PMC

Omics datasets containing multiple time points can be presented in the form of omics popups on individual full-detail pathway diagrams. The user can select from several layouts and drag the popups to modify their location.

Adding MIGS [Minimal Information about a (Meta)Genome Sequence] data to PGDBs enables searching the organism list for organisms that match particular phenotypes. In this example, BioCyc was queried for PGDBs for organisms that are facultative in respect to oxygen, retrieving 327 matches.

The new layout of the gene/protein page adds tabs, enabling the user to switch quickly among different data fields, including a summary, GO terms, essentiality data, protein features, operons, and references. A Show All tab places all the information on a single scrollable page.

New electron transfer pathway diagrams enable connecting multiple reactions via any electron carrier. This type of diagram provides more information for electron transfer chains than does the typical metabolic pathway diagram, and clearly depicts the direction of the electron flow, the cell-compartment locations where the substrates are transformed, and the optional translocation of protons across membranes.

The new pathway collage diagram combines multiple pathway diagrams for a selected set of pathways. Users can edit pathway collages within their web browser, such as by adding additional pathways; zooming in or out; manually moving pathways or metabolite nodes; showing or hiding connections; highlighting objects of interest; and displaying omics data (transcriptomics data are shown in this image).

The new BioCyc app, which works on iOS devices, enables users to access any database in BioCyc, and any database in any other Pathway-Tools-based website that is running version 18.5 or later of Pathway Tools. The app lets users select a PGDB, query it for genes, and display related information, such as gene/protein data, catalyzed reactions, and metabolic pathways that the gene products participates in.