Name
Title | ||
|---|---|---|
TopoFilter: a MATLAB package for mechanistic model identification in systems biology. |
Abstract | ||
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To develop mechanistic dynamic models in systems biology, one often needs to identify all (or minimal) representations of the biological processes that are consistent with experimental data, out of a potentially large set of hypothetical mechanisms. However, a simple enumeration of all alternatives becomes quickly intractable when the number of model parameters grows. Selecting appropriate dynamic models out of a large ensemble of models, taking the uncertainty in our biological knowledge and in the experimental data into account, is therefore a key current problem in systems biology. The TopoFilter package addresses this problem in a heuristic and automated fashion by implementing the previously described topological filtering method for Bayesian model selection. It includes a core heuristic for searching the space of submodels of a parametrized model, coupled with a sampling-based exploration of the parameter space. Recent developments of the method allow to balance exhaustiveness and speed of the model space search, to efficiently re-sample parameters, to parallelize the search, and to use custom scoring functions. We use a theoretical example to motivate these features and then demonstrate TopoFilter’s applicability for a yeast signaling network with more than 250’000 possible model structures. TopoFilter is a flexible software framework that makes Bayesian model selection and reduction efficient and scalable to network models of a complexity that represents contemporary problems in, for example, cell signaling. TopoFilter is open-source, available under the GPL-3.0 license at https://gitlab.com/csb.ethz/TopoFilter. It includes installation instructions, a quickstart guide, a description of all package options, and multiple examples. |
Year | DOI | Venue |
|---|---|---|
2020 | 10.1186/s12859-020-3343-y | BMC Bioinformatics |
Keywords | DocType | Volume |
Ensemble modeling, Bayesian model selection, Topological filtering, Signal transduction | Journal | 21 |
Issue | ISSN | Citations |
1 | 1471-2105 | 0 |
PageRank | References | Authors |
0.34 | 0 | 5 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Mikołaj Rybiński | 1 | 2 | 1.11 |
| Simon Möller | 2 | 0 | 0.34 |
| Mikael Sunnåker | 3 | 44 | 3.02 |
| Claude Lormeau | 4 | 0 | 0.34 |
| Jörg Stelling | 5 | 1 | 0.68 |