Adding / removing sbml:reaction nodes

[bmoreau]

= Description =

• Provide the API for adding or removing reactions in SBML models through the Change mechanism in SED-ML.

= Context =

• Biochemical reactions are central to the SBML language; it should be made possible to manipulate them through the SED-ML language in !BioPreDyn, using the elementary XML manipulation tools it provides.
• The sedml:Change object (and all its derived classes) encodes for a modification to be applied to a sedml:Model before a simulation run. Writing a Change element requires a deep understanding of both the SBML model (the user usually has it) and the XML philosophy (the user does not necessarily have it).

= Success criteria =

• High-level API exists for adding / removing sbml:reaction nodes from a SBML model through the use of sedml:change-derived nodes attached to a sedml:model node.

= Expected issues =

• Amount of information required when creating a reaction?
• Should we use external biochemical reaction databases?

[bmoreau]

Imported from trac issue 40. Created by bmoreau on 2014-06-10T15:51:16, last modified: 2014-06-10T15:55:36