Graphical & Computational Modelling of Biological Pathways

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Download the datasets used in the tutorial videos.

1.Introduction


2. Many Views of A Pathway(Lecture)

Content:

  • a biologists view of the world, Prof Lee Smith’s world view, testicular development
  • a mathematician’s view of a pathway
  • an interactome view of a pathway
  • an analyst’s (my) data driven view of a pathway
  • many views of what constitutes a pathway model

3.Pathway Models & Pathway Types (Lecture)

Content:

  • why build pathway models?
  • why should we want to construct pathway models?
  • pathway types

4. Sources of ‘Pathway Data’ (Lecture)

Content:

  • sources of ‘pathway data’
  • KEGG(Kyoto Encyclopaedia of Genes and Genomes)
  • eMIM
  • wikipathways
  • wikipathways. Most ‘edited’: Breast cancer
  • Pathway Interaction Database
  • reactome

5. Issues (Lecture)

Content:

  • issues
  • views of apoptosis

6. SBGN (Lecture)

Content:

  • SBGN (The Systems Biology Graphical Notation)
  • SBGN tools: cellDesigner, SBGN-ED

7. mEPN (Lecture)

Content:

  • why build models
  • mEPN(Modified Edinburgh Pathway Notation Scheme)
  • mEPN(Modified Edinburgh Pathway Notation Scheme) 2014
  • basics of mEPN usage
  • comparison between mEPN and SBGN
  • basic Layout Rules for Modified Edinburgh Process Notation

8. Practical Session: Pathway to Pathway Construction – yED(1)

Content:

  • pathway to pathway construction
  • yED by yWorks
  • edges, edge annotation
  • layout algorithms
  • navigation tools, zoom in/out

9. Practical Session: Pathway to Pathway Construction – yED(2)

Content:

  • properties menu
  • Preferences, display
  • align nodes
  • tools, graph analysis

10. Practical Session: Pathway to Pathway Construction – yED(3)

Content:

  • create a customized pallet(pallet manager)
  • IFNB Pathway Description

11. Practical Session: IFNB Pathway Description & Diagram

Content:

  • IFNB Pathway Description
  • IFNB Pathway Diagram

12. Practical Session: IFNB Pathway Description & Diagram (Cont.)

Content:

  • IFNB Pathway Description
  • IFNB Pathway Diagram

13. Framework Map of Macrophage Signalling Pathways (Lecture)

Content:

  • framework map of macrophage signalling pathways

14. Analysis & Visualization of Rule-Based Stochastic Flow (Lecture)

Content:

  • analysis and visualization of rule-based stochastic flow through large network diagrams of biological pathways
  • objectives
  • options for DynamicModelling
  • starting assumptions

15. Petri nets, Basis of The Flow of Tokens using SPN, and Flow of Tokensthrough Transitions (Lecture)

Content:

  • Petri nets
  • Signaling Petri Net: stochastic flow simulation
  • basis of the flow of tokens using SPN
  • SPN implementation
  • stochastic linear flow
  • flow of tokensthrough transitions

16. Practical Session: SPN Simulation

Content:

  • flow of tokensthrough transitions
  • SPN Simulation
  • animation control
  • view node name and simulation profile

17. Practical Session: SPN Simulation (Cont.)

Content:

  • IFNB pathway – SPN feedback
  • run SPN Simulation
  • graph properties
  • animation control
  • view node name and simulation profile
  • choose SPN stochastic distribution, numbers of run, Size transition
  • accuracy

18. Sample Case: The Influenza Virus & Macrophage Diagram (Lecture)