Differences between revisions 20 and 75 (spanning 55 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 Sequence 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 Prac3	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: Biofilm formation in opportunistic human pathogen Staphylococcus epidermidis	Prac4
	15:00	Tea/Coffee Break
	15:30	P4: Continue
	17:00	Close
Day 3 Wed (25/09)
AM	10:00	Lecture 5: Identification of nutrient requirements for growth of Campylobacter jejuni	Slides	DS
	11:00	P5: Identification of nutrient requirements for growth of Campylobacter jejuni	Prac5	All
PM	12:00	Lunch
	14:00	Lecture 6: Antimicrobial target identification by GSMM	Slides	PV/MP
		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.
	17:00	Close
Day 4 - Thurs (26/09)
AM	10:00	P6: continue		All
APM	12:00	Lunch
	13:00	Participants to present the outcome of the group discussion		All
	15:00	Finish Practicals/General Discussion		All
		Go Home!

-  ⇤ ← Revision 20 as of 2024-09-11 13:23:57 → 
  Size: 22111
  Editor: trunil
  Comment:
+   ← Revision 75 as of 2024-09-24 07:26:33 → ⇥
  Size: 3385
  Editor: dipali
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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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- * 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 9:
-||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot">'''Day''' ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">'''Time''' ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">'''Activity''' ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">'''Links''' ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">'''Lecturer''' ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot">'''Mon''' ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">10:00 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Welcome and introduction to the course - why do modelling? ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">MP||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks. ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">PV/TD ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">12:30 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lunch ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lecture 2: Python and computational representation of metabolic networks. ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">TD ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">P1. Computers: Checking internet connectivity, software installation. ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">All ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">P2. Python and [[https://mudshark.brookes.ac.uk/ScrumPy|ScrumPy]] ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">All ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">17:00 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Close ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot">'''Tues''' ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">10:00 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lecture 3: Null space and elementary modes ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">MP||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot">'''<<BR>>''' ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">P3. Null space, subsets and elementary modes ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">All ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">12:30 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lunch ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lecture 4: Linear programming and Flux Balance Analysis ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">MP ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">P4. Central metabolism of S. epidermidis ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">All ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">17:00 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Close ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot">'''Wed''' ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">10:00 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lecture 5: Determination of minimal media requirements for Campylobacter jejuni ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">DS ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">P5: Determination of minimal media requirements for Campylobacter jejuni ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">All ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">12:30 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lunch ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lecture 6: Phaeodactylum tricornutm for biofuel synthesis ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">DS ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">P5: Continued ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">All ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">17:00 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Close ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;36px&quot"><<BR>>Thur ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>>10:00 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>>Case study project presentation by the participants ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">12:30 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Lunch ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">P6. Identifying pathways for TAG synthesis in P. tricornutm ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">All ||
||<height="&quot" style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left;20px&quot"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:right">17:00 ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left">Closing dinner ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||<style="&quot;border-top:1px solid #000000;border-bottom:1px solid #000000;border-left:1px solid #000000;border-right:1px solid #000000&quot; ;text-align:left"><<BR>> ||
+== 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 Sequence 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/Nepal2024/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|ScrumPy]] ||[[https://mudshark.brookes.ac.uk/Meetings/Nepal2024/Prac2|Prac2]] [[https://mudshark.brookes.ac.uk/Meetings/Nepal2024/Prac3|Prac3]] ||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: Biofilm formation in opportunistic human pathogen ''Staphylococcus epidermidis'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/P4|Prac4]] || ||
|| ||15:00 ||Tea/Coffee Break || || ||
|| ||15:30 ||P4: Continue || || ||
|| ||17:00 ||Close || || ||
||Day 3 Wed (25/09) || || || || ||
||AM ||10:00 ||Lecture 5: Identification of nutrient requirements for growth of ''Campylobacter jejuni '' ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L7.pdf|Slides]] ||DS ||
|| ||11:00 ||P5: Identification of nutrient requirements for growth of ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All ||
||PM ||12:00 ||Lunch || || ||
|| ||14:00 ||Lecture 6: Antimicrobial target identification by GSMM ||[[http://mudsharkstatic.brookes.ac.uk/Nepal2024/L6.pdf|Slides]] ||PV/MP ||
|| || ||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. || || ||
|| ||17:00 ||Close || || ||
||Day 4 - Thurs (26/09) || || || || ||
||AM ||10:00 ||P6: continue || ||All||
||APM ||12:00 ||Lunch || || ||
|| ||13:00 ||Participants to present the outcome of the group discussion || ||All ||
|| ||15:00 ||Finish Practicals/General Discussion || ||All ||
|| || ||Go Home! || || ||