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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
Day |
Time |
Activity |
Lecturer |
Mon |
10:00 |
Welcome and introduction to the course - why do modelling? |
TBD |
|
|
Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks. |
TBD |
|
12:30 |
Lunch |
|
|
|
Lecture 2: Python and computational representation of metabolic networks. |
TBD |
|
|
P1. Computers: Checking internet connectivity, software installation. |
All |
|
|
P2. Python and ScrumPy |
All |
|
17:00 |
Close |
|
Tues |
10:00 |
Lecture 3: Null space and elementary modes |
TBD |
|
|
P3. Null space, subsets and elementary modes |
All |
|
12:30 |
Lunch |
|
|
|
Lecture 4: Linear programming and Flux Balance Analysis |
TBD |
|
|
P4. Central metabolism of S. epidermidis |
All |
|
17:00 |
Close |
|
Wed |
10:00 |
Lecture 5: Determination of minimal media requirements for Campylobacter jejuni |
DS |
|
|
P5: Determination of minimal media requirements for Campylobacter jejuni |
All |
|
12:30 |
Lunch |
|
|
|
Lecture 6: Phaeodactylum tricornutm for biofuel synthesis |
DS |
|
|
P5: Continued |
All |
|
17:00 |
Close |
|
Thur |
10:00 |
Case study project presentation by the participants |
|
|
12:30 |
Lunch |
|
|
|
P6. Identifying pathways for TAG synthesis in P. tricornutm |
All |
|
17:00 |
Closing dinner |
|
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. |
|
PV/TD |
|
|
Lecture 2: Python and computational representation of metabolic networks. |
|
TD |
|
|
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 |
|
MP |
|
|
P3. Null space, subsets and elementary modes |
All |
|
|
12:00:00 |
Lunch |
|
|
PM |
13:00:00 |
Lecture 4: Linear programming and Flux Balance Analysis |
|
MP |
|
|
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 target identification by GSMM - INNOTARGETS |
|
PV/MP |
|
|
Lunch |
|
|
PM |
13:00:00 |
P5: Antimicrobial target identification by GSMM - INNOTARGETS |
|
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 |
|
|