Welcome to OneModel’s documentation!

OneModel is an open-source text-based tool for defining SBML models in a modular and incremental way that minimizes the user’s programming knowledge requirements.

With the advent of the Systems Biology Markup Language (SBML), a large community of SBML-compliant tools has been created. However, these tools can only be used to their full potential by expert users with advanced programming knowledge. OneModel is an open-source text-based tool for defining SBML models in a modular and incremental way that minimizes the user’s programming knowledge requirements. It is focused on accessibility, simplicity, and modularity. OneModel syntax allows the user to define models based on chemical (and pseudo-chemical) reactions, differential equations, and algebraic equations. OneModel is written in Python and it provides two interfaces: a command-line interface for expert-users, and a graphical user interface for non-expert users.

Check out the Installation and Quick Start sections for further information.

Note

This project is under active development.

Contents:

• Introduction
• Installation
• Quick Start
  • Usage
• OneModel workflow
• OneModel design philosophy
• OneModel implementation
• Subpackage SBML2dae
• OneModel syntax
  • Comments
  • Parameters
  • Species
  • Reactions
  • Substitution, rate, and algebraic rules
  • Model and objects
  • Import
  • Standalone
• Examples
  • Constitutive protein expression
  • Induced protein expression
  • Antithetic controller
  • Host-aware antithetic controller
• src
  • onemodel package

Indices and tables

• Index

• Module Index

• Search Page