Guided tour

N.B.: all screenshots on this page are from an alpha version of Arcadia. The current release slightly differs in appearance, but the main features remain the same.

Graphical User Interface:
list view (left), property view (bottom), graphic view (top right)

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Open the SBML model (up to L2v4):
SBO annotations are used to determine rendering style (SBGN PD compliant)

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Browse species and reactions in the list view:

• sorted according to relevant properties
• linked to the graphic view (standard commands on selected nodes can be executed from there)

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Select and move groups of species and reactions:
edges are updated in real time

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Switch to (+ between and from) the local views with a right click

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Zoom in/out

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Clone individual species with a double click:
good candidates are well-known currency molecules, high connectivity species, modifiers, ...

For more convenience, a menu command allows to clone all modifiers at a time

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Update the layout by double-clicking the background:
the layout is computed according to local strategies defined for subparts of the network (cf. dashed rectangles)

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Create a transversal branch

by double-clicking a species involved in a single reaction

... or double-clicking a reaction

to create a regular branch, pointing out of the main flow

or a triangle's branch connecting two parts of the main flow

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Save and/or export your work:

• save as annotated SBML (proprietary annotations and layout extension)
• export as vector image (SVG, PDF, PS)