Showing posts with label Paper Reading. Show all posts
Showing posts with label Paper Reading. Show all posts

Friday, November 28, 2008

The Basic Knowledge on Random Forest

In machine learning, a random forest is a classifier that consists of many decision trees and outputs the class that is the mode of the classes output by individual trees. The algorithm for inducing a random forest was developed by Leo Breiman and Adele Cutler. The term came from random decision forests that was first proposed by Tin Kam Ho of Bell Labs in 1995. The method combines Breiman's "bagging" idea and Ho's "random subspace method" to construct a collection of decision trees with controlled variations.

Learning Algorithm
Each tree is constructed using the following algorithm:
1. Let the number of training cases be N, and the number of variables in the classifier be M. (假设有N个训练样本,M个变量)
2. We are told the number m of input variables to be used to determine the decision at a node of the tree; m should be much less than M. (给定m个输入变量,用来确定树上一个节点的决策,m应小于M)
3. Choose a training set for this tree by choosing N times with replacement from all N available training cases(i.e. take a bootstrap sample)。 Use the rest of the cases to estimate the error of the tree, by predicting their classes.(从N个训练样本中随机重复取样N次得到一组训练集,即bootstrap取样)。预测剩余样本的类别,并用以估计决策树的误差。
4. For each node of the tree, randomly choose m variable on which to base the decision at that node. Calculate the best split based on these m variable in the training set.(对每个节点都随机选取m个基于此节点决策的变量。根据着m个变量计算其最佳分割方式)
5. Each tree is fully grown and not pruned(as may be done in constructing a normal tree classifier). (每棵树都会完整生长,不会像其他许多正常树分类器构建完成后经常做的那样被剪枝)

Advantages
The advantages of random forest are:
  • For many data sets, it produces a highly accurate classifier (分类准确度高)
  • It handles a very large number of input variables (处理大量输入变量)
  • It estimates the importance of variables in determine classification(在决策类别时,评估变量的重要性)
  • It generates an internal unbiased estimate of the generalization error as the forest building progresses(在构建森林过程中产生对泛化误差的内部无偏差估计)
  • It includes a good method for estimating missing data and maintains accuracy when a large proportion of the data are missing (具有一个比较好的方法可以估计缺失值,并且如果有一大部分数据缺失,它仍可以维持准确度)
  • It provides an experimental way to detect variable interactions(提供一种试验方法侦测变量之间的相互作用)
  • It can balance error in class population unbalanced data sets(对于非平衡数据集中的分类数据,可以平衡误差)
  • It computes proximities between cases, useful for clustering, detecting outliers, and(by scaling) visualizing the data(计算各种用例之间的相似性,对于聚类、侦测离群值和数据可视化(扩大或缩小)都非常游泳)
  • Using the above, it can be extended to unlabeled data, leading to unsupervised clustering, outlier detection and data views (它也可被拓展到无标记数据的应用,形成非监督聚类、侦测离群值和数据可视化的方法)
  • Learning is fast.(学习过程很快)
Reference:
Wiki for Random Forest
中文
Random Forest from Berkeley
RandomForest on the main page of Breiman

Wednesday, November 26, 2008

When 'JUNK' DNA meets with the p53 network

Yesterday The Molecular Systems Biology of NATURE published a paper in its News and Views column: 'Junk' DNA meets the p53 network.
The original article is addressed here.

[What is Junk-DNA]
A major part of the genome of higher eukaryotes consists of non-coding sequences. In former times, these sequences were called 'junk-DNA' as no specific function could not be attributed to them. More recent research has shown that small non-coding RNAs are contained in these parts of the genome. These non-coding RNAs have a fundamental role in gene regulation.

[What is MicroRNA(miRNA)]
MicroRNAs(miRNAs) are a relatively recently indentified means for gene regulation. They are small, endogeous non-coding RNAs, between 19 and 25 nt in length. Unlike siRNA, miRNAs are of endogenous origin and alterations in their expression are associated with a number of diseases, including cancer.

