PSS explore options
Newt interface
Available at: Newt interface
In order to display PSS from a systems biology perspective, SKM utilizes Newt, an open source, browser based Systems Biological Graphical Notation (SBGN) editor and viewer. For more information on Newt, and for tutorial and user instructions, please see: Newt Pathway Viewer & Editor.
Within the Newt representation, the reactions grouped by biologically relevant pathways. Nodes are coloured by type, and to be able to also discern the cellular compartment, node borders are coloured by compartment.
The colour legend is as below:
Search result nodes are highlighted by a thick red border:
Note: on entry of a new reaction, the page needs to be fully refreshed for the new reaction to appear.
Biomine interface
Available at: Biomine interface
The biomine exploration interface allows for interactive search queries of PSS, shortest path, and neighbourhood extraction.
Right clicking on a node brings up a sub-menu, including expanding node neighbours. Right clicking on the canvas brings up the option to freeze all node positions. More information on the biomine interface is available in the side panel.
When applicable, the sub-menu of the node also contains a link to query the Arabidopsis identifiers associated with the node in KnetMiner.
Note: on entry of a new reaction, the page needs to be fully refreshed for the new reaction to appear.
Searching by property
Available at: Search
In the "Search" interface, users can find reactions and FunctionalClusters entered into PSS via a number of properties (such as DOI, PMID , or node identifiers).