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Contains methods to load supplementary data and export networks into Petri nets.

Overview

Protein annotations

Opens a window in which the user manages protein annotations. Protein annotations are key/value pairs associated with a given protein identifier. Annotations must be loaded from the file system (note: the Java API contains methods to generate such annotation file). These protein annotations can be used to create filtered protein sets to restrict networks or complex sets to the filtered protein space.

See also:

Name mappings

Opens a window for managing name mappings. Name mappings are loaded as directed networks from the file system.

See also: Name mappings

GO settings

Manages Gene Ontology (GO) functional similarity calculators. A GO setting consists of the following parameters:
Ontology and annotation files can be downloaded from the Gene Ontology website.

Important note: The protein identifier types used in the GO files might not be the same as in the other data files. You might have to use a name mapping file. ProCope provides such a name mapping file for yeast in data/yeastmappings_YYMMDD.txt.

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Localization data

Manages localization data for proteins. Localization data must be loaded from files in a specific format.

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Petri nets

Contains methods to export and convert Petri nets.

Generate Petri net

Generates a Petri net which integrates information from all selected networks, complex sets and purification datasets. The Petri net is stored in a GZIPed file.

See also: Petri nets

Convert to Cytoscape/XGMML

Converts a given Petri net file to a Cytoscape-compatible XGMML format file.

See also: Petri nets

Convert to ToPNet

Converts a given Petri net file to a pair of ToPNet .places/.interactions files.

See also: Petri nets


ProCope documentation