Digest of 'Why extends is evil'

The original article is addressed in JavaWorld: Why extends is evil.
The extends keyword is evil, maybe not at the Charles Manson Level, but bad enough that it should be shunned whenever possible. The Gang of Four Design Patterns book discusses at length implementation inheritance (extends) with interface inheritance(implements).

Good designers write most of their code in terms of interfaces, not concrete base classes. This article describes why designers have such odd habits, and also introduces a few interface-based programming basics.

Interface versus classes

Losing flexibility
Why should you avoid implementation inheritance? The first problem is that explicit use of concrete class names locks you into specific implementations, making down-the-line changes unnecessarily difficult.

Many successful projects have proven that you can develop high-quality code more rapidly ( and cost effectively ) this way than with the traditional pipelined approach.

Rather than implement features you might need, you implement only the features you definitedly need, but in a way that accommodates change.

A better solution to the base-class issue is encapsulating the data structure instead of using inheritance.

Summing up fragile base classes
In general, it is best to avoid concrete base classes and extends relationships in favor of interfaces and implements relationships. My rule of thumb is that 80 percent of my code at minimum should be written entirely in terms of interfaces. I never use references to a HashMap, for example; I use references to the Map interface.(I use the word "interface" loosely here. An InputStream is effectively an interface when you look at how it's used, even though it's implemented as an abstract class in Java.)

The more abstraction you add, the greater the flexibility. In today's business environment, where requirements regularly change as the program develops, this flexibility is essential. Moreover, most of the Agile developement methodologies simply won't work unless the code is written in the abstract.

If you examine the Gang of Four patterns closely, you'll see that many of them provide ways to eliminate implementation inheritance, and that's a common characteristic of most patterns. The significant fact is the one we started with: patterns are discovered, not invented. Patterns emerge when you look at well-written, easily maintainable working code. It is telling that so much of this well-written, easily maintainable code avoids implementation inheritance at all cost.

Monday, November 24, 2008

The graph representation in JUNG

1. Network and graph data sets have often been described mathematically as matrices which are commonly implemented as 2D arrays. The represantation facilitates fast retrieval of the edges, which operations is called findEdge in JUNG.
However, this representation is generally not feasible for large-scale networks. First, it requires O(|V|2) space. Second, existing algorithms for network analysis, which involve matrix multiplication or matrix inversion, generally require O(|V|3) time on 2D arrays. Third, this representation is problematic for dynamic networks(those whose vertex set may grow larger or smaller) and for networks with parallel edges. Finally, large-scale networks are almost invariably very sparse, so almost all the the space in a 2D array representing such a network is wasted on representing absent links.
2. A common alternative representation for sparse graphs and networks is the adjacency list representation, in which each vertex maintains a list of incident edges (or adjacent vertices); this requires O(|V|+|E|) space. This representation does NOT permit an efficient implementation of findEdge.
3. Most of the current JUNG vertex implementations employ a variant of the adjacency list representation, which is termed as adjacency map representation: each vertex maintains a map from each adjacent vertex to the connecting edge(or connecting edge set, in the case of graphs that permit parallel edges). ( Separate maps are maintained, if appropriate, for incoming directed edges, outgoing directed edges, and undirected edges.) This uses slightly more memory than the adjacency list representation, but makes findEdge approximately as fast as the corresponding operation on the 2D array representation.

Friday, November 21, 2008

POPE—a tool to aid high-throughput phylogenetic analysis

Thorhildur Juliusdottir *, Fredrik Pettersson and Richard R. Copley

Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK



Abstract:

Summary: POPE (Phylogeny, Ortholog and Paralog Extractor) provides an integrated platform for automatic ortholog identification. Intermediate steps can be visualized, modified and analyzed in order to assess and improve the underlying quality of orthology and paralogy assignments.

Availability: POPE is available for download from the website: http://www.well.ox.ac.uk/~tota/pope.

