= !!           Under Construction - Contents Liable to Change       !! =
= Workshop  on Metabolic Modelling =
== Nottingham 2024 ==
== Tutors ==
 * Mark Poolman   (MP: Oxford Brookes University)
 * Trunil Desai       (DS:  Oxford Brookes University)
 * Pareena Verma (PV:  Oxford Brookes University)
 * Cristiana Sebu  (CS: University of Malta)

== Reading List ==
 . A reading list for topics covered in the course is provided [[Meetings/Nottingham2022/Reading|here]]

== Course Timetable and Resources ==
||'''Day''' ||'''Time''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' ||
||Monday ||AM           ''' ''' || || || ||
||09/12/2024 ||09:00 ||Arrival, Admin & Registration || || ||
|| ||PM || || || ||
|| ||12:00 ||Lunch || || ||
|| ||13:00 ||Welcome and introduction to the course.    Outline of the week. || ||MP et al ||
|| || ||( Keynote DF online?) || || ||
|| || ||Lecture:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DF ?? ||
|| || ||Tea/coffee || || ||
|| || ||Python and computational representation of metabolic networks. +Minor updates ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software installation.-> P2 ||[[https://gitlab.com/MarkPoolman/scrumpy/-/wikis/Manual/Install|Installation]]  of !ScrumPy. ||All ||
|| || || || || ||
||Tuesday ''' ''' ||AM           ''' ''' || || || ||
|| ||09:00 ||P2. Python ||[[Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
|| || ||Lecture: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||CS ||
|| ||11:00 ||Break || || ||
|| || ||P3.  Null space, subsets and elementary modes ||[[Meetings/Nottingham2022/Prac3|Prac3]] ||All ||
|| ||13:00 ||Lunch || || ||
|| ||PM          ''' ''' ||Lecture. Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DF ||
|| || ||P4.   Elementary Modes of the Woods-Ljungdahl Pathway ||[[Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
|| || || || || ||
||Wednesday ''' ''' || || || || ||
|| ||09:00 ||Lecture: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||MP ||
|| || ||Lecture: Validation and construction of models ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] ||TD ||
|| ||11:00 ||Break || || ||
|| || ||Lecture: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]] ||PV ||
|| || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All ||
|| ||13:00 ||Lunch || || ||
|| ||PM          ''' ''' ||Lecture: ''Phaeodactylum tricornutm'' for biofuel synthesis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L9.pdf|Slides]] ||DS ||
|| || ||P6. Identifying pathways for TAG  synthesis in ''P. tricornutm'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P6|Prac6]] ||All ||
|| ||16:45 || || || ||
|| || || || || ||
||Thursday ''' ''' ||AM          ''' ''' || || || ||
|| ||09:00 ||Lecture. ''Cupriavadus necator''        ''' ''' ''' ''' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L10.pdf|Slides]] ||NP ||
|| || ||P6 (ctd) P7: KOs for ethelene production in ''C. necator'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P7|Prac7]] || ||
|| ||13:00 ||Lunch || || ||
|| ||14:00 ||Practical or Lecture here (LPEMs ?? Reaction CCs ??) || || ||
|| || || || || ||
||Friday ||AM || || || ||
|| ||09:00 ||Complete  unfinnished practicals || || ||
|| ||11:00 ||General discussion. AOB || || ||
|| ||13:00 ||Lunch ||
|| ||14:00 ||Go Home ! ||