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#Cytoscape Network Inference Toolbox (Cyni)
Cytoscape Network Inference Toolbox (Cyni) is a new Cytoscape App that puts together several tools that allow infering networks from biological data. Each of the tools can be used independently or together to perform several tasks.
The goal of Cyni is to make network inference more accessible to biologists by providing user-friendly solution as well as provide a framework to bio-informaticiens to develop and apply their new techniques. Data imputation and discretization techniques are provided along with several known inference algorithms to make this tool fully operational for any kind inference requirement. While data imputation and discretization techniques allow you modify Cytoscape tables, network inference algorithms produce a new network after applying the chosen technique. Cyni requires 3.0 version or newer of Cytoscape and is available in the Cy3 App Store.
##Contents
- Installation
- Using Cyni Toolbox
- App Development through Cyni API
- Loading Data Tables
- Data Imputation Algorithms
- Zero Imputation Algorithm
- Row Average (RAV)
- Bayesian Principal Component Analysis (BPCA)
- Discretization Algorithms
- Equal Frequency/Width Algorithm
- Manual Discretization
- Network Inference Algorithms
- Basic Correlation Algorithm
- Mutual Information Algorithm
- Bayesian K2 Algorithm
- Hill Climbing Algorithm
- Measurements
- Correlation Metrics
- Local Score Metrics
- Cyni through commands
- Authors
- Acknowledgments
- Downloads
- References
##1.Installation
Cyni is already available through Cy3 App Store. However, its installation could also be done by using the App Manager found in the Apps Menu. Once App Manager is open, you should click on Install from File. A new dialog will appear to help you find the Cyni app jar file that you should have previously saved it in your computer. After installing the right jar file, cyni will be already available to be used without need to restart Cy3. Moreover, next time Cytoscape is opened, cyni will be always available. If Cyni is not longer needed, it can be uninstalled easily by using the App Manager. The Cyni App Jar file can be found in the Downloads section.
#2.Using Cyni Toolbox
Once Cyni is installed, it will install a new Cyni Toolbox menu option under the Apps main menu. At the same time, a new tab Cyni Toolbox is created in Cytoscape Control Panel. Under this new Cyni Toolbox panel, there are three available tabs that represent all tools available in Cyni. The functionality that these three tabs provide is explained in the next sections.
##3.App Development through Cyni API
Cyni Toolbox is not only an application to perform a result, but it also provides a framework to other app developers to facilitate the implementation of other algorithms. The goal of Cyni framework is to provide standarized, extensible and configurable default solutions for all components different from the core algorithms, such as GUI, parameter handling, configuration of distance/similarity measures. Thereby, developers can focus on their core expertise, instead of trying to spend significant effort constructing software components foreign to their expertise. You can find all documentation to produce new apps through Cyni framework at the Cyni App Development documentation.
##4.Loading Data Tables
Latest release of Cyni Tool Box does not longer provide an option to load tables that are independent of any network into Cytoscape. This feature is already available in Cytoscape 3.1 and any later release. Users can find this option under "File, Import, Table, File... " menu. The user interface is similar to previous Cytoscape relases (3.0.x) but provides the option to choose loading data to an unassigned table. Once the table is loaded, a new tab in the table panel is shown, this tab is called Unassigned Tables. Under this tab, there will be any table that its data is not assigned to a network.
##9. Cyni through commands
Cyni App is also available through commands thanks to the Cytoscape Command line dialog tool. This tool can be found in the Tools Menu. By typing help cyni, all available algorithms in cyni are enumerated. Then only typing help cyni <Algo name>, the information for all parameters required by that algorithm is displayed, so users know which parameters need to be typed on the command line to execute the chosen algorithm.
##10. Authors
CYNI was implemented by Oriol Guitart Pla, and conceived by Frank Rügheimer and Benno Schwikowski.
##11. Acknowledgments
The implementation of Bayesian Principal Component Analysis (BPCA) incorporates the original java code by Shigeyuki Oba (Oba et al. 2003). The CYNI project is part of http://nrnb.org, and funded by NIH grant P41 GM103504.
##12. Downloads
##13. References
- Cytoscape Original Paper: Shannon P, Markiel A, Ozier O, Baliga N, Amin N, Ramage D, Schwikowski B, Ideker T (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res' 13 (11): 2498-2504
- Cooper GF, Herskovits E: A Bayesian Method for the Induction of Probabilistic Networks from Data. Machine Learning 1992, 9:309:347
- Oba, S., Sato, M., Takemasa, I., Monden, M., Matsubara, K., and Ishii, S. A Bayesian Missing value estimation method for gene expression profile data, Bioinformatics 2003 19, pp.2088-2096 (2003).
- Jose A. Gamez, Juan L. Mateo, and Jose M. Puerta. 2011. Learning Bayesian networks by hill climbing: efficient methods based on progressive restriction of the neighborhood. Data Min. Knowl. Discov. 22, 1-2 (January 2011)
- Mark Hall, Eibe Frank, Geoffrey Holmes, Bernhard Pfahringer, Peter Reutemann, Ian H. Witten (2009) The WEKA Data Mining Software: An Update. SIGKDD Explorations, Volume 11, Issue 1.
- Butte AJ, Kohane IS (2000) Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput, pp 418–429b.