Contact: tota@well.ox.ac.uk

Thursday, October 30, 2008

Cytoscape and its plug-in

Cytoscape is so famous and popular recently in the biological network research field that Wikipedia has a term for it: Cytoscape in Wiki

Now, Cytoscape has 64 plugins in total; they are divided into 6 categories. With the list of plug-ins which are probably useful to use, the categories are:

  • Analysis -- Used for analyzing existing networks (20)
    • APID2NET

      • Description: Plugin designed to visualize, explore and analyze the proteins and interactions retrieved from the unified interactome platform APID (which integrates BIND, BioGrid, DIP, HPRD, IncAct and MINT). The retrieved data include the annotations and attributes associated to the network: GO terms, InterPro domains, experimental methods that validate each interaction, PubMed IDs, UniProt IDs. The tool provides interactive graphical representation of the protein-protein interaction (PPI) networks within Cytoscape, plus new automatic tools to find hubs and concurrent attributes (functional and structural) along the protein pairs of a given network.
        Project website: http://bioinfow.dep.usal.es/apid/apid2net.html
        License: click here
        Version: 1.52
        Reference: Juan Hernandez-Toro, Carlos Prieto and Javier De Las Rivas. APID2NET: unified interactome graphic analyzer. Bioinformatics 2007 23(18): 2495-2497. PMID: 17644818
        Release Date: 2008-05-14
        Released by: Hernandez-Toro J, Prieto C, De Las Rivas J. Bioinformatics and Functional Genomic Research Group, Cancer Research Center, (CIC-IMBCC,CSIC/USAL)
        Release notes: http://bioinfow.dep.usal.es/apid/apid2net.html
        Verified to work in: 2.6
        Download Jar/zip: click here (414.4KB)


    • BioQualiPlugin

      • Description: BioQuali analyses regulatory networks and expression datasets by checking a global consistency between the regulatory model and the expression data. It diagnoses a regulatory network searching for the regulations that are not consistent with the expression data, and it outputs a set of genes which predicted expression is decided in order to explain the expression data provided. The BioQuali Cytoscape Plugin proposes the user to visualize this analysis automatically and in few minutes no matter the size of the network.
        Project website: http://www.irisa.fr/symbiose/projects/bioqualiCytoscapePlugin/
        --

        Version: 1.0
        Release Date: 2008-09-17
        Released by: Annabel Bourdé , Centre INRIA Rennes Bretagne Atlantique, IRISA
        Carito Guziolowski , Centre INRIA Rennes Bretagne Atlantique, IRISA
        Verified to work in: 2.6
        Download Jar/zip: click here (2.19MB)


    • CABIN
    • CentiScaPe
    • clusterExplorerPlugin
    • clusterMaker
    • COMA

      • Description: This plugin performs consistency checks for gene expression data given gene regulatory networks (refer to citation for details).

        Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.

        If you use it for your research please cite:

        Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Project website: https://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/v4/CytoscapePlugins/index.html
        License: click here


        --

        Version: 1.101
        Reference: Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Release Date: 2008-04-21
        Released by: Jan Baumbach , Bielefeld University
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (17.7KB)


    • dynamicXpr

      • Description: A Plug-In that colors nodes according to their expression across many conditions, as in a movie
        --

        Version: 1.2
        Release Date: 2008-03-18
        Released by: Iliana Avila-Compillo , ISB
        John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (18.4KB)

        --

        Version: 1.3
        Release Date: 2008-09-18
        Released by: Iliana Avila-Compillo , ISB
        John "Scooter" Morris , UCSF
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (18.4KB)
        Download source: http://chianti.ucsd.edu/svn/csplugins/trunk/ucsf/scooter/dynamicXpr

    • EnhancedSearch
    • jActiveModules

      • Description: ActiveModules is a plugin that searches a molecular interaction network to find expression activated subnetworks, i.e., modules.

        --
        Version: 2.23
        Release Date: 2008-08-13
        Released by: Ryan Kelley , UCSD
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (115.4KB)


    • MCODE

      • Description: MCODE finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.

