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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
pV-Diagrams01:18

pV-Diagrams

The pV diagram, which is a graph of pressure versus volume of the gas under study, is helpful in describing certain aspects of the substance. When the substance behaves like an ideal gas, the ideal gas equation describes the relationship between its pressure and volume. On a pV diagram, it is common to plot an isotherm, which is a curve showing p as a function of V with the number of molecules and the temperature fixed. Then, for an ideal gas, the product of the pressure of the gas and its...
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

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Related Experiment Video

Updated: Jun 19, 2026

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo
08:32

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo

Published on: May 4, 2018

VANLO--interactive visual exploration of aligned biological networks.

Steffen Brasch1, Lars Linsen, Georg Fuellen

  • 11Department of Mathematics and Computer Science, Ernst-Moritz-Arndt-University, Greifswald, Germany. sbrasch@uni-greifswald.de

BMC Bioinformatics
|October 14, 2009
PubMed
Summary

We developed VANLO, a 3D visualization system for aligned protein-protein interaction networks. This tool aids in understanding evolutionary relationships and biological network evolution through interactive exploration and optimized layout.

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Related Experiment Videos

Last Updated: Jun 19, 2026

Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo
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Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein-protein interactions (PPI) are crucial for biological processes.
  • Evolutionary analysis of biological networks requires aligning networks across species using orthologs.
  • Visualizing aligned networks aids in understanding evolutionary relationships.

Purpose of the Study:

  • To present a novel 3D visualization system for aligned biological networks.
  • To provide insights into inter-network relationships and evolutionary patterns.
  • To facilitate the exploration of aligned protein-protein interaction networks.

Main Methods:

  • Developed a 3D visualization system embedding existing 2D layouts.
  • Implemented a global layout optimization considering intra- and inter-network relationships.
  • Integrated network merging, layout, splitting, and layered display.
  • Incorporated interactive techniques for data exploration.

Main Results:

  • The system visualizes aligned biological networks in 3D space with layered structures.
  • Optimized layout considers both intra- and inter-network connections.
  • Interactive features allow for task-specific data exploration.

Conclusions:

  • The VANLO system offers an intuitive understanding of aligned PPI networks.
  • It enables the investigation of key biological and evolutionary questions.
  • The tool is accessible online for real-world biological data analysis.