= C1Net Workshop 3 on Metabolic Modelling = == Tutors == * David Fell (DF: Oxford Brookes University) * Mark Poolman (MP: Oxford Brookes University) * Noah Mesfin (NM: Oxford Brookes University) * Rupert Norman (RN: University of Nottingham) * Nicole Pearcy (NP: University of Nottingham) == Course Timetable and Resources Index == ||'''Day''' ||'''Time''' ||'''Place''' ||'''Activity''' ||'''Links''' ||'''Lecturer''' || ||'''Monday''' ||12:00 || ||Registration opens at St James Hotel || || || ||23/1/17 ||12:30 ||Oak Room ||Lunch || || || || ||13:30 ||Great Room ||Opening and introductions || ||DF || || ||14:00 || ||L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L1.pdf|Slides]] ||DF || || ||15:30 || ||Tea/coffee || || || || ||16:00 || ||L2. Computational representation of metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L2.pdf|Slides]] ||MP || || ||17:00 || ||P1. Computers: checking internet connectivity, software installation. ||[[Meetings/C1netWork3/Prac1|Installation]] of !ScrumPy. ||DF, MP, NM,RN,NP || || ||18:00 || ||Close and room registration (cont) || || || || || || || || || || || ||19:00 ||Oak Room ||Dinner || || || || || || || || || || ||'''Tuesday''' ||08:00 || ||Breakfast || || || ||24/1/17 ||09:00 || ||L3. Sources of data for metabolic models ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L3.pdf|Slides]] ||DF || || ||10:00 || ||L4. Null space and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L3.pdf|Slides]] ||DF || || ||10:30 || ||Coffee/Tea || || || || ||11:00 || ||P2. Python and !ScrumPy ||[[Meetings/C1netWork3/Prac2|Instructions]] ||DF, MP, NM,RN,NP || || ||12:30 || ||Lunch || || || || ||13:30 || ||P2 continued || ||DF, MP, NM,RN,NP || || ||15:30 || ||Tea/Coffee || || || || ||16:00 || ||L5. Biotechnological applications of metabolic network analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L5.pdf|Slides]] ||DF || || ||17:00 || ||P3. Models, kernels, subsets and elementary modes ||[[Meetings/C1netWork3/Prac3|Instructions]] ||DF, MP, NM,RN,NP || || ||17:30 || ||Close || || || || ||19:00 || ||Dinner || || || || || || || || || || ||'''Wednesday''' ||08:00 || ||Breakfast || || || ||25/1/17 ||09:00 || ||L6. Linear Programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L6.pdf|Slides]] ||MP || || || || ||L7. Building genome-scale metabolic networks ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L7.pdf|Slides]] ||MP || || ||10:30 || ||Coffee/Tea || || || || ||11:00 || ||P4. Elementary modes of a simple model ||[[Meetings/C1netWork3/Prac4|Instructions]] ||DF, MP, NM,RN,NP || || ||12:30 || ||Lunch '''+ free time (Nottingham Castle and Caves?)''' || || || || ||'''15:30 ''' || ||Tea/Coffee || || || || ||'''15:45 ''' || ||L8. Accessing !BioCyc databases from !ScrumPy ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L8.pdf|Slides]] ||MP || || ||16:00 || ||P5. Building models from !MetaCyc with !ScrumPy ||[[Meetings/C1netWork3/P5|Instructions]] ||DF, MP, NM,RN,NP || || ||'''18:00''' || ||Close || || || || ||19:00 || ||Dinner || || || || || || || || || || ||'''Thursday''' ||08:00 || ||Breakfast || || || ||26/1/17 ||09:00 || ||L9. Examples of genome scale modelling ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L9_NM.pdf|Noah's slides]]; [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L9_RN.pdf|Rupert's slides]]; [[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L9_NP.pdf|Nicole's slides]] ||NM, RN, NP || || ||10:30 || ||Coffee/Tea || || || || ||11:00 || ||P6. Flux Balance Analysis of fatty acid biosynthesis in ''E coli''. ||[[Meetings/C1netWork3/P6|Instructions]] ||DF, MP, NM,RN,NP || || ||12:30 || ||Lunch || || || || ||13:30 || ||L10. Identification of novel anti-microbial targets ||[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop3/L10.pdf|Slides]] ||MP || || ||14:30 || ||P6 continued || ||DF, MP, NM,RN,NP || || ||15:30 || ||Tea/Coffee || || || || ||16:00 || ||P7. Analysing a genome scale model ||[[Meetings/C1NetWork1/Prac7|Instructions]] ||DF, MP, NM,RN,NP || || ||17:30 || ||Close || || || || || || || || || || || ||19:00 || ||'''Workshop dinner''' || || || || || || || || || || ||'''Friday''' ||08:00 || ||Breakfast || || || ||27/1/17 ||09:00 || ||P7 continued || ||DF, MP, NM,RN,NP || || ||10:30 || ||Coffee/Tea || || || || ||11:00 || ||Discussion of results and prospective applications of modelling in attendees' projects || ||DF, MP, NM,RN,NP || || ||12:00 || ||Any questions? Closing remarks || ||DF& MP || || ||12:30 || ||(Sandwich?) lunch and departure || || || || || || || || || ||