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Course102106068105 lectures

Computational Systems Biology

Prof. Karthik Raman · IIT Madras

Start with lecture 1 At NPTEL

Lectures

Week 1

  1. 01 - Introduction Video
  2. 02 - Introduction to Modelling Video
  3. 03 - Introduction to Modelling Video
  4. 04 - Fundamentals of Mathematical Modelling Video
  5. 05 - Fundamentals of Mathematical Modelling Video
  6. 06 - Fundamentals of Mathematical Modelling Video
  7. 07 - Some Example Models Video
  8. 08 - Representation of Biological Networks Video
  9. 09 - Lab: MATLAB Basics Video
  10. 10 - Lab: MATLAB Basics Video
  11. 11 - Lab: MATLAB Basics Video
  12. 12 - Lab: MATLAB Basics Video

Week 2

  1. 13 - Introduction to Networks Video
  2. 14 - Introduction to Networks Video
  3. 15 - Introduction to Network Biology Video
  4. 16 - Introduction to Network Biology Video
  5. 17 - Introduction to Network Biology Video
  6. 18 - Network Biology Video
  7. 19 - Network Models Video
  8. 20 - Network Models Video

Week 3

  1. 21 - Biological Networks Video
  2. 22 - Network Perturbations Video
  3. 23 - Community Detection Video
  4. 24 - Network Motifs Video
  5. 25 - Lab: Cytoscape Video
  6. 26 - Lab: Cytoscape Video
  7. 27 - Lab: Network Biology Video

Week 4

  1. 28 - Network Biology: Recap Video
  2. 29 - Lab: Network Models & Perturbations Video
  3. 30 - Lab: Network Models & Perturbations Video
  4. 31 - Reconstruction of Gene Regulatory Networks Video
  5. 32 - Reconstruction of Protein Networks Video
  6. 33 - Reconstruction of Signalling Networks Video
  7. 34 - Reconstruction of Signalling Networks Video

Week 5

  1. 35 - Introduction to Dynamic Modelling Video
  2. 36 - Introduction to Dynamic Modelling Video
  3. 37 - Introduction to Dynamic Modelling Video
  4. 38 - Lab: Solving ODEs in MATLAB Video
  5. 39 - Lab: Example Biological Model Video
  6. 40 - Parameter Estimation Video
  7. 41 - Parameter Estimation Video
  8. 42 - Parameter Estimation Video
  9. 43 - Methods for Parameter Estimation Video
  10. 44 - Direct Search Methods Video

Week 6

  1. 45 - Genetic Algorithms Video
  2. 46 - Genetic Algorithms Video
  3. 47 - Other Evolutionary Algorithms Video
  4. 48 - PyGMO Video
  5. 49 - Dynamic Modelling Recap Video
  6. 50 - Lab: Parameter Estimation Video
  7. 51 - Guest Lecture: Modelling in Drug Development Video
  8. 52 - Guest Lecture: Modelling in Drug Development Video
  9. 53 - Guest Lecture: Quantitative Systems Pharmacology Video
  10. 54 - Guest Lecture: Quantitative Systems Pharmacology Video
  11. 55 - Guest Lecture: Quantitative Systems Pharmacology Video

Week 7

  1. 56 - Constraint-based Modelling of Metabolic Networks Video
  2. 57 - Flux Balance Analysis Video
  3. 58 - Flux Balance Analysis Video
  4. 59 - Flux Balance Analysis Video
  5. 60 - Other Constraint-Based Approaches Video
  6. 61 - Other Constraint-Based Approaches Video
  7. 62 - Lab: FBA using MATLAB Video

Week 8

  1. 63 - Perturbations to Metabolic Networks: Deletions Video
  2. 64 - Lab: COBRA Toolbox Video
  3. 65 - Understanding FBA Video
  4. 66 - Understanding FBA Video
  5. 67 - Perturbations to Metabolic Networks: Over-expression Video
  6. 68 - Perturbations to Metabolic Networks: Synthetic Lethals Video
  7. 69 - Perturbations to Metabolic Networks: Synthetic Lethals Video
  8. 70 - Constraint-based Modelling of Metabolic Networks Video

Week 9

  1. 71 - Lab: Gene Deletions Video
  2. 72 -Integrating Regulatory Information into Constraint-Based Models Video
  3. 73 - Elementary Modes Video
  4. 74 - Elementary Modes Video
  5. 75 -Constraint-based Modelling of Metabolic Networks: Applications Video
  6. 76 - Constraint-based Modelling of Metabolic Networks: Applications Video
  7. 77 - Constraint-based Modelling of Metabolic Networks: Applications Video
  8. 78 - Lab: Gene Deletions Video

Week 10

  1. 79 - Constraint-based Modelling of Metabolic Networks: Recap Video
  2. 80 - Constraint-based Modelling of Metabolic Networks: Recap Video
  3. 81 - Constraint-based Modelling of Metabolic Networks: Recap Video
  4. 82 - $^{13}$C-Metabolic Flux Analysis using Mass Spectrometry Video
  5. 83 - $^{13}$C-Metabolic Flux Analysis using Mass Spectrometry Video
  6. 84 - $^{13}$C-Metabolic Flux Analysis using Mass Spectrometry Video
  7. 85 - Lab: $^{13}$C-Metabolic Flux Analysis using Mass Spectrometry Video

Week 11

  1. 86 - Modelling Gene Regulatory Networks Video
  2. 87 - Modelling Gene Regulatory Networks Video
  3. 88 - Modelling Gene Regulatory Networks Video
  4. 89 - Lab: Modelling Gene Regulatory Networks Video
  5. 90 - Lab: Modelling Gene Regulatory Networks Video
  6. 91 - Computational Modelling of Host--Pathogen Interactions Video
  7. 92 - Computational Modelling of Host--Pathogen Interactions Video
  8. 93 - Robustness in Biological Systems Video
  9. 94 - Robustness in Biological Systems: Mechanisms Video
  10. 95 - Robustness in Biological Systems: Organising Principles Video
  11. 96 - Robustness in Biological Systems: Trade-offs Video

Week 12

  1. 97 - Obustness and Evolvability Video
  2. 98 - obustness and Evolvability Video
  3. 99 - Introduction to Synthetic Biology Video
  4. 100 - Advanced Topics Video
  5. 101 - Advanced Topics Video
  6. 102 - Advanced Topics Video
  7. 103 - Course Recap Video

Live Session

  1. Live Session 05-03-2021 Video
  2. Live Session 20-02-2020 Video

Syllabus and materials

At NPTEL, as the course publishes them.

Credits and licence

Institution
IIT Madras
Department
Biotechnology
Teacher
Prof. Karthik Raman
Level
Undergraduate
Language
English
Subjects
Biology
Source
NPTEL
Licence
CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
Attribution
NPTEL states: "Distributed under Creative Commons Attribution-ShareAlike / CC BY - NC - SA", beside a BY-NC-SA badge.
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