Abstract
The understanding of complex biological networks often relies on both a dedicated layout and a topology. Currently, there are three major competing layout-aware systems biology formats, but there are no software tools or software libraries supporting all of them. This complicates the management of molecular network layouts and hinders their reuse and extension. In this paper, we present a high-level overview of the layout formats in systems biology, focusing on their commonalities and differences, review their support in existing software tools, libraries and repositories and finally introduce a new conversion module within the MINERVA platform. The module is available via a REST API and offers, besides the ability to convert between layout-aware systems biology formats, the possibility to export layouts into several graphical formats. The module enables conversion of very large networks with thousands of elements, such as disease maps or metabolic reconstructions, rendering it widely applicable in systems biology.
Highlights
Systems biology aims at a detailed understanding of mechanisms underlying complex biological processes
We addressed the issue of conversion between layout-aware formats in a recently developed tool, which allows users to convert between Systems Biology Markup Language (SBML) with layout and render packages, CellDesigner SBML and Systems Biology Graphical Notation (SBGN)-ML Process Description diagrams
The current situation, when one format is used for encoding the structure, dynamics and annotations of molecular network and the other is used representing layout, is clearly unsatisfactory
Summary
Systems biology aims at a detailed understanding of mechanisms underlying complex biological processes. A format capable of storing a diagram layout needs to handle information about the network structure and positions of elements and labels, space they occupy and how they should be rendered, i.e. their shape, color and other visual aspects. Besides its ability to encode molecular network information, SBML provides the ability to store visual diagrams via its layout and render packages. These extend the core language of SBML, used for describing the structure and dynamics of the underlying system. We addressed the issue of conversion between layout-aware formats in a recently developed tool, which allows users to convert between SBML with layout and render packages, CellDesigner SBML and SBGN-ML Process Description diagrams. The API can be accessed from any programming language or from the command line using the cURL tool (see examples in the documentation [56])
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