        --

        Version: 1.3
        Release Date: 2007-12-07
        Released by: Gary Bader, Vuk Pavlovic , University of Toronto
        Verified to work in: 2.5
        Download Jar/zip: click here (95.3KB)


    • NetAtlas

      • Description: NetAtlas is a Java plugin application designed to use tissue gene expression data to filter genes in a cellular signaling network. The NetAtlas plugin allows the creation of tissue-defined networks, identification of network components that are more highly expressed in specific tissues, and the identification of network components that show correlated expression across tissues. The default tissue gene expression data available in NetAtlas is from SymAtlas and contains human, mouse, and rat gene expression data for a wide range of tissues and has been previously published by the Genomics Institute of the Novartis Research Foundation. The user is also allowed to import their own tissue gene expression data in text file format.
        Project website: http://sourceforge.net/projects/netatlas/
        License: click here

        --

        Version: 1.1
        Reference: Longlong Yang, John R. Walker, John B. Hogenesch and Russell S. Thomas NetAtlas: A Cytoscape Plugin to Examine Signaling Networks Based on Tissue Gene Expression. In Silico Biol. 8:0005, 2007. http://www.bioinfo.de/isb/2007/08/0005/
        Release Date: 2007-11-20
        Released by: Russell S. Thomas , The Hamner Institutes for Health Sciences
        Longlong Yang , The Hamner Institutes for Health Sciences
        Release notes: http://sourceforge.net/projects/netatlas/
        Verified to work in: 2.4,2.5
        Note: A tutorial can be found at: http://sourceforge.net/projects/netatlas/
        Download Jar/zip: click here (985.3KB)
        Download source: http://sourceforge.net/projects/netatlas/

    • NetworkAnalyzer

      • This plugin is not available through the Plugin Manager!

        Description: NetworkAnalyzer performs analysis of biological networks and calculates network topology parameters including the diameter of a network, the average number of neighbors, and the number of connected pairs of nodes. It also computes the distributions of more complex network parameters such as node degrees, average clustering coefficients, topological coefficients, and shortest path lengths. It displays the results in diagrams, which can be saved as images or text files.
        Project website: http://med.bioinf.mpi-inf.mpg.de/networkanalyzer/
        License: click here

        --

        --

        Version: 2.6.1
        Reference: Reference: Assenov, Y., Ramirez, F., Schelhorn, S.E., Lengauer, T., Albrecht, M. Computing topological parameters of biological networks. Bioinformatics, 24(2):282-284, 2008
        Release Date: 2008-07-10
        Released by: Yassen Assenov , Max Planck Institute for Informatics
        Mario Albrecht , Max Planck Institute for Informatics
        Verified to work in: 2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • OmicsViz

      • This plugin is not available through the Plugin Manager!

        Description: OmicsViz is a Cytoscape plugin (cytoscape2.4 and 2.5) dedicated to providing useful visualization and an integrated analysis tool for large-scale omics data. OmicsViz imports omics data into Cytoscape and visualizes it on a graph according to the change of gene experimental values (Figure 1). OmicsViz also provides a mapping function between two different species or between probe set and experimental names and node names in a network. For example, when you load an Arabidopsis metabolic pathway in Cytoscape and you have a Grape gene expression file, OmicsViz can associate the file with the Arabidopsis pathway based on gene mapping file which contains orthologous genes between the two species.
        Project website: http://metnet.vrac.iastate.edu/MetNet_fcmodeler.htm
        --
        Verified to work in: 2.4,2.5,2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • RandomNetworks
    • RDFScsape

      • This plugin is not available through the Plugin Manager!

