PM ||<style="&quot;text-align:right;vertical-align:bottom&quot;">13:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">P5:  Antimicrobial target identification by GSMM - INNOTARGETS ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">15:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied. ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">17:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Close ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||<style="&quot;text-align:left&quot;"> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot&quot; ;&amp;quot&quot"> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">Day 4 – Thursday ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">AM ||<style="&quot;text-align:right;vertical-align:bottom&quot;">10:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Participants to present the outcome of the group discussion ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lunch ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot">PM ||<style="&quot;text-align:right;vertical-align:bottom&quot;">13:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Lecture 7: Determination of minimal media requirements for Campylobacter jejuni ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">DS ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">14:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">P6: Determination of minimal media requirements for Campylobacter jejuni ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;">All ||
||<height="&quot" style="&quot;text-align:left; 17px&amp; quot; ;vertical-align:bottom&quot; ;&amp;quot&quot"><<BR>> ||<style="&quot;text-align:right;vertical-align:bottom&quot;">17:00:00 ||<style="&quot;text-align:left;vertical-align:bottom&quot;">Close ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||<style="&quot;text-align:left;vertical-align:bottom&quot;"><<BR>> ||
+ * Dr Anu Raghunathan (AR: National Chemical Laboratory, Pune - online)
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+== Course Timetable and Resources ==
||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Tutor''' ||
||Day 1 - Mon(23/09) || || || || ||
||AM ||09:30 ||Arrival, Admin & Registration etc || || ||
|| ||10:00 ||Welcome and introduction to the course || ||DS ||
|| || ||From genome to pathway using Pathway Tools ||Demo ||DS ||
|| || ||Lecture 1:  Introduction to metabolic modelling. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L1.pdf|Slides]] ||TD/MP ||
|| || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/ScrumPyInstall|Prac1]] ||All ||
||PM ||12:00 ||Lunch || || ||
|| || ||P1: Continue || || ||
|| ||14:00 ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L2.pdf|Slides]] ||TD/MP ||
|| || ||Lecture 3: Why do metabolic modelling? || ||MP ||
|| ||15:00 ||Tea/Coffee Break || || ||
|| ||15:30 ||P2: Python and [[https://mudshark.brookes.ac.uk/ScrumPy/Doc/Tutorial/ScrumPyIntro|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/India2024/Prac2|Prac2]] ||All ||
|| ||17:00 ||Close || || ||
||Day 2 - Tues(24/09) || || || || ||
||AM ||10:00 ||Lecture 4: Linear programming, Flux Balance Analysis and Applications ||Guest Lecture ||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) || || || || ||
||AM||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/India2024/L7.pdf|Slides]] ||PV/MP ||
|| ||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 || ||All ||
|| ||15:00 ||Finish Practicals/General Discussion || ||All ||
|| || ||Go Home! || || ||