= 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. ||[[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! || || ||