Similarity measures for automated comparison of in silico and in vitro experimental results

@article{Ropella2003SimilarityMF,
  title={Similarity measures for automated comparison of in silico and in vitro experimental results},
  author={Glen E. P. Ropella and Dev A. Nag and C. Anthony Hunt},
  journal={Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE Cat. No.03CH37439)},
  year={2003},
  volume={3},
  pages={2933-2936 Vol.3}
}
  • Glen E. P. Ropella, D. A. Nag, C. Hunt
  • Published 17 September 2003
  • Computer Science
  • Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE Cat. No.03CH37439)
The overwhelming complexity of biological systems prevents exhaustive description of the processes and mechanisms that cause system functionality. There are large numbers of processes to be considered with options for manifold hypotheses describing each. The long-term goal of this project, for a particular biological system, is to put the computer to work weeding out the weaker hypotheses and, even, weeding out posited processes that do not pertain directly to specific functionality. An… 
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9 Citations
Background Citations
3
Methods Citations
5

9 Citations

Citation Type

Citation Type

Similarity Measures and Validation in Automated Modeling
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A generic vector time series similarity measure is described in the context of output-driven validation and a formal category theoretic framework for the modeling process and the specific role of similarity measures is provided.
In Silico Hepatocyte: Agent-Based Modeling of the Biliary Excretion of Drugs In Vitro
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This work uses a stochastic agent directed, cellular automatabased synthetic method to instantiate, test, and partially validate simulation models of cultured primary hepatocytes (the primary cell of the liver), and validated the ISH using in vitro measures of cellular uptake and biliary clearance of the four compounds.
Prediction of in Vitro Hepatic Biliary Excretion using Stochastic Agent-Based Modeling and Fuzzy Clustering
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The method enables the ISH to interact with simulated drugs to reasonably match results from in vitro hepatocyte excretion studies and makes the estimation method available to the model, itself, to enable it to reasonably anticipate the biliary transport and excretion properties of a new compound based on the acceptable parameter values for previously encountered compounds.
Using Heuristic Models to Bridge the Gap Between Analytic and Experimental Models in Biology
TLDR
The basics of a modeling method, FURM (Functional Unit Representation Method), is presented that attempts to address this breakdown in the extent to which any computer model can represent its biological referent.
PISL : A Large-Scale In Silico Experimental Framework for Agent-Directed Physiological Models
TLDR
In silico, physiologically-based rat liver models that are designed for large-scale and high-performance experimentation and analysis are presented that use multi-scale parallelism, parallel parameter sweeping, parallel partitioning and batch processing, and a posteriori analysis.
Tracing Multiscale Mechanisms of Drug Disposition in Normal and Diseased Livers
TLDR
It is proposed that changes in ISL micromechanistic details may have disease-causing counterparts, and in silico transformations from normal to diseased ISLs stand as concrete theories for disease progression from the disposition perspective.
Agent-Based Simulations of In Vitro Multicellular Tumor Spheroid Growth
TLDR
This in silico, agent-based, discrete event analogue successfully simulates the three phases of spheroid growth and achieves the balance of cell gain and loss that is necessary for saturation.
Affects of Surface Detection on Shape and Growth of Model Tumor Spheroids
TLDR
It is demonstrated that different proliferation algorithms will create distinctly dissimilar cross section shapes and growth curves, and algorithms that minimize surface irregularity and area are the most likely to produce simulated MTS that achieve and maintain a constant size.
Application and processing of Time Domain Reflectometry: a model-based approach
TLDR
A full featured workflow for the implementation of integrated diagnosis and monitoring systems based on Time Domain Reflectometry (TDR) is proposed, and the jDE optimization algorithm is applied to successfully solve the inverse problem in both synthetic and real life scenarios.

References

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