Differences between revisions 3 and 33 (spanning 30 versions)

Innotargets: Introduction to Metabolic Modelling

DRAFT - slightly incomplete and subject to change.

Barcelona 2023

Tutors

Mark Poolman (MP: Oxford Brookes University)
Oliver Ebenhoeh (OE: Heinrich Heine University, Dusseldorf)
Yanica Said (YS: Oxford Brookes University)
Dipali Singh (DS: Quadram Institute, Norwich)

Guest Speaker

Dr. Rodriguez-Caso (University of Malaga)

Course Timetable and Resources

Day	Time	Activity	Links	Lecturer
30/05/23 Tuesday
AM	09:00	Arrival, Admin & Registration Hotel check-in etc
	13:00	Lunch

PM	14:00	Welcome and introduction to the course - why do modelling?	Slides	MP (Not Yet Created)
		Lecture 1: Introduction to metabolic modelling. Mathematical representation of metabolic networks.	Slides	YS
	15:30	Tea/coffee
		Lecture 2: Python and computational representation of metabolic networks.	Slides	MP
		P1. Computers: checking internet connectivity, software installation.	Prac1	All
		P2. Python and ScrumPy	Prac2	All
	1800	Close

Wednesday
AM	09:00	Lecture 3: Null space, elementary modes and conserved cycles (? keep the latter ? something else ?)	Slides	OE (review - ensure aligned w/ L2 and P3)
		P3. Null space, subsets and elementary modes	Prac3	All (review - do we need more?)
	10:30	tea/coffee
		P3 continues
	13:00	Lunch

PM	14:00	Guest lecture - Synthetic Biology: Uncovering principles of biological design applying math and experiments.		Dr. Rodriguez-Caso
	15:00	Depart social activity		All

Thursday
AM	09:00	Lecture 4. Linear programming and Flux Balance Analysis	Slides	OE
		Lecture 5: S. typhim model	Slides	MP
	10:30	Break
		P4 TBC	TBC	YS/DS

	13:00	Lunch
		Lecture 6: Determination of minimal media requirements for Campylobacter jejuni	Slides	DS
		P5: Determination of minimal media requirements for Campylobacter jejuni	Prac5	All

Friday
AM	09:00	Lecture 7: construction and validation	Slides	DS
		Finish practicals/General discussion/Something else	Prac6	(Optional if time allows)
	13:00	Lunch
		Go home!

None: Meetings/Barcelona2023/Timetable (last edited 2023-05-29 12:34:39 by mark)

-  ⇤ ← Revision 3 as of 2023-05-02 14:02:20 → 
  Size: 3706
  Editor: mark
  Comment:
+   ← Revision 33 as of 2023-05-22 14:49:15 → ⇥
  Size: 3489
  Editor: mark
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-== DRAFT/UNDER CONSTRUCTION - STUDENTS PLEASE IGNORE ==
+== DRAFT - slightly incomplete and subject to change. ==
 Line 9:
- * Hester Chapman (HC: University of Nottingham)
-Line 11:
+Line 10:
-== Guest Speaker ?? ==
 * TBA ??