        Description: RDFScape is a project that brings Semantic Web \"features\" to the popular Systems Biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape. A full list of features is reporte in Features. Unlike other ontology-based features in Cytoscape, RDFScape doesn\'t consider ontologies as annotation, but as a knowledge-base that can be interpreted through standard inference processes and through custom inference rules. The result is that ontologies can be interpreted for specific analysis needs. For instance, a pathway ontology such as biopax can be easily abstracted to an interaction network. Or as a causal network, once of notion on causal effect is defined on the ontology. Beside this, RDFScape offers reach query capabilities on ontologies (SPARQL,RDQL,Strings, interactive browsing) and a customizable visualization features.
        Project website: http://www.bioinformatics.org/rdfscape/
        License: click here

        --

        Version: 0.4
        Reference: To appear in BMC Bioinformtics
        Release Date: 2008-02-07
        Released by: Andrea Splendiani , University of Rennes 1
        , Leaf Bioscience s.r.l.
        Verified to work in: 2.5
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://www.bioinformatics.org/rdfscape/

    • ShortestPath Plugin

      • Description: ShortestPath is a plugin for Cytoscape 2.1 to show the shortest path between 2 selected nodes in the current network. It supports both directed and undirected networks and it gives the user the possibility to choose which node (of the selected ones) should be used as source and target (useful for directed networks). The plugin API makes possible to use its functionality from another plugin.
        License: click here

        --

        Version: 1.1
        Release Date: 2007-07-25
        Released by: Marcio Rosa da Silva
        Verified to work in: 2.4,2.5
        Download Jar/zip: click here (8KB)

  • Network and Attribute I/O -- Used for importing networks and attributes in different file formats (14)
    • BiNoM

      • Description: BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure.
        • Import of BioPAX, SBML and CellDesigner formats
        • Export to BioPAX, SBML and CellDesigner formats after user manipulations
        • Conversion between standards (CellDesigner->BioPAX, BioPAX->SBML)
        • Full support of BioPAX information (reaction network, interaction network, pathway structure, references), concept of BioPAX index and network interfaces
        • Browsing, editing, extracting parts, merging BioPAX files with network graph interface
        • Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)
        • Support of generating network modular view
        • BioPAX network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)
        • Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.)

        Project website: http://bioinfo.curie.fr/projects/binom
        License: click here

        --

        Version: 1.0
        Reference: Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2007. Accepted in Bioinformatics.
        Release Date: 2007-09-01
        Released by: Andrei Zinovyev , Institut Curie
        Eric Viara , Institut Curie
        Laurence Calzone , Institut Curie
        Emmanuel Barillot , Institut Curie
        Release notes: http://bioinfo.curie.fr/projects/binom
        Verified to work in: 2.5
        Note: The jar provided is dependent on many other jars. For self-containing versions of jar, visit http://bioinfo.curie.fr/projects/binom
        Download Jar/zip: click here (1.26MB)
        Download source: http://bioinfo.curie.fr/projects/binom/docs/BiNoM_src.zip

    • BioNetBuilder

      • Description: Accesses BIND,BioGrid,DIP,HPRD,KEGG,IntAct,MINT,MPPI, and Prolinks as well as interolog networks derived from these sources for all species represented in NCBI HomoloGene.
        --

        Version: 2.0
        Reference: Iliana Avila-Campillo, Kevin Drew, John Lin, David J. Reiss and Richard Bonneau BioNetBuilder: automatic integration of biological networks Bioinformatics 2007 23(3):392-393; doi:10.1093/bioinformatics/btl604
        Release Date: 2008-06-18
        Released by: Jay Konieczka , University of Arizona
        Kevin Drew , Courant Institute, NYU.
        Release notes: http://err.bio.nyu.edu/cytoscape/bionetbuilder/index.php
        Verified to work in: 2.6
        Download Jar/zip: click here (2.21MB)
        Download source: https://err.bio.nyu.edu/svn/bionetbuilder/

    • CoryneRegNetLoader

      • Description: This plugin downloads gene regulatory networks from the corynebacterial reference database CoryneRegNet (compatible with at least release 4.0). Downloaded are the gene/protein IDs, the gene/protein names, the evidence, and the regulation type (-1 for repression and +1 for activation).

        Please contact Jan Baumbach (jan.baumbach@cebitec.uni-bielefeld.de) if you have further questions.

