Maxwell Lewis Neal

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We introduce and define the Ontology of Physics for Biology (OPB), a reference ontology of physical principles that bridges the gap between bioinformat-ics modeling of biological structures and the bio-simulation modeling of biological processes. Where-as modeling anatomical entities is relatively well-studied, representing the physics-based semantics of(More)
Accurate clinical assessment of a patient's response to treatment for glioblastoma multiforme (GBM), the most malignant type of primary brain tumor, is undermined by the wide patient-to-patient variability in GBM dynamics and responsiveness to therapy. Using computational models that account for the unique geometry and kinetics of individual patients'(More)
There now exists a rich set of ontologies that provide detailed semantics for biological entities of interest. However, there is not (nor should there be) a single source ontology that provides all the necessary semantics for describing biological phenomena. In the domain of physiological biosimulation models, researchers use annotations to convey(More)
Currently, biosimulation researchers use a variety of computational environments and languages to model biological processes. Ideally, researchers should be able to semiautomatically merge models to more effectively build larger, multi-scale models. However, current modeling methods do not capture the underlying semantics of these models sufficiently to(More)
As a case-study of biosimulation model integration, we describe our experiences applying the SemSim methodology to integrate independently-developed, multiscale models of cardiac circulation. In particular, we have integrated the CircAdapt model (written by T. Arts for MATLAB) of an adapting vascular segment with a cardiovascular system model (written by M.(More)
Dynamic simulation models of physiology are often represented as a set of mathematical equations. Such models are very useful for studying and understanding the dynamic behavior of physiological variables. However, the sheer number of equations and variables can make these models unwieldy, difficult to under-stand, and challenging to maintain. We describe a(More)
The human physiome is envisioned as the quantitative description of the whole of human physiology. Researchers actively working toward achieving this grand challenge have populated publicly available repositories of quantitative physiological models; however, no mechanism has been developed that integrates the information from these models into a single(More)
SUMMARY We describe libSBMLReactionFinder, a C library for retrieving specific biochemical reactions from the curated systems biology markup language models contained in the BioModels database. The library leverages semantic annotations in the database to associate reactions with human-readable descriptions, making the reactions retrievable through simple(More)