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Related Concept Videos

Studying the Cytoskeleton01:17

Studying the Cytoskeleton

The cytoskeletal architecture can be studied using different microscopic and biochemical techniques. Electron microscopy was instrumental in discovering the cytoskeletal architecture around the 1960s, which allowed obtaining structural information at a high-resolution level. However, the sample preparation procedure often limits this ability in biological samples. Several protocols have been developed over the years to optimize sample preparation. In one of the protocols known as rotary...
Introduction to Cytoskeleton01:33

Introduction to Cytoskeleton

Overview of the Cytoskeleton
The cytoskeleton is a network of protein filaments present within the cell, having three distinct filaments ̶   microfilaments, microtubules, and intermediate filaments. Each has characteristic features that distinguish them, including the dynamics of their assembly and disassembly, mechanical properties, polarity, and the type of molecular motors associated with them. Earlier, they were thought to be present only in eukaryotic cells; however, their homologs were...
Introduction to the Cytoskeleton01:33

Introduction to the Cytoskeleton

Overview of the Cytoskeleton
The cytoskeleton is a network of protein filaments present within the cell, having three distinct filaments ̶   microfilaments, microtubules, and intermediate filaments. Each has characteristic features that distinguish them, including the dynamics of their assembly and disassembly, mechanical properties, polarity, and the type of molecular motors associated with them. Earlier, they were thought to be present only in eukaryotic cells; however, their homologs were...
Cytoskeletal Coordination in Cell Migration01:32

Cytoskeletal Coordination in Cell Migration

A migrating cell changes its shape during the cyclic events of attachment and detachment from the substratum and repositions the cell organelles correspondingly. These complex events are orchestrated by the dynamic cytoskeletal network comprising actin filaments, intermediate filaments, and microtubules. Cytoskeletal crosstalk — the direct and indirect communication between the different components — is crucial for this coordination. Direct communication involves various linker proteins that...
Molecular Models02:00

Molecular Models

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.
Assembly of Cytoskeletal Filaments01:18

Assembly of Cytoskeletal Filaments

Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...

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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Cytoscape: a community-based framework for network modeling.

Sarah Killcoyne1, Gregory W Carter, Jennifer Smith

  • 1Institute for Systems Biology, Seattle, WA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 15, 2009
PubMed
Summary
This summary is machine-generated.

Cytoscape is a versatile software for network visualization and data analysis, particularly in systems biology. Its plugin architecture allows for extensive customization and community-driven enhancements, expanding its utility across diverse research areas.

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Cytoscape is a widely adopted software package for network visualization, data integration, and analysis.
  • Its primary focus has been on meeting the modeling needs of systems biology research.
  • The software's flexibility has led to its application in various scientific domains beyond systems biology.

Purpose of the Study:

  • To provide a comprehensive overview of Cytoscape's capabilities and development.
  • To highlight the role of its plugin framework in extending functionality for specialized research.
  • To illustrate the collaborative development model driven by a community of users and developers.

Main Methods:

  • Discussion of Cytoscape's core features and architecture.
  • Explanation of the plugin framework for dynamic extension of functionality.
  • Case study detailing the development and application of a specific plugin for systems biology analysis.

Main Results:

  • Cytoscape's adaptability through plugins allows for tailored data analysis, integration, and visualization.
  • Community contributions have significantly enhanced the core software and expanded its plugin ecosystem.
  • A practical example demonstrates the application of a Cytoscape plugin for a systems biology research question.

Conclusions:

  • Cytoscape serves as a powerful and extensible platform for biological network analysis.
  • The plugin architecture fosters innovation and broadens the software's applicability.
  • Community-driven development is key to Cytoscape's ongoing success and evolution in scientific research.