Proposal for SED-ML extension to cover models in SBML Qual format

Quantitative modeling is used in computational biology to study interaction networks (predominantly regulatory and signalling networks). The SBML Qual package is an extension to the SBML Level 3 standard.

SBML Qual supports the encoding of qualitative models. It defines the structure and syntax for qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved (Chaouiya et al 2013).

SED-ML Level 1 Version 2 already supports different types of simulation experiments on SBML models. However, a few concepts are missing in order to fully support the encoding of models based on the SBML Qual extension. Here is a first proposal for how the missing concepts could be added to the current SED-ML Level 1 Version 2.