        If you use it for your research please cite:

        Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Project website: https://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/v4/CytoscapePlugins/index.html
        License: click here

        --

        --

        Version: 1.101
        Reference: Baumbach J, Apeltsin L (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184.
        Release Date: 2008-04-21
        Released by: Jan Baumbach , Bielefeld University
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (15.5KB)

    • NCBIClient
    • NCBIEntrezGeneUserInterface
    • PICRClient
    • ReConn

      • This plugin is not available through the Plugin Manager!

        Description: ReConn connects Cytoscape to the Reactome database. ReConn offers the user the following features: 1. Loading pathways by name. 2. Generating a new pathway by taking a given metaboliteas a starting point. Cytoscape can then display all reactions that are related to the reactions that consumes the given metabolite. 3. After a pathway has been loaded into Cytoscape, one can load data (e.g. from micro-array experiments) on top of it. This data is then visualized by changing the node colours. For instance, with micro-array data the colour and its intensity corresponds to the level of expression of the gene associated with the reaction. 4. ReConn can work also in the oposite direction: the user can see how the data is mapped onto the various pathways of Reactome. Therefore one can select the pathway of interest by looking at the data, instead of starting with a pathway. 5. ReConn can generate a subgraph containing all paths from one reaction to another. This is possible because of the graph-like data structure of Reactome. For clarity, one can limit the subgraph to paths shorter than a certain cut-off length. It is also possible to exclude certain reactions from this subgraph.
        Project website: http://bmi.bmt.tue.nl/reconn/
        License: click here

        --

        Version: 1.0
        Release Date: 0000-00-00
        Released by: Willem P.A. Ligtenberg , BioModeling & bioInformatics, Department of BioMedical Engineering, Eindhoven University of Technology
        Verified to work in: 2.6
        Download Jar/zip: Please follow the Project URL to download and install manually. Download source: http://bmi.bmt.tue.nl/reconn/ReConn_source.zip

  • Network Inference -- Used for inferring new networks (6)
    • AgilentLiteratureSearch

      • Description: Creates a CyNetwork based on searching the scientific literature.
        Project website: http://www.agilent.com/labs/research/litsearch.html
        License: click here

        --

        Version: 2.55
        Release Date: 2007-07-17
        Released by: Allan Kuchinsky and Aditya Vailaya, , Agilent Labs
        Michael Creech, , Blue Oak Software
        Verified to work in: 2.5
        Note: See plugin.props file for various field info.
        Download Jar/zip: click here (4.14MB)

        --

        Version: 2.68
        Release Date: 2008-03-28
        Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (4.28MB)

        --

        Version: 2.69
        Release Date: 2008-09-08
        Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (4.28MB)


    • Cytoprophet

      • Description: Cytoprophet is a Cytoscape plugin that helps researchers infer new potential protein (PPI) and domain (DDI) interactions. Users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score.
        Project website: http://cytoprophet.cse.nd.edu/
        License: click here

        --

        Version: 1.0
        Reference: Morcos, F., Lamanna, C., Sikora, M. and Izaguirre, J. Cytoprophet: A Cytoscape plug-in for protein and domain interaction network inference. Bioinformatics. (Submitted)
        Release Date: 2008-04-18
        Released by: Faruck Morcos, Charles Lamanna, Marcin Sikora and Jesus Izaguirre , University of Notre Dame
        Release notes: http://cytoprophet.cse.nd.edu/
        Verified to work in: 2.6
        Note: More information, documentation and the API are available at the website (http://cytoprophet.cse.nd.edu/).
        Download Jar/zip: click here (61.1KB)
        Download source: http://cytoprophet.cse.nd.edu/

    • DomainGraph

      • This plugin is not available through the Plugin Manager!

        Description: DomainGraph decomposes protein networks into domain-domain interactions and generates a new network of interacting domains. It also allows the integration of exon expression data measured using the Affymetrix Human Exon 1.0 ST Array, which supports the analysis of alternative splicing events and the characterization of their effects on protein and domain interaction networks.
        Project website: http://domaingraph.bioinf.mpi-inf.mpg.de/
        --

        Version: 1.0
        Release Date: 2008-08-15
        Released by: Dorothea Emig, Thomas Lengauer, Mario Albrecht , Max Planck Institute for Informatics
        Melissa S. Cline , Department of Molecular Cell and Developmental Biology, UCSC
        Verified to work in: 2.5,2.6
        Download Jar/zip: Please follow the Project URL to download and install manually.

