Computational Systems Biology

COURSE OUTLINE: Every living cell is the result of beautifully concerted interplay of metabolic, signalling and regulatory networks. Systems biology has heralded a systematic quantitative approach to study these complex networks, to understand, predict and manipulate biological systems. Systems biology has had a positive impact on metabolic engineering as well as the pharmaceutical industry. This course seeks to introduce key concepts of mathematical modelling, in the context of different types of biological networks. The course will cover important concepts from network biology, modelling of dynamic systems and parameter estimation, as well as constraint-based metabolic modeling. Finally, we will also touch upon some of the cutting-edge topics in the field. The course has a significant hands-on component, emphasizing various software tools and computational methods for systems biology

103 - Course Recap.
102 - Advanced Topics.
101 - Advanced Topics.
100 - Advanced Topics.
99 - Introduction to Synthetic Biology.
98 - Robustness and Evolvability.
96 - Robustness in Biological Systems: Trade-offs.
97 - Robustness and Evolvability.
95 - Robustness in Biological Systems: Organising Principles.
94 - Robustness in Biological Systems: Mechanisms.
93 - Robustness in Biological Systems.
92 - Computational Modelling of Host--Pathogen Interactions.
91 - Computational Modelling of Host--Pathogen Interactions.
90 - Lab: Modelling Gene Regulatory Networks.
89 - Lab: Modelling Gene Regulatory Networks.
88 - Modelling Gene Regulatory Networks.
87 - Modelling Gene Regulatory Networks.
86 - Modelling Gene Regulatory Networks.
85 - Lab: $^{13}$C-Metabolic Flux Analysis using Mass Spectrometry.
84 - $^{13}$C-Metabolic Flux Analysis using Mass Spectrometry.
83 - $^{13}$C-Metabolic Flux Analysis using Mass Spectrometry.
82 - $^{13}$C-Metabolic Flux Analysis using Mass Spectrometry.
81 - Constraint-based Modelling of Metabolic Networks: Recap.
80 - Constraint-based Modelling of Metabolic Networks: Recap.
79 - Constraint-based Modelling of Metabolic Networks: Recap.
78 - Lab: Gene Deletions.
77 - Constraint-based Modelling of Metabolic Networks: Applications.
76 - Constraint-based Modelling of Metabolic Networks: Applications.
75 -Constraint-based Modelling of Metabolic Networks: Applications.
74 - Elementary Modes.
73 - Elementary Modes.
72 -Integrating Regulatory Information into Constraint-Based Models.
71 - Lab: Gene Deletions.
70 - Constraint-based Modelling of Metabolic Networks.
69 - Perturbations to Metabolic Networks: Synthetic Lethals.
68 - Perturbations to Metabolic Networks: Synthetic Lethals.
67 - Perturbations to Metabolic Networks: Over-expression.
66 - Understanding FBA.
65 - Understanding FBA.
64 - Lab: COBRA Toolbox.
63 - Perturbations to Metabolic Networks: Deletions.
62 - Lab: FBA using MATLAB.
61 - Other Constraint-Based Approaches.
60 - Other Constraint-Based Approaches.
59 - Flux Balance Analysis.
58 - Flux Balance Analysis.
57 - Flux Balance Analysis.
56 - Constraint-based Modelling of Metabolic Networks.
55 - Guest Lecture: Quantitative Systems Pharmacology.
54 - Guest Lecture: Quantitative Systems Pharmacology.
53 - Guest Lecture: Quantitative Systems Pharmacology.
52 - Guest Lecture: Modelling in Drug Development.
51 - Guest Lecture: Modelling in Drug Development.
50 - Lab: Parameter Estimation.
49 - Dynamic Modelling Recap.
48 - PyGMO.
47 - Other Evolutionary Algorithms.
46 - Genetic Algorithms.
45 - Genetic Algorithms.
44 - Direct Search Methods.
43 - Methods for Parameter Estimation.
42 - Parameter Estimation.
41 - Parameter Estimation.
40 - Parameter Estimation.
39 - Lab: Example Biological Model.
38 - Lab: Solving ODEs in MATLAB.
37 - Introduction to Dynamic Modelling.
36 - Introduction to Dynamic Modelling.
35 - Introduction to Dynamic Modelling.
34 - Reconstruction of Signalling Networks.
33 - Reconstruction of Signalling Networks.
32 - Reconstruction of Protein Networks.
31 - Reconstruction of Gene Regulatory Networks.
30 - Lab: Network Models & Perturbations.
29 - Lab: Network Models & Perturbations.
28 - Network Biology: Recap.
27 - Lab: Network Biology.
26 - Lab: Cytoscape.
25 - Lab: Cytoscape.
24 - Network Motifs.
23 - Community Detection.
22 - Network Perturbations.
21 - Biological Networks.
20 - Network Models.
19 - Network Models.
18 - Network Biology.
17 - Introduction to Network Biology.
16 - Introduction to Network Biology.
15 - Introduction to Network Biology.
14 - Introduction to Networks.
13 - Introduction to Networks.
12 - Lab: MATLAB Basics.
11 - Lab: MATLAB Basics.
10 - Lab: MATLAB Basics.
09 - Lab: MATLAB Basics.
08 - Representation of Biological Networks.
07 - Some Example Models.
06 - Fundamentals of Mathematical Modelling.
05 - Fundamentals of Mathematical Modelling.
04 - Fundamentals of Mathematical Modelling.
03 - Introduction to Modelling.
02 - Introduction to Modelling.
01 - Introduction.