ITM Probe: Channel Model

Model Parameters

Interaction Network

Interaction Graph: [?]

Select the interaction network for the query. more...

Excluded Nodes: enter here [?]

Enter the list of nodes (proteins) to exclude from the graph. The nodes can be entered as NCBI Gene IDs or canonical gene symbols appropriate for the selected network. Identifiers may be separated by spaces, commas, semicolons, tabs or line breaks. The unrecognised identifiers are ignored and a warning is printed. Note that the identifiers uploaded from the file are appended to those entered through the form.

or submit a file [?]

Upload a text file with the list of proteins to exclude from the graph. The nodes can be entered as NCBI Gene IDs or canonical gene symbols appropriate for the selected network. Identifiers may be separated by (one or many) spaces, commas, semicolons, tabs or line breaks. The unrecognised identifiers are ignored and a warning is printed. Note that the identifiers uploaded from the file are appended to those entered through the form.

Channel Model Parameters

Sources (max. 6): [?]

Enter the origins of the random walks (information flow) as NCBI Gene IDs or canonical gene symbols appropriate for the selected network. Identifiers may be separated by spaces, commas, semicolons, tabs or line breaks. Up to six sources among all contexts can be specified and each active context must contain at least one source.

Sinks (max. 6): [?]

Enter the destinations of the random walks (information flow) as NCBI Gene IDs or canonical gene symbols appropriate for the selected network. Identifiers may be separated by spaces, commas, semicolons, tabs or line breaks. Up to six sinks among all contexts can be specified and each active context must contain at least one sink.

Dissipation Criterion (choose one):

Termination (dissipating) probability:
[?]

Enter the probability for a random walk to terminate (dissipate) at each step. Allowed values range from 0.0 to 1.0 - 1e-14. more...

Expected drift from shortest path (absolute):
[?]

Enter the average amount of steps a random walk can drift from its shortest possible path as it moves from a source to a sink, in absolute units. With more than one source, the length of the shortest path should be interpreted as the average of the lengths of shortest paths from each source to the sink closest to it.

A value close to 0 corresponds to termination probability close to 0 and means that random walks can only visit the nodes on the shortest paths from each source to its closest sinks. The value of 2 means that on average, each random walk visits two nodes more than necessary on the way from its origin to its destination. more...

Expected drift from shortest path (relative):
[?]

Enter the average amount of steps a random walk can drift from its shortest possible path as it moves from a source to a sink, as proportion of the length of the shortest path. With more than one source, the length of the shortest path should be interpreted as the average of the lengths of shortest paths from each source to the sink closest to it.

For example, if the length of the shortest path is 4, the value of 0.8 means that on average, each random walk visits 3.2 nodes more than necessary on the way from its origin to its destination. more...

Display Parameters

Output Format

Output Format: [?]

Choose output format for the results.

Layout Options

Layout by: [?]

Choose the values used to selecting the most significant nodes from the results for display in the table and in the graphical image. Presently restricted to a single choice. more...

Criterion: [?]

Choose the criterion to select the number of top ranking nodes to be shown. more...

Cutoff Value:

Maximum Shown: [?]

Enter the maximum number (up to 200) of network nodes to be shown. This option overrides the 'Criterion' selection if it would display a larger number of nodes. more...

Layout Seed: [?]

Enter the seed to initialize the graphics layout. Each seed produces a different layout and hence this parameter can be used to obatain different layouts of the same ITM subragraph. more...

Rendering Options

Color by: [?]

Select the values used to color the nodes in the ITM subgraph image. more...

Scaling: [?]

Choose the scaling function to apply to the node values before coloring. more...

Color Map: [?]

Choose the color palette to color the nodes. more...

Image Format: [?]

Choose the format of the ITM subraph image. The 'SVG in Navigator' format is best for viewing and exploring the image online while others can be used to save the image. more...

QMBP

ITM Probe

NCBI

WEB SERVICE

DOCUMENTATION

Interaction Network

Channel Model Parameters

Output Format

Layout Options

Rendering Options