BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4:92

European Bioinformatics Institute, Hinxton, UK.
BMC Systems Biology (Impact Factor: 2.44). 06/2010; 4(1):92. DOI: 10.1186/1752-0509-4-92
Source: PubMed


Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification.
BioModels Database is aimed at addressing exactly these needs. It is a freely-accessible online resource for storing, viewing, retrieving, and analysing published, peer-reviewed quantitative models of biochemical and cellular systems. The structure and behaviour of each simulation model distributed by BioModels Database are thoroughly checked; in addition, model elements are annotated with terms from controlled vocabularies as well as linked to relevant data resources. Models can be examined online or downloaded in various formats. Reaction network diagrams generated from the models are also available in several formats. BioModels Database also provides features such as online simulation and the extraction of components from large scale models into smaller submodels. Finally, the system provides a range of web services that external software systems can use to access up-to-date data from the database.
BioModels Database has become a recognised reference resource for systems biology. It is being used by the community in a variety of ways; for example, it is used to benchmark different simulation systems, and to study the clustering of models based upon their annotations. Model deposition to the database today is advised by several publishers of scientific journals. The models in BioModels Database are freely distributed and reusable; the underlying software infrastructure is also available from SourceForge under the GNU General Public License.

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Available from: Melanie I. Stefan, Oct 02, 2015
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    • "Such systems are often arise in biology and biochemistry (for biochemical applications see BioModel database [20]). Note that in the case when all coefficients b i , M ij and K ijk equal zero, system (1.1) reduces to a generalized Lotka-Volterra system [10]. "
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    ABSTRACT: We consider systems of differential equations with quadratic nonlinearities having applications for biochemistry and population dynamics, which may have a large dimension n. Due to the complexity of these systems, reduction algorithms play a crucial role in study of their large time behavior. Our approach aims to reduce a large system to a smaller one consisting of m differential equations, where . Under some restrictions (that allow us to separate slow and fast variables in the system) we obtain a new system of differential equations, involving slow variables only. This reduction is feasible from a computational point of view for large n that allows us to investigate sensitivity of dynamics with respect to random variations of parameters. We show that the quadratic systems are capable to generate all kinds of structurally stable dynamics including chaos.
    Studies in Applied Mathematics 03/2015; DOI:10.1111/sapm.12083 · 1.25 Impact Factor
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    • "Moreover, the requirement for a model repository is different in systems biology approaches. For example, the BioModels database [Li et al. 2010] provides models that can be simulated or can be used in computational analyses. However, for a model-driven design approach, models may be incomplete and may require additional information for the model composition process. "
    ACM Journal on Emerging Technologies in Computing Systems 12/2014; 11(3):1-19. DOI:10.1145/2631921 · 0.73 Impact Factor
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    • "The model has been deposited in the BioModels database (Li et al., 2010) and assigned the identifier MODEL1406060000. "
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