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Innotargets: Introduction to Metabolic Modelling

India 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

TBD

Day	Time	Activity	Links	Tutor
Day 1 – Monday
AM	09:30:00	Arrival, Admin etc
	10:00:00	Welcome and introduction to the course - why do modelling?		MP
	10:30:00	Lecture 1: Introduction to metabolic modelling.		TBD
		Lecture 2: Python and computational representation of metabolic networks.		TBD
		P1. Computers: checking internet connectivity, software installation.		All
	12:00:00	Lunch
PM	13:00:00	P1. Contd.		All
	13:30:00	P2. Python and ScrumPy		All
	17:00:00	Close

Day 2 – Tuesday
AM	10:00:00	Lecture 3: Null space, elementary modes and conserved cycles		TBD
		P3. Null space, subsets and elementary modes		All
	12:00:00	Lunch
PM	13:00:00	Lecture 4: Linear programming and Flux Balance Analysis		TBD
		P4. LP – Central metabolism of Staphylococcus epidermidis		All
	17:00:00	Close

Day 3 – Wednesday
AM	10:00:00	Lecture 5: Construction, Validation and Applications of GSMs		DS
	11:00:00	Lecture 6: Antimicrobial resistance mechanism in E.coli		PV
		Lunch
PM	13:00:00	P5: LP – Antimicrobial resistance		All
	15:00:00	Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied.		All
	17:00:00	Close


Day 4 – Thursday
AM	10:00:00	Participants to present the outcome of the group discussion		All
		Lunch
PM	13:00:00	Lecture 7: Determination of minimal media requirements for Campylobacter jejuni		DS
	14:00:00	P6: Determination of minimal media requirements for Campylobacter jejuni		All
	17:00:00	Close

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- * Dr Anu Raghunathan (AR: NCL, Pune)
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-||<(v  height="17px">'''Day'''||<(v>'''Time'''||<(v>'''Activity'''||<(v>'''Links'''||<(v>'''Tutor'''||
||<(v  height="17px">Day 1 – Monday||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||
||<(v  height="17px">AM||<)v>09:30:00||<(v>Arrival, Admin etc ||<(v><<BR>>||<(v><<BR>>||
||<(  height="17px"> ||<)>10:00:00||<(>Welcome and introduction to the course - why do modelling?||<(> ||<(>MP||
||<(  height="17px"> ||<)>10:30:00||<(v>Lecture 1: Introduction to metabolic modelling. ||<(> ||<(>TBD||
||<(  height="17px"> ||<(> ||<(v>Lecture 2: Python and computational representation of metabolic networks.||<(> ||<(>TBD||
||<(  height="17px"> ||<(> ||<(v>P1. Computers: checking internet connectivity, software installation.||<(> ||<(>All||
||<(v  height="17px"><<BR>>||<)v>12:00:00||<(v>Lunch ||<(v><<BR>>||<(v><<BR>>||
||<(v  height="17px">PM||<)v>13:00:00||<(v>P1. Contd.||<(v><<BR>>||<(v>All||
||<(v  height="17px"><<BR>>||<)v>13:30:00||<(>P2. Python and ScrumPy||<(v><<BR>>||<(v>All||
||<(v  height="17px"><<BR>>||<)v>17:00:00||<(v>Close||<(v><<BR>>||<(v><<BR>>||
||<(  height="17px"> ||<(> ||<(> ||<(> ||<(> ||
||<(v  height="17px">Day 2 – Tuesday||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||
||<(v  height="17px">AM||<)v>10:00:00||<(v>Lecture 3: Null space, elementary modes and conserved cycles||<(v><<BR>>||<(v>TBD||
||<(v  height="17px"><<BR>>||<(v><<BR>>||<(v>P3. Null space, subsets and elementary modes||<(v><<BR>>||<(v>All||
||<(v  height="17px"><<BR>>||<)v>12:00:00||<(v>Lunch||<(v><<BR>>||<(v><<BR>>||
||<(v  height="17px">PM||<)v>13:00:00||<(v>Lecture 4: Linear programming and Flux Balance Analysis||<(v><<BR>>||<(v>TBD||
||<(v  height="17px"><<BR>>||<(v><<BR>>||<(v>P4. LP – Central metabolism of Staphylococcus epidermidis||<(v><<BR>>||<(v>All||
||<(v  height="17px"><<BR>>||<)v>17:00:00||<(v>Close||<(v><<BR>>||<(v><<BR>>||
||<(  height="17px"> ||<(> ||<(> ||<(> ||<(> ||
||<(v  height="17px">Day 3 – Wednesday||<(> ||<(> ||<(> ||<(> ||
||<(v  height="17px">AM||<)v>10:00:00||<(v>Lecture 5: Construction, Validation and Applications of GSMs||<(v><<BR>>||<(v>DS||
||<(v  height="17px"><<BR>>||<)v>11:00:00||<(v>Lecture 6: Antimicrobial resistance mechanism in E.coli||<(v><<BR>>||<(v>PV||
||<(v  height="17px"><<BR>>||<(v><<BR>>||<(v>Lunch||<(v><<BR>>||<(v><<BR>>||
||<(  height="17px">PM||<)v>13:00:00||<(v>P5: LP – Antimicrobial resistance ||<(v><<BR>>||<(v>All||
||<(v  height="17px"><<BR>>||<)v>15:00:00||<(v>Group discussion: Please form a group of 4-5 to discuss project ideas where metabolic modelling can be applied.||<(v><<BR>>||<(v>All||
||<(v  height="17px"><<BR>>||<)v>17:00:00||<(v>Close||<(v><<BR>>||<(v><<BR>>||
||<(v  height="17px"><<BR>>||<(> ||<(> ||<(> ||<(> ||
||<(  height="17px"> ||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||
||<(v  height="17px">Day 4 – Thursday||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||<(v><<BR>>||
||<(v  height="17px">AM||<)v>10:00:00||<(v>Participants to present the outcome of the group discussion||<(v><<BR>>||<(v>All||
||<(v  height="17px"><<BR>>||<(v><<BR>>||<(v>Lunch||<(v><<BR>>||<(v><<BR>>||
||<(v  height="17px">PM||<)v>13:00:00||<(v>Lecture 7: Determination of minimal media requirements for Campylobacter jejuni||<(v><<BR>>||<(v>DS||
||<(v  height="17px"><<BR>>||<)v>14:00:00||<(v>P6: Determination of minimal media requirements for Campylobacter jejuni||<(v><<BR>>||<(v>All||
||<(v  height="17px"><<BR>>||<)v>17:00:00||<(v>Close||<(v><<BR>>||<(v><<BR>>||
+||<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>> ||
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