Visualizing Complex Networks with Cytoscape Visualizing Complex Networks with Cytoscape

Visualizing Complex Networks with Cytoscape

Uncover Patterns and Insights: Exploring Network Data with Cytoscape

Cytoscape is a javascript library. Since the invention of the high programming language of JavaScript, all problem-solving software and Ajax applications have been integrating it due to its functionalities. However, web development through JavaScript become time taking task due to the integration of different class and elements. Thus, different web designers and software engineers come up with different pre-designed libraries of JavaScript. So, these assist in new feature insertion in previously designed coding of a website and enhance its complexity.  

A lot of categories of these JavaScript libraries assist in designing and integrating classes/elements in websites. Hence, one of these libraries is Cytoscape which integrates for graphical visualization on software. However, this classification of JavaScript libraries defines the specificity and its functionality for websites. Thus, the above described JavaScript library belongs to the Graphical java category, used for 3D graphics and data visualization on different software. 

Moreover, Cytoscape, being an open-source JavaScript library, provides visualization of molecular interaction networks, integrations of these networks, and biological pathways on bioinformatics software. Hence, the coding language used in designing this library is Java.   

History of Cytoscape and reason behind its invention 

The major reason behind designing of Cytoscape is the data visualization of biological research. The bioinformatics software requires proper programming for the visualization of molecular interactions, biological pathways, gene expression profiles, and genetic integrations. Thus, the first design of this JavaScript library was made by the Institute of Systems Biology in Seattle in 2002. Therefore, the first version came into the programming world as an innovation in 2002, and later on, v1.0 came in 2003 with more tempting features of data visualization. From 2000 to 2016, about 8 advanced versions have innovated the strategies of biological data interpretations and much more. Hence, the library is available for download under the license of GNU Lesser General Public License.   


However, the designing of this JavaScript library urged developers to design better versions for other software. Therefore, the first official and common data visualizing JavaScript Library was released with the title of Cytoscape 3.0 in 2013. This official version has advanced features of maintenance and expand-ability with modern architecture. So, its additional features are an expression of gene profiling through different plug-ins. Moreover, Cytoscape. JS is another extension and sister project of this graphical JavaScript library that helps for the analysis and visualization of data on browsers. 

Astonishing features of Cytoscape Java library 

 The development of plugins in the Cytoscape library makes it more demanding for molecular profiling analyses and bioinformatic data visualization. Hence, the features which make it more popular among web designer for graphical visualization purposes are given below: 

Visualization of molecular data 

The Cytoscape JavaScript library provides the 3D visualization of molecular data with advanced visual styles. However, it also enables the researcher to customize the network data and choose its display method. Hence, expression of statistical data, gene expression ratios, and p-values are major tasks, completed by using visualization schemes. So, Customization of data visualization including mapping, border lining, colour, or texture enables the researcher to display uniquely.   

Inputs for molecular interaction networks 


Raw interaction files contain the protein-protein and protein–DNA interaction pairs listings, used for input and construction of molecular interaction through Cytoscape. For example, the molecular pairwise data of yeasts and other unicellular organisms are larger and expressed in TRANSFAC databases of the library. Hence, the programming of the library helps the researchers to load and save previous files in form of an XML document. Thus, this document contains the graphs of molecular interactions as well as mRNA expression profiles.    

Analysis of genetic profiles and their expressions    

The more tempting feature of the JavaScript library Cytoscape is that it provides plugins for molecular data analysis. However, these plugins may be designed by the open Java software architecture and the library encourages the apps (plugins). Hence, this graphical library helps to design the modules for molecular data analysis and gene profiling of different species. 

Application of Cytoscape Graphical library

The major application of this JavaScript graphical library is in biological research and in the field of bioinformatics. Moreover, there is the application of libraries in social networks to visualize network graphs of edges and nodes. Hence, a major speciality of the module is the integration of plugins for different purposes. 


From input to analyses of molecular data, all are functions of Cytoscape graphical JavaScript library. Moreover, being community modular, it invites the development and integration of new plugins. That helps to modify the library for further functionalities. hence, it will help future genetic researchers to innovate bioinformatics research by using new visualization and analysis techniques. 

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