**Setting parameters in the model: general methodologies and details**

Parameters in the model are set according to a number of rules, some very general and others quite specific. The parameters actually needed by the model essentially divide into those which are taken (or estimated) directly from the literature, and those which are calculated indirectly from information in the literature and model constraints.

Here we first detail the general principles used in setting parameters. Readers wishing simply for a reference database of all parameters in the model can go to the list of model parameters at the end, which are arranged alphabetically. Within this very long table are links to the functional forms, and where parameters are set by a complicated or non-standard process, to the sections describing how this is done.

- Basics

- Estimating rate constants for reactions
- Estimating rate constants from equilibrium and turnover data for reactions not normally at equilibrium
- Estimating rate constants for reactions from equilibrium, concentration and half-time data
- Carrier mediated transport

- Metabolic rates and accounting

- Particular calculations: biochemistry
- The rate constants for adenylate kinase
- NAD/NADH concentrations
- The rate constants for haemoglobin
- Calcium dynamics
- NO dynamics
- Myosin phosphorylation and dephosphorylation
- Electron transport

- Particular calculations: ion channels
- Total potassium channel conductivity of a given VSM segment
- General methodology for working out normal channel conductivity
- Normal potassium channel conductivities
- Calcium channels in VSM
- The total effect of extracellular potassium on the membrane potential

- A list of model parameters
- Bibliography

2004-07-08