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Overview of Metabolism01:40

Overview of Metabolism

Living cells constantly carry out various chemical reactions which are necessary for their proper functioning. These reactions are interlinked to one another via multiple pathways. The collection of these chemical reactions is known as metabolism.
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The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
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Introduction to Metabolism01:30

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Metabolism encompasses all biochemical reactions in a living organism, facilitating both the breakdown and synthesis of biomolecules. These metabolic processes are categorized into catabolic and anabolic pathways, which operate in a coordinated manner to ensure energy balance and cellular function.Catabolic Pathways and Energy ReleaseCatabolic pathways involve the breakdown of complex macromolecules such as carbohydrates, lipids, and proteins into smaller structures like monosaccharides, fatty...
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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Published on: February 8, 2017

Arcadia: a visualization tool for metabolic pathways.

Alice C Villéger1, Stephen R Pettifer, Douglas B Kell

  • 1School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK. alice.villeger@manchester.ac.uk

Bioinformatics (Oxford, England)
|May 11, 2010
PubMed
Summary
This summary is machine-generated.

Arcadia software converts Systems Biology Markup Language (SBML) files into Systems Biology Graphical Notation Process Description (SBGN PD) maps. This tool allows users to visualize and customize biological network diagrams for better understanding.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Biological networks are complex and require standardized visualization methods.
  • Systems Biology Markup Language (SBML) is a standard for representing biochemical reaction networks.
  • Standardized diagrams are crucial for clear communication and analysis of biological models.

Purpose of the Study:

  • To develop a software tool, Arcadia, for translating SBML files into standardized diagrams.
  • To provide users with flexible visualization options for biological network models.
  • To facilitate the emulation of traditional textbook representations of biological pathways.

Main Methods:

  • Arcadia software is implemented in C++.
  • The software translates Systems Biology Markup Language (SBML) files.
  • The output format is standardized Systems Biology Graphical Notation Process Description (SBGN PD) maps.

Main Results:

  • Arcadia successfully translates SBML files into SBGN PD maps.
  • Users can interact with the generated diagrams, changing perspectives and layouts.
  • The tool enables the creation of visualizations resembling traditional textbook diagrams.

Conclusions:

  • Arcadia provides a valuable tool for visualizing and understanding biological networks.
  • The software enhances the interpretability of complex biological models through standardized diagrams.
  • Arcadia facilitates the communication of biological network information by offering customizable layouts.