Arcadia

Arcadia converts SBML-encoded biological network models into Systems Biology Graphical Notation (SBGN) Process Description diagrams to visualize and explore metabolic pathways and signaling cascades.

Key Features:

• Standardized visualization: Converts Systems Biology Markup Language (SBML) files into Systems Biology Graphical Notation (SBGN) Process Description (PD) maps to represent network structure in a standardized graphical format.
• Multiple perspectives: Produces alternative views of the same biological model to present network structure from different perspectives.
• Customizable layouts: Supports alteration of diagram layouts to emulate textbook-style representations or alternative visual arrangements.
• Cross-platform implementation and licensing: Implemented in C++ with compatibility for Mac OS and Windows and distributed with source code under the GNU General Public License (GPL).

Scientific Applications:

• Systems biology model visualization: Visualizes systems biology models encoded in SBML for structural interpretation of networks.
• Metabolic pathway representation: Represents metabolic pathways as SBGN PD diagrams to clarify reaction and metabolite relationships.
• Signaling network analysis: Depicts signaling cascades to facilitate analysis of pathway connectivity and information flow.
• Model validation and hypothesis generation: Aids interpretation of model-derived results and supports generation and communication of hypotheses based on network representations.

Methodology:

Arcadia performs an automated translation of SBML files into SBGN Process Description maps.