Differences between revisions 2 and 24 (spanning 22 versions)

C1Net Workshop on Metabolic Modelling

Course Timetable and Resources Index (Provisional)

Day	Time	Place	Activity	Links	Lecturer
Monday	13:00		Room registration opens at St Anne's Lodge
15/12/14	13:30	S8	Workshop registration opens.		DF, DS, KA
	14:00	S8	Opening and introductions		DF
	14:30	S8	L1. Introduction to metabolic modelling. Mathematical representation of metabolic networks. Outline of the week	Slides	DF
	15:30	S9	Tea/coffee
	16:00	S8	L2. Sources of data for metabolic models	Slides	DF
	17:00	S9	P1. Computers: checking internet connectivity, software installation. Enzyme and metabolism databases.	Installation of ScrumPy. Database Instructions	DF, MP, DS, KA,TK
	18:30		Room registration (cont)
	19:00	S9	Opening reception
	19:30	S9	Dinner

Tuesday	08:00	Hall	Breakfast
16/12/14	09:00	S8	L3. Null space and elementary modes	Slides	DF
	10:00		L4. Computational representation of metabolic networks	Slides	MP
	10:30	S9	Coffee/Tea
	11:00	S8	P2. Python and ScrumPy	Instructions	MP, DF, DS, TK
	12:30	S9	Lunch
	13:30	S8	L5. Biotechnological applications of metabolic network analysis	Slides	DF
	14:30	S8	P3. Null space analysis with ScrumPy	As P2 plus these instructions	DF, HH, DS, TK
	15:30	S9	Tea/Coffee
	16:00	S8	L6. Linear Programming and Flux Balance Analysis	Slides	HH
	17:00	S8	P2 and P3 continued
	17:30		Close
	19:00	S9	Dinner

Wednesday	08:00	Hall	Breakfast
17/12/14	09:00	S8	L7. Building genome-scale metabolic networks	Slides	MP
	10:30	S9	Coffee/Tea
	11:00	S8	P4. Elementary modes of a simple model	Instructions	MP, DF, KA
	12:30	S9	Lunch + Oxford walking tour
	14:30	S8	L8. Examples of analyzing genome scale metabolic models	Slides	MP or DF
	15:00	S8	P5. Building models from MetaCyc with ScrumPy – group work	Instructions	MP, DF, HH, KA
	15:30	S9	Tea/Coffee
	17:00	S8	P5 continued		MP, DF, HH, KA
	18:00		Close
	19:00	S9	Dinner (changed back to S9)

Thursday	08:00	Hall	Breakfast
18/12/14	09:00	S8	L9. Examples of genome scale modelling	Slides	DS KA
	10:30	S9	Coffee/Tea
	11:00	S8	P6. Flux Balance Analysis of a simple model	Instruction	DF, KA, DS
	12:30	S9	Lunch
	13:30	S8	L10. Modelling energy metabolism in Salmonella	Slides	HH
	14:30	S8	P7 (Group work) Analysing a genome scale model of Salmonella	Instructions	DF, MP, DS, KA
	15:30	S9	Tea/Coffee
	16:00	S8	P7 continued		DF, MP, DS, KA
	17:30		Close
	18:30	S9	Pre-dinner drinks
	19:00	S9	Workshop dinner with cash bar

Friday	08:00	Hall	Breakfast
19/12/14	09:00	S8	P7 continued		DF, MP, HH, DS, KA
	10:30	S9	Coffee/Tea
	11:00	S8	Reports from groups		DF, MP, HH, DS, KA
	12:00	S8	Any questions? Closing remarks		DF
	12:30	S9	Sandwich lunch (packed)
	13:30		Departure

-  ⇤ ← Revision 2 as of 2014-12-05 17:00:48 → 
  Size: 26625
  Editor: david
  Comment: Provisional timetable created
+   ← Revision 24 as of 2014-12-18 14:45:24 → ⇥
  Size: 24080
  Editor: hassan
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-||<tablewidth="1099px" tableheight="1801px"height="23px" style="text-align:left;vertical-align:top">'''Date''' ||<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="23px" style="text-align:left;vertical-align:top">15/12/14 ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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">Workshop registration opens. ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||<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">Slides ||<style="text-align:left;vertical-align:top">DF ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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">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">                        ||<style="text-align:left;vertical-align:top">17:30 ||<style="text-align:left;vertical-align:top">S9 ||<style="text-align:left;vertical-align:top">P1. Computers: checking internet connectivity, software installation ||<style="text-align:left;vertical-align:top">Instructions ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" 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">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">16/12/14 ||<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="23px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<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">Slides ||<style="text-align:left;vertical-align:top">MP? DF ||
||<height="38px" style="text-align:left;vertical-align:top">                        ||<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">Slides ||<style="text-align:left;vertical-align:top">MP ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||<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">Instructions ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||<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">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">                        ||<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">Instructions ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||<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">Slides ||<style="text-align:left;vertical-align:top">HH? ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" 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">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">17/12/14 ||<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">                        ||<style="text-align:left;vertical-align:top">                        ||<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">Slides ||<style="text-align:left;vertical-align:top">MP ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||<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">Instructions ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||<style="text-align:left;vertical-align:top">13:30 ||<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">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">                        ||<style="text-align:left;vertical-align:top">14:30 ||<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">Instructions ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||<style="text-align:left;vertical-align:top">16:00 ||<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">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">19:30 ||<style="text-align:left;vertical-align:top">UCR ||<style="text-align:left;vertical-align:top">Dinner (Upper Common Room) ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" 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">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">18/12/14 ||<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="38px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">09:00 ||<style="text-align:left;vertical-align:top">S8 ||<style="text-align:left;vertical-align:top">L8.    Modelling energy metabolism in Salmonella ||<style="text-align:left;vertical-align:top">Slides ||<style="text-align:left;vertical-align:top">HH ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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">Instructions ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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">L9.  Examples of genome scale modelling ||<style="text-align:left;vertical-align:top">Slides ||<style="text-align:left;vertical-align:top">DS KA ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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.  FB mini-projects (Group work) ||<style="text-align:left;vertical-align:top">Instructions ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||<style="text-align:left;vertical-align:top">19:30 ||<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="23px" 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">                        ||<style="text-align:left;vertical-align:top">                        ||
||<height="23px" style="text-align:left;vertical-align:top">19/12/14 ||<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="23px" style="text-align:left;vertical-align:top">                        ||<style="text-align:left;vertical-align:top">                        ||<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">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||
||<height="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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="23px" style="text-align:left;vertical-align:top">                        ||<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">                        ||
+||<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">[[http://mudshark.brookes.ac.uk/AccliPhot/WorkshopOne/prac3|Instruction]] ||<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">[[http://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">                        ||