Macrophage pathways

Modelling pathways is fundamental to our understanding of the workings of biological systems. This resource brings together pathway-models of macrophage signalling or other systems with relevance to this cell. Including:

Pathway Diagrams

The following pathway models have been assembled using the modified Edinburgh Pathway Notation (mEPN) scheme, a graphical language for depicting relationships between pathway components.  All pathways were created manually using the free network-diagramming software yEd Graph Editor and are based on published literature. 

Find out more about the below pathways here.

Upon clicking upon the pathway title the pathways can be accessed in a number of software tools suited for different needs: 

  • pdf for high definition zoomable viewing of the pathway image.
  • flash html for zoomable viewing of pathway image in a web browser.
  • yEd (.graphml file). yEd Graph Editor was used to create these diagrams and when opened in this tool pathways can be edited, nodes can be hyperlinked out to other resources, and additional notes added and viewed.
  • Biolayout Express3D  (.graphml file). supports the input of graphml files and includes a parser that converts the notation scheme into a 3D equivalent.  In this tool the results of other analyses e.g. microarray analyses can be overlaid upon these diagrams and it also contains a Signalling Petri Net algorithm for running stochastic flow simulations of pathway activity based upon predefined parameters/assumptions.
  • VANTED/ SBGN-ED format (sbgn file). Download VANTED and SBGN-ED (both free) to open the SBGN compliant version of the pathway.
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Creation of the above pathway diagrams has been a collaborative effort between members of:

Specifically the pathways have been compiled with the help of University of Edinburgh students studying on the Division of Pathway Medicine’s MSc  in Genomics and Pathway Biology and final year BSc BioMedical students who undertake the ‘Making sense of Disease Pathways’ elective course.

Other Relevant Pathway Resources

For information on a wide range of other pathway resources follow this link.