Notions of similarity for systems biology models
@article{Henkel2017NotionsOS, title={Notions of similarity for systems biology models}, author={Ron Henkel and R. Hoehndorf and Tim Kacprowski and Christian Kn{\"u}pfer and Wolfram Liebermeister and Dagmar Waltemath}, journal={Briefings in Bioinformatics}, year={2017}, volume={19}, pages={77 - 88} }
Abstract Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of ‘similarity’ may greatly vary. A general notion of model similarity, applicable to…
19 Citations
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References
SHOWING 1-10 OF 71 REFERENCES
A graphical method for reducing and relating models in systems biology
- Computer ScienceBioinform.
- 2010
The generality of the graphical method is concluded, on its limits with respect to the representation of the structure of the interactions in SBML, and on some perspectives for dealing with the dynamics.
Structure, function, and behaviour of computational models in systems biology
- Biology, Computer ScienceBMC Systems Biology
- 2012
A conceptual framework – the meaning facets – which can be used to rigorously specify the semantics of bio-models is presented and constitutes a basis for computer-aided collaborative research.
Retrieval, alignment, and clustering of computational models based on semantic annotations
- Computer Science, BiologyMolecular systems biology
- 2011
By using general and flexible similarity measures for Systems Biology models computed from semantic annotations and a large extensible ontology, this work proposes a platform that can retrieve, cluster, and align systems Biology models and experimental data sets.
An algorithm to detect and communicate the differences in computational models describing biological systems
- Computer ScienceBioinform.
- 2016
Focusing on SBML and CellML, an algorithm to accurately detect and describe differences between coexisting versions of a model with respect to (i) the models’ encoding, (ii) the structure of biological networks and (iii) mathematical expressions is presented.
Integration of Boolean models exemplified on hepatocyte signal transduction
- Computer Science, BiologyBriefings Bioinform.
- 2012
This work proposes modelling standards for Boolean models as a prerequisite for smooth model integration and demonstrates the coupling of two logical models on two different examples concerning cellular interactions in the liver.
Finding patterns in biochemical reaction networks
- Computer SciencePeerJ Prepr.
- 2016
A tool chain that identifies reoccurring patterns in biochemical reaction networks and how the identified patterns can serve as a tool to measure the similarity of models is introduced.
Revision history aware repositories of computational models of biological systems
- Computer ScienceBMC Bioinformatics
- 2010
The Physiome Model Repository software is extended to be fully revision history aware, by building it on top of Mercurial, an existing DVCS, to build and understand more complex models.
Propagating semantic information in biochemical network models
- Computer ScienceBMC Bioinformatics
- 2011
This work aligns partially annotated models and finds annotations for non-annotated model elements based not only on their own annotations, but also on annotations of surrounding elements in the network.
Boolean modeling in systems biology: an overview of methodology and applications.
- Biology, Computer SciencePhysical biology
- 2012
This paper builds on research to provide a methodology overview of Boolean modeling in systems biology, including Boolean dynamic modeling of cellular networks, attractor analysis of Boolean dynamic models, as well as inferring biological regulatory mechanisms from high-throughput data using Boolean models.
Sustainable model building the role of standards and biological semantics.
- Computer ScienceMethods in enzymology
- 2011