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Arcadia Description

A visualisation tool for metabolic pathways

As the amount of data available on biological systems increases, so does the need for computing tools supporting their analysis.
In particular, by enabling the interactive exploration on various kind of pathways, visualisation software provides considerable assistance in making sense of complex networks.
Unfortunately, existing tools struggle to address adequately the specific case of metabolic pathways: automatic layouts computed by generic graph-drawing algorithms usually require time-consuming manual adjustments.

Arcadia has been designed specifically to provide relevant visualisation options for metabolic pathways.

Arcadia is a viewer, not an editor: this means a simpler interface, offering multiple perspectives on the same data, with a focus on navigation.

As a light-weight, standalone component, Arcadia is easy to deploy and maintain. In order to ensure interoperability with other tools, an effort is made to support existing or emerging standards such as SBML and SBGN.

A reference framework for the development of Arcadia is Utopia: an open-source, interoperable set of desktop tools for protein analysis, built according to the Model/View/Controller pattern. This approach, along with Object Oriented Programming, makes up for flexible, evolutive software.

Implementation

Written in C++, Arcadia makes use of powerful existing open-source libraries:

* LibSBML => an interface to SBML pathway files
* the Boost Graph Library => an efficient graph structure
* GraphViz => classic layout algorithms
* libavoid => dynamic edge routing
* Qt => the Graphical User Interface

Cross-platform, the code can be compiled to run on Mac, UNIX or Windows systems.

Features

Arcadia enables navigation between multiple interconnected views of the same model:

* sorted lists of reactions and biochemical species
* detailed properties of selected elements
* graphic representations of the whole network
* local maps for groups of neighbouring molecules

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