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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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Clearance measures drug elimination from the central compartment, including plasma and highly perfused organs like kidneys and liver. Its calculation varies depending on pharmacokinetic models and administration routes. The one-compartment model, for instance, portrays the pharmacokinetics of polar drugs such as aminoglycoside antibiotics administered intravenously and readily excreted in urine. In this case, clearance is influenced by the terminal rate constant (λz) and the total volume...
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Related Experiment Video

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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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ModelView for ModelDB: Online Presentation of Model Structure.

Robert A McDougal1, Thomas M Morse2, Michael L Hines2

  • 1Department of Neurobiology, Yale University, PO Box 208001, New Haven, CT, 06520-8001, USA. robert.mcdougal@yale.edu.

Neuroinformatics
|April 22, 2015
PubMed
Summary
This summary is machine-generated.

ModelView enhances ModelDB by providing graphical views of computational neuroscience models, aiding reuse and reproducibility. This web tool offers a simulator-independent way to explore model structures without software installation.

Keywords:
Code analysisModelDBRepositoryVisualization

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Area of Science:

  • Computational Neuroscience
  • Bioinformatics
  • Scientific Software Development

Background:

  • ModelDB hosts over 950 computational neuroscience models, but code sharing alone hinders model reuse and reproducibility.
  • Understanding complex model source code is a significant barrier for researchers.
  • A standardized, accessible method for exploring model structures is needed.

Purpose of the Study:

  • To develop ModelView, a web application for ModelDB, to visualize and contextualize computational neuroscience model structures.
  • To facilitate model understanding and assessment for researchers without requiring software installation or code reading.
  • To promote greater model reuse and reproducibility within the computational neuroscience community.

Main Methods:

  • Developed ModelView, a web application integrated with ModelDB.
  • Generated graphical representations of model structures for NEURON and NEURON-runnable models (NeuroML, PyNN).
  • Combined manual curation, text-mining, ModelDB queries, and simulator introspection for data generation.

Main Results:

  • ModelView provides a rich, simulator-independent environment for interacting with model graphs.
  • Researchers can examine and assess hundreds of ModelDB models through a standardized web presentation.
  • The tool eliminates the need for software installation, model downloads, or direct source code analysis.

Conclusions:

  • ModelView significantly improves the accessibility and understandability of computational neuroscience models in ModelDB.
  • The application promotes efficient model exploration, assessment, and reuse.
  • ModelView represents a key advancement in fostering reproducibility in computational neuroscience research.