Welcome to SBMLDiagrams’s documentation!

Contents:

• Introduction
  • Installation
  • Figure Examples
• Tutorial
• Network
• Compartment
  • Read the compartment information.
  • Edit the compartment information.
• Node
  • Read the node information.
  • Edit the node information.
• Reaction
  • Read the reaction information.
  • Edit the reaction information.
• ArbitraryText
  • Read the information of arbitrary text.
  • Edit the information of arbitrary text.
  • Add and remove the an arbitrary text.
• ArbitraryShape
  • Read the information of arbitrary shape.
  • Add or remove an arbitrary shape.
• Colors

Introduction

SBMLDiagrams is a Python package to visualize networks embedded in SBML Level 3 models. If the SBML layout and render extension are used, the package will use this data to display the network. SBMLDiagrams can export PNG, JPG, PDF files. SBMLDiagrams can be used to add SBML layout and render to an existing valid SBML model which can be subsequently be exported.

We also have an interface of SBMLDiagrams to NetworkX to exploit the variety of layout algorithms as well as SBbadger which is a tool for generating realistic but random biochemical networks. If you are using any of the code, please cite the article (https://doi.org/10.1093/bioinformatics/btac730) and the PYPI web page (https://pypi.org/project/SBMLDiagrams/). Thanks.