Table 5.
Evaluation of the neuronal signal transduction models.
| Model | Online | Language | Equations | Parameters | Init. cond. | Repro., Repli. | Compa. |
|---|---|---|---|---|---|---|---|
| d'Alcantara et al., 2003 | No | MATLABⓇ | All appendix | Most text | Most appendix, text | ++ | Tested |
| Hayer and Bhalla, 2005 | DOQCS | GENESIS/Kinetikit, MATLABⓇ, SBML | All code, suppl, tab | All code, suppl, tab | All code, suppl, tab | Not tried | Tested |
| Lindskog et al., 2006 | ModelDB | XPPAUT | All code, tab, text | All code, tab | All code | Not tried | Tested |
| Delord et al., 2007 | No | Not given | All text | All text | All text | +++ | Tested |
| Nakano et al., 2010 | ModelDB | GENESIS/Kinetikit | All code, suppl, tab, text | All code, suppl, tab | All code, suppl, tab | Not tried | Tested |
| Kim et al., 2010 | ModelDB | XPPAUT | All code, tab, text | All code, tab, text | All code | Not tried | Tested |
| Zachariou et al., 2013 | No | XPPAUT | Most text | Most tab, text | Some text | – | Not tried |
Online: availability of the model implementation in a model repository by the original authors. Language/Simulation tool: programming language or simulation tool used by the original authors to implement the model. Equations: availability and format of equations—embedded in the text, appendix, or supplementary material, presented in a table, or described in the publicly available model implementation (code). Parameters: availability and format of model parameters (same categories as for Equations). Init. cond.: availability and format of initial conditions (same categories as for Equations). Repro., Repli.: reproducibility or replicability of the original results with the information given in the original publication. Compa.: comparability of the models to each other. We described model implementation in the original publication using the following categories: none, some (at least about one third of the details necessary for model reimplementation is given), most (at least about two thirds are given), or all. Models for which we were not able to reproduce any results are marked by − sign. Models for which we reproduced at least some of the results are marked by one to three + signs depending how well we reproduced the results. We implemented the chosen models with MATLABⓇ. See more details in section 3 and in our previous publications (Manninen and Linne, 2008; Manninen et al., 2011).