• Register
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.


Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.


Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

Pubmed ID: 14597658


  • Shannon P
  • Markiel A
  • Ozier O
  • Baliga NS
  • Wang JT
  • Ramage D
  • Amin N
  • Schwikowski B
  • Ideker T


Genome research

Publication Data

November 4, 2003

Associated Grants

  • Agency: NIGMS NIH HHS, Id: P20 GM64361

Mesh Terms

  • Algorithms
  • Archaeal Proteins
  • Bacteriophage lambda
  • Computational Biology
  • Halobacterium
  • Internet
  • Models, Biological
  • Neural Networks (Computer)
  • Phenotype
  • Software
  • Software Design
  • Stochastic Processes