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Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...

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The three-compartment open model is a pharmacokinetic model used to describe the distribution and elimination of drugs following extravascular administration. It comprises a central compartment representing the plasma and two peripheral compartments. The highly perfused peripheral compartment represents organs and tissues with a rich blood supply, such as the liver, kidneys, and lungs. The scarcely perfused peripheral compartment represents tissues with lower blood supply, such as adipose...

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Modeling an Enzyme Active Site using Molecular Visualization Freeware

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Published on: December 25, 2021

An online model composition tool for system biology models.

Sarp A Coskun¹, A Ercument Cicek, Nicola Lai

¹Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH, USA. tekin@case.edu.

BMC Systems Biology

|September 7, 2013

Summary

This summary is machine-generated.

The PathCase-SB web portal simplifies Systems Biology model composition with user-friendly tools. These tools enable easy model merging, simulation, and comparison, benefiting both students and researchers.

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A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Area of Science:

Systems Biology
Computational Biology
Bioinformatics

Background:

Systems Biology Markup Language (SBML) is a widely used format for computational models.
Existing Systems Biology data sources and researchers need advanced, integrated web-based solutions for model management.
There is a need for tools supporting SBML functionalities like uploading, editing, composing, visualizing, simulating, querying, and browsing models.

Purpose of the Study:

To present the design and implementation of the Model Composition Tool within the PathCase-SB web portal.
To introduce supporting tools for model composition, simulation, and comparison.
To provide accessible platforms for Systems Biology models from BioModels Database and SBML Test Suite.

Main Methods:

Development of the Model Composition Tool within the PathCase-SB web portal.
Implementation of supporting tools: Model Simulation Interface, iModel Tool, and SimCom Tool.
Hosting of BioModels Database and SBML Test Suite models on dedicated websites.

Main Results:

The Model Composition Tool facilitates the merging of Systems Biology models.
The Model Simulation Interface generates visual plots of simulations.
The iModel Tool allows users to upload and compose their own models.
The SimCom Tool enables side-by-side comparison of composed models.

Conclusions:

The Model Composition Tool and supporting tools require minimal SBML knowledge, benefiting students and learners.
Beginners can utilize SBML Test Suite models, while advanced users can access BioModels Database models.
The developed tools enhance accessibility and usability of Systems Biology models and their composition.