== Reading List ?? ==
 . Suggestions ?
+== Guest Speaker ==
 * Dr. Rodriguez-Caso (University of Malaga)
-Line 19:
+Line 15:
-||Tuesday ||AM           ''' ''' || || || ||
||03/04/22 ||09:00 ||Arrival, Admin & Registration || || ||
|| ||PM || || || ||
|| ||12:00 ||Lunch || || ||
|| ||13:00 ||Welcome and introduction to the course.    Outline of the week. || ||MP et al ||
|| || ||Lecture 1: Who? What? ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L1.pdf|Slides]] ||??? ||
|| || ||Lecture 2:  Introduction to metabolic modelling.   Mathematical                     representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L2.pdf|Slides]] ||DS ||
|| || ||Tea/coffee || || ||
|| || ||Lecture 3: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L3.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/ScrumPyInstall|Installation]]  of ScrumPy. ||All ||
|| || ||Close || || ||
||Wednesday           ''' ''' ||AM           ''' ''' || || || ||
|| ||09:00 ||P2. Python and ScrumPy ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
|| || ||Lecture 4: Null space, subsets and elementary modes ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L4.pdf|Slides]] ||MP ||
|| ||11:00 ||Break || || ||
|| || ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All ||
|| ||13:00 ||Lunch + Social Acitivity - visit to the Sagrada Familia || || ||
|| ||PM          ''' ''' ||Lecture 5. Biotechnological applications of elementary modes analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L5.pdf|Slides]] ||DF ||
|| || ||P4.   Elementary Modes of the Woods-Ljungdahl Pathway ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac4|Prac4]] ||All ||
||Thursday          ''' ''' || || || || ||
|| ||09:00 ||Lecture 6: Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L6.pdf|Slides]] ||MP ||
|| || ||Lecture 7 : Validation and construction of models ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L7.pdf|Slides]] ||DS ||
|| ||11:00 ||Break || || ||
|| || ||Lecture 8: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Nottingham2022/L8.pdf|Slides]] ||DS ||
|| || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||DS ||
+||30/05/23 Tuesday || || || || ||
||AM ||09:00 ||Arrival, Admin & Registration Hotel check-in etc || || ||
-Line 45:
+Line 18:
-|| ||PM          ''' ''' ||Lecture 9: ''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 ||close || || ||
-Line 49:
+Line 19:
+||PM ||14:00 ||Welcome and introduction to the course - why do modelling? ||[[https://mudsharkstatic.brookes.ac.uk/Barcelona2023/L0.pdf|Slides]] ||MP  ('''Not Yet Created''') ||
|| || ||Lecture 1:  Introduction to metabolic modelling.   Mathematical  representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L1.pdf|Slides]] ||YS ||
|| ||15:30 ||Tea/coffee || || ||
|| || ||Lecture 2: Python and computational representation of metabolic networks. ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L2.pdf|Slides]] ||MP ||
|| || ||P1. Computers: checking internet connectivity, software installation. ||[[https://mudshark.brookes.ac.uk/Meetings/Barcelona2023/ScrumPyInstall|Prac1]] ||All ||
|| || ||P2. Python and ScrumPy ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac2|Prac2]] ||All ||
|| ||1800 ||Close || || ||
-Line 50:
+Line 27:
+||Wednesday || || || || ||
||AM ||09:00 ||Lecture 3: Null space, elementary modes and conserved cycles (? keep the latter ? something else ?) ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L3.pdf|Slides]] ||OE (review - ensure aligned w/ L2 and P3) ||
|| || ||P3.  Null space, subsets and elementary modes ||[[https://mudshark.brookes.ac.uk/Meetings/Nottingham2022/Prac3|Prac3]] ||All (review - do we need more?) ||
|| ||10:30 ||tea/coffee || || ||
|| || ||P3 continues || || ||
|| ||13:00 ||Lunch || || ||
-Line 51:
+Line 34:
+||PM ||14:00 ||Guest lecture - Synthetic Biology: Uncovering principles of biological design applying math and experiments. || ||Dr. Rodriguez-Caso ||
|| ||15:00 ||Depart social activity || ||All ||
-Line 52:
+Line 37:
+||Thursday || || || || ||
||AM ||09:00 ||Lecture 4. Linear programming and Flux Balance Analysis ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L4.pdf|Slides]] ||OE ||
|| || ||Lecture 5: S. typhim model ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L5.pdf|Slides]] ||MP ||
|| ||10:30 ||Break || || ||
|| || ||P4 TBC ||TBC||YS/DS ||
-Line 53:
+Line 43:
+|| ||13:00 ||Lunch || || ||
|| || ||Lecture 6: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L6.pdf|Slides]] ||DS ||
|| || ||P5: Determination of minimal media requirements for ''Campylobacter jejuni'' ||[[https://mudsharkstatic.brookes.ac.uk/Nottingham2022/P5|Prac5]] ||All ||
-Line 54:
+Line 47:
-|| || || || || ||
|| || || || || ||
+||Friday || || || || ||
||AM ||09:00 ||Lecture 7: construction and validation ||[[http://mudsharkstatic.brookes.ac.uk/Barcelona2023/L7.pdf|Slides]] ||DS ||
|| || ||Finish practicals/General discussion/Something else ||[[https://mudshark.brookes.ac.uk/Meetings/C1NetWork1/Prac7|Prac6]]||(Optional if time allows)||
|| ||13:00 ||Lunch || || ||
|| || ||Go home! || || ||