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BioCyc Database Plug-In

Image The BioCyc Database Plug-In allows to search for pathways and reactions in the BioCyc database collection and to load them as networks into Omix.

Using the Plug-In

After installation, you can find the BioCyc access in the File -> New menu.

File menu containing access to BioCyc
File menu containing access to BioCyc


After choosing this option, a dialog appears that requests to choose an organism database. BioCyc is a database collection of nearly 3000 databases about different organims and strains. Select the desired organism and continue with OK.

Selecting target BioCyc database
Selecting target BioCyc database


Then, the BioCyc plug-in loads all available pathways from the corresponding database. After finishing, you can select from these pathways in the following dialog window. Use the quick launch in order to search for specific pathways in the list. By double click, all reactions belonging to the pathway are listed. You can select individual reactions to be imported to Omix as well as entire pathways.
The list at the bottom shows all reactions selected to be imported.

BioCyc pathway browser
BioCyc pathway browser


If you need more information about the individual pathway or reaction in the list click with right mouse button on the list item. A context menu allears that contains the entry "Show pathway/reaction on BioCyc website". By clicking the menu entry your webbrowser opens with the corresponding website of the reaction or pathway.

Many reactions provide a number of alternative names and synonyms which you can select for each individual reaction in the bottom selection list. Likewise, you can specify, to which pathway the reaction shall belong in Omix.

After collecting an arbitrary number of reactions, the network can be finally assembled. Therefore, the plug-in again connects the database in order to download all necessary information about the reactions and reactants. Finally, the network is loaded as new document in Omix.

Non-positioned network components in the component view
Non-positioned network components in the component view


After loading the network all reactions and metabolites are not drawn on the drawing area but listed in the component view (highlighted red) because, currently, no positioning information is downloaded by the BioCyc plug-in. You can place the individual items on the drawing area by drag and drop, you can use the layout pattern and motif stamp feature of Omix (see User Manual) and/or you can use the AutoLayout Plug-In in order to arrange the network on the drawing area.

It is highly recommended not to load too many reactions in one step but to begin with a small selection (e.g. one pathway), finishing the diagram layout and then import further sets of reactions into the document.

1.2. Importing into other Documents

Instead of loading BioCyc database content into new Omix documents as described, you can also choose to import content into existing documents. Therefore, choose the menu entry File -> Import... -> Import Network from BioCyc.

1.3. Cache

By default, all content downloaded from the BioCyc databases will be cached in your local user directory. This makes later access to the same data much faster. In the configuration window of Omix, you can enable/disable caching and specify how often the cache shall be updated (go to menu Extra -> Configure; on OS X go to menu Omix -> Preferences).

Configuring BioCyc plug-in
Configuring BioCyc plug-in


1.4. Chemical Structures and Atom Mappings


In case that the Chemical Structure Plug-In is installed in Omix, the BioCyc Database Plug-In offers the option to import a network including the chemical structures available in the databases.
If the Atomic Layer Plug-In is installed, the BioCyc plug-in can also download atom mappings for most of the reactions. Both options are provided for choice after collecting the list of reactions.

Imported structures and atom mappings in the network
Imported structures and atom mappings in the network