    • ExpressionCorrelation

      • Description: ExpressionCorrelation plugin computes a similarity network from
        either the genes or conditions in an expression matrix.
        Project website: http://www.baderlab.org/Software/ExpressionCorrelation
        --

        Version: 1.01
        Release Date: 2008-10-07
        Released by: Elena Potylitsine, Weston Whitaker and Gary Bader , Memorial Sloan-Kettering Cancer Center
        Chris Sander , Memorial Sloan-Kettering Cancer Center
        Shirley Hui and Laetitia Morrison , University of Toronto
        Release notes: click here
        Verified to work in: 2.5,2.6
        Note: This is an update to the previously submitted version 1.0 that contains a bug fix and some updated author information.
        Download Jar/zip: click here (94.9KB)

        --

        Version: 1.0
        Release Date: 2008-09-24
        Released by: Elena Potylitsine, Weston Whitaker and Gary Bader , MSKCC
        Shirley Hui and Laetitia Morrison , University of Toronto
        Release notes: click here
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (94.9KB)
        Download source: http://www.baderlab.org/Software/ExpressionCorrelation

    • MetaNetter

      • Description: Plugin for the inference of metabolic networks based on high resolution metabolomic data.
        Project website: http://compbio.dcs.gla.ac.uk/fabien/abinitio/abinitio.html
        License: click here

        --

        Version: 2.1
        Reference: Jourdan F, Breitling R, Barrett M and Gilbert D. MetaNetter: inference and visualization of high-resolution metabolomic networks. (2007) In press Bioinformatics.
        Release Date: 2007-07-24
        Released by: Fabien Jourdan , INRA
        Release notes: http://compbio.dcs.gla.ac.uk/fabien/abinitio/abinitio.html
        Verified to work in: 2.5
        Note: MetaNetter is a plugin for the inference of metabolomic networks based on high resolution mass spectrometry data.
        Download Jar/zip: click here (67.2KB)


    • MONET

      • Description: MONET is a genetic interaction network inference algorithm based on Bayesian networks, which enables reliable network inference with large-scale data(ex. microarray) and genome-scale network inference from expression data. Network inference can be finished in reasonable time with parallel processing technique with supercomputing center resources.
        Project website: http://delsol.kaist.ac.kr/~monet/home/index.html
        --

        Version: 1.1
        Reference: Phil Hyoun Lee, Doheon Lee (2005) Modularized learning of genetic interaction networks from biological annotations and mRNA expression data. Bioinformatics. 21, 2739-2747.
        Release Date: 2007-12-20
        Released by: Younghoon Kim , BISL Lab, Dept. of Bio and Brain Engineering, KAIST
        Doheon Lee , BISL Lab, Dept. of Bio and Brain Engineering, KAIST
        Release notes: http://delsol.kaist.ac.kr/~monet/home/news.html
        Verified to work in: 2.3,2.4,2.5
        Download Jar/zip: click here (1.97MB)
        Download source: http://delsol.kaist.ac.kr/~monet/home/downloads.html

  • Functional Enrichment -- Used for functional enrichment of networks (4)
    • BiNGO

      • Description: BiNGO is a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network.
        Project website: http://www.psb.ugent.be/cbd/papers/BiNGO/
        License: click here

        Version: 2.3
        Reference: Maere, S., Heymans, K. and Kuiper, M. (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449.
        Release Date: 2008-08-05
        Released by: Steven Maere , VIB
        Martin Kuiper , VIB
        Release notes: http://www.psb.ugent.be/cbd/papers/BiNGO/
        Verified to work in: 2.6
        Download Jar/zip: click here (12.05MB)
        Download source: http://www.psb.ugent.be/cbd/papers/BiNGO/

    • CommonAttributes

      • Description: Find attributes shared between selected nodes.

