CellML Models Containing the Deprecated Reaction Element
While it is possible to specify a CellML model purely in terms of equations expressed in MathML, when the CellML 1.0 language was first defined a reaction element was included. This described reaction kinetics, the identites of the reactants and products, and also identified any reaction catalysts or inhibitors.
However, in practice we found implementing the reaction element in a CellML model often required the equations to be re-written, such that they no longer reflected those in the original publication. At best this created extra work and some confusion, at worst it broke the model.
As a result, we are now deprecating the reaction element, and we intend it to be removed from the CellML1.2 specification. A document discussing the motivation for this change, and also describing the process of how the reaction element can be removed from a model can be downloaded here.
We have identified all the models in the repository which contained the reaction element, and the vast majority of these have now been successfully recoded. At the end of this process we have been left with 13 models which we were unable to translate. The main reason for this is because the CellML models were originally taken from papers (often review papers) which did not contain a (complete) mathematical model. They were qualitative models which were usually based on a schematic figure of a reaction pathway. All the reaction kinetics were assumed to be mass action and all the parameters were assigned a default value of 1.0.
Although it is possible to recode these models to remove the reaction element, the end product will be pretty meaningless, and the CellML model will not represent a published model. Consequently we have removed these 13 models from the main repository and they are now listed below as a legacy of a learning process.
However, in practice we found implementing the reaction element in a CellML model often required the equations to be re-written, such that they no longer reflected those in the original publication. At best this created extra work and some confusion, at worst it broke the model.
As a result, we are now deprecating the reaction element, and we intend it to be removed from the CellML1.2 specification. A document discussing the motivation for this change, and also describing the process of how the reaction element can be removed from a model can be downloaded here.
We have identified all the models in the repository which contained the reaction element, and the vast majority of these have now been successfully recoded. At the end of this process we have been left with 13 models which we were unable to translate. The main reason for this is because the CellML models were originally taken from papers (often review papers) which did not contain a (complete) mathematical model. They were qualitative models which were usually based on a schematic figure of a reaction pathway. All the reaction kinetics were assumed to be mass action and all the parameters were assigned a default value of 1.0.
Although it is possible to recode these models to remove the reaction element, the end product will be pretty meaningless, and the CellML model will not represent a published model. Consequently we have removed these 13 models from the main repository and they are now listed below as a legacy of a learning process.
- condorelli_george_2001
- haugh_wells_lauffenburger_2000
- hefti_harder_eppenberger_schaub_1997
- kamp_hell_2000
- kodama_fukuda_pan_sano_takahashi_kato_makino_manabe_murata_ogawa_2000
- mulquiney_bubb_kuchel_1999
- mulquiney_kuchel_1999
- ren_samson_sowers_1999
- rizzi_baltes_reuss_1997
- takahashi_cannon_2001
- vojtek_der_1998
- wang_2002
- wang_lipsius_1995
Release candidates PCEnv 0.5 (rc1) and CellML API 1.5 (rc1)