= C1Net Workshop on Metabolic Modelling =
== Course Timetable and Resources Index ==
||<height="20px" style="text-align:left;vertical-align:top">'''Day''' ||<style="text-align:left;vertical-align:top">'''Time''' ||<style="text-align:left;vertical-align:top">'''Place''' ||<style="text-align:left;vertical-align:top">'''Activity''' ||<style="text-align:left;vertical-align:top">'''Links''' ||<style="text-align:left;vertical-align:top">'''Lecturer''' ||
||<height="20px" style="text-align:left;vertical-align:top">'''Monday''' ||<style="text-align:left;vertical-align:top">13:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Room registration opens at St Anne's Lodge ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">15/12/14 ||<style="text-align:left;vertical-align:top">13:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">Workshop registration opens. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, DS, KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">14:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">Opening and introductions ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF ||
||<height="56px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks.  Outline of the week ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L1.pdf|Slides]] ||<style="text-align:left;vertical-align:top">DF ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">15:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Tea/coffee ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L2. Sources of data for metabolic models ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L2.pdf|Slides]] ||<style="text-align:left;vertical-align:top">DF ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">17:00 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">P1. Computers: checking internet connectivity, software installation.  Enzyme and metabolism databases. ||<style="text-align:left;vertical-align:top">[[http://mudshark.brookes.ac.uk/Meetings/Riga2013/Practicals/ScrumPyVM|Installation]] of ScrumPy. [[Meetings/C1netWork1/Prac1|Database Instructions]] ||<style="text-align:left;vertical-align:top">DF, MP, DS, KA,TK ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">18:30 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Room registration (cont) ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">19:00 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Opening reception ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">19:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Dinner ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">'''Tuesday''' ||<style="text-align:left;vertical-align:top">08:00 ||<style="text-align:left;vertical-align:top">Hall ||<style="text-align:left;vertical-align:top">Breakfast ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">16/12/14 ||<style="text-align:left;vertical-align:top">09:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L3.  Null space and elementary modes ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L3.pdf|Slides]] ||<style="text-align:left;vertical-align:top">DF ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">10:00 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">L4. Computational representation of metabolic networks ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L4.pdf|Slides]] ||<style="text-align:left;vertical-align:top">MP ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">10:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Coffee/Tea ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P2.  Python and !ScrumPy ||<style="text-align:left;vertical-align:top">[[http://mudshark.brookes.ac.uk/AccliPhot/WorkshopOne/prac1|Instructions]] ||<style="text-align:left;vertical-align:top">MP, DF, DS, TK ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">12:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Lunch ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">13:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L5. Biotechnological applications of metabolic network analysis ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L5.pdf|Slides]] ||<style="text-align:left;vertical-align:top">DF ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P3. Null space analysis with !ScrumPy ||<style="text-align:left;vertical-align:top">As P2 plus these [[http://mudshark.brookes.ac.uk/Meetings/Riga2013/Practicals/Practical_2/ScrumPyIntro|instructions]] ||<style="text-align:left;vertical-align:top">DF, HH, DS, TK ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">15:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Tea/Coffee ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L6. Linear Programming and Flux Balance Analysis ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L6.pdf|Slides]] ||<style="text-align:left;vertical-align:top">HH ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">17:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P2 and P3 continued ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">17:30 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Close ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">19:00 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Dinner ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">'''Wednesday''' ||<style="text-align:left;vertical-align:top">08:00 ||<style="text-align:left;vertical-align:top">Hall ||<style="text-align:left;vertical-align:top">Breakfast ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="38px" style="text-align:left;vertical-align:top">17/12/14 ||<style="text-align:left;vertical-align:top">09:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L7.  Building genome-scale metabolic networks ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L7.pdf|Slides]] ||<style="text-align:left;vertical-align:top">MP ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">10:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Coffee/Tea ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="56px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P4.  Elementary modes of a simple model ||<style="text-align:left;vertical-align:top">[[http://mudshark.brookes.ac.uk/AccliPhot/WorkshopOne/prac2|Instructions]] ||<style="text-align:left;vertical-align:top">MP, DF, KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">12:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Lunch '''+ Oxford walking tour''' ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">'''14:30 ''' ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left">L8. Examples of analyzing genome scale metabolic models ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L8.pdf|Slides]] ||<style="text-align:left;vertical-align:top">MP or DF ||
||<height="56px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">'''15:00 ''' ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P5. Building models from !MetaCyc with ScrumPy – group work ||<style="text-align:left;vertical-align:top">[[Meetings/C1netWork1/Prac5|Instructions]] ||<style="text-align:left;vertical-align:top">MP, DF, HH, KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">15:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Tea/Coffee ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="56px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">'''17:00''' ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P5 continued ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">MP, DF, HH, KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">'''18:00''' ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Close ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">19:00 ||<style="text-align:left;vertical-align:top">'''S9''' ||<style="text-align:left;vertical-align:top">Dinner (changed back to S9) ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">'''Thursday''' ||<style="text-align:left;vertical-align:top">08:00 ||<style="text-align:left;vertical-align:top">Hall ||<style="text-align:left;vertical-align:top">Breakfast ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">18/12/14 ||<style="text-align:left;vertical-align:top">09:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L9.  Examples of genome scale modelling ||<style="text-align:left;vertical-align:top">Slides ||<style="text-align:left;vertical-align:top">DS KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">10:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Coffee/Tea ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P6.  Flux Balance Analysis of a simple model ||<style="text-align:left;vertical-align:top">[[../Prac6|Instructions]] ||<style="text-align:left;vertical-align:top">DF, KA, DS ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">12:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Lunch ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">13:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L10.    Modelling energy metabolism in Salmonella ||<style="text-align:left;vertical-align:top">[[http://mudsharkstatic.brookes.ac.uk/C1Net/Wshop1/L10.pdf|Slides]] ||<style="text-align:left;vertical-align:top">HH ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">14:30 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P7  (Group work)  Analysing a genome scale model of Salmonella ||<style="text-align:left;vertical-align:top">[[Meetings/C1NetWork1/Prac7|Instructions]] ||<style="text-align:left;vertical-align:top">DF, MP, DS, KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">15:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Tea/Coffee ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">16:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P7 continued ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, MP, DS, KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">17:30 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Close ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">18:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Pre-dinner drinks ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">19:00 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">'''Workshop dinner with cash bar''' ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="18px" style="text-align:left;vertical-align:top">'''Friday''' ||<style="text-align:left;vertical-align:top">08:00 ||<style="text-align:left;vertical-align:top">Hall ||<style="text-align:left;vertical-align:top">Breakfast ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">19/12/14 ||<style="text-align:left;vertical-align:top">09:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">P7 continued ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, MP, HH, DS, KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">10:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Coffee/Tea ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">11:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">Reports from groups ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF, MP, HH, DS, KA ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">12:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">Any questions?  Closing remarks ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">DF ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">12:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">Sandwich lunch (packed) ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="20px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">13:30 ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">Departure ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||