        Requires background knowledge network files available at the CommonAttributes download site hanalyzer.sourceforge.net.
        License: click here

        --

        Version: 1.3
        Reference: Sonia M. Leach, Hannah Tipney, Weiguo Feng, William A. Baumgartner Jr. Priyanka Kasliwa, Ron Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter, "3R Systems for Biomedical Discovery Acceleration, with Applications to Craniofacial Development" PLoS Computational Biology, submitted.
        Release Date: 2008-08-12
        Released by: Ronald Schuyler , University of Colorado Health Sciences Center
        Release notes: hanalyzer.sourceforge.net
        Verified to work in: 2.5,2.6
        Download Jar/zip: click here (14.2KB)
        Download source: hanalyzer.sourceforge.net

    • HyperEdgeEditor

      • Description: Add, remove, and modify HyperEdges in a Cytoscape Network.

        --

        Version: 2.62
        Release Date: 2008-04-03
        Released by: Allan Kuchinsky and Aditya Vailaya , Agilent Labs
        Michael Creech , Blue Oak Software
        Release notes: click here
        Verified to work in: 2.6
        Download Jar/zip: click here (161.5KB)


  • Communication/Scripting -- Used for communicating with or scripting Cytoscape (7)
    • CyGoose

      • Description: The CyGoose Cytoscape Plugin gives any network in Cytoscape full access to the Gaggle.
        As of version 2.6 of the plugin, it works with the current (2007-04) revision of the Gaggle API.

        Version: 2.6
        Release Date: 2007-10-29
        Released by: Sarah Killcoyne and Dan Tenenbaum , Institute for Systems Biology
        John Lin, Kevin Drew and Richard Bonneau , NYU Bonneau Lab
        Release notes: click here
        Verified to work in: 2.5
        Download Jar/zip: click here (1.06MB)


    • JavaScriptEngine

      • Description:

        Rhino JavaScript engine version 1.7.1. You can run JavaScript on Cytoscape. To use this, you need ScriptEngineManager Plugin.


        License: click here

        --

        Version: 0.01
        Release Date: 2008-04-15
        Released by: Keiichiro Ono , UCSD Bioengineering
        Release notes: http://www.cytoscape.org/cgi-bin/moin.cgi/ScriptingPlugins
        Verified to work in: 2.6
        Download Jar/zip: click here (964.6KB)


    • MiSink

      • Description: Network interface to MiSink-enabled Web sites, including DIP (The Database of Interacting Proteins: http://dip.doe-mbi.ucla.edu).
        Project website: http://dip.doe-mbi.ucla.edu/dip/Software.cgi

        Version: 2.04
        Reference: Salwinski L, Eisenberg D. The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins. Bioinformatics 23:2193-5 (2007)
        Release Date: 2008-05-28
        Released by: Lukasz Salwinski , UCLA
        Verified to work in: 2.6
        Note: This is a minor fix to make plugin compatible with Cytoscape 2.6. The downloaded file has been tested from a local download site. It seems to install/work fine with Cytoscape 2.6 and java 1.6 running on linux and windows xp
        Download Jar/zip: click here (74.8KB)


    • PythonScriptingEngine
    • RubyScriptingEngine
    • ScriptEngineManager
  • Other -- None of the above (13)
There are also several useful plugins in this categories, for example, AdvancedNetworkMerg which is for merging networks by set operations (union, intersection and difference), BiLayout which is for computing a bipartite network layout for two user-selected disjoint groups of nodes, edgeLengthPlugin which is for calculating edge lengths and stores them in an edge attribut, edgeLister which is for tracking edge selection( it will be very useful in the random trail), NamedSelection which is for "remembering" a group of selected nodes, and so on.


Here are some tutorials:
  1. Network analysis with Cytoscape, 15-16.12.2005
  2. Cytoscape Wiki -- Getting started guide
  3. Cytoscape Wiki -- Plugin tutorial. It will help us a lot in case we are to develop our approach into a software, say, a plugin of Cytoscape.
  4. Cytoscape Wiki -- User manual