Friday, October 31, 2008

Convert KEGG pathway files to SBML

This afternoon, I happen to find a useful tool on the mainpage of SBML: KEGG2SBML. The 1.5.8 version is released on 28 July 2008. Now it is currently limited to converting only KEGG Metabolic Pathway files and not other types of KEGG files. It is using the KEGG LIGAND database(not the xml files in the ftp).

Fortunatedly, I even found the converted files on one page of SBML, and the files can be downloaded directly.


I downloaded the three files: * SBML files without CellDesigner's tag : [Level-2 Ver-1 |Level-2 Ver-3] as well as * SBML files with CellDesigner's tag : [Level-2 Ver-1]. As is statemented, The version of Source Databases files are * KEGG Metabolic Pathways Release 47 and * LIGAND 2008-07-28 (daily snapshot) . I must note it down.

Tonight, I'd like to try to display these files by use of the CellDesign or Cytoscape. If this network reconstruction way works, then it might be the best one among my thoughts.
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How to statement two guys as the joint First Authors

Last week Ma asked me how to declare that she and another guy, both of them, should be treated as the first authors of their paper. I had no idea what was the formal way of this statement at that time.
By chance I saw one paper, which statemented their joint First authors in this way formally:
"The authors wish it to be known that, in their opinion, the first two authors are to be regarded as joint First Authors."
That's it.
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Labels:

How to add a plug-in in the Cytoscape

  1. Download the necessary jar files for the right website.
  2. Copy the jar files into the Cytoscape plugin directory.
When Cytoscape starts, all the plugins contained in this directory will be loaded. The plugin will be available from the Cytoscape "Plugins" item menu.
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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
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Add a user library into a project

There are two steps to follow when you plan to add an exist library into your project. The library may be either yours or some public one.

As the first step, you need to create a new User Library for the adding library. Consider adding the jaxb ri-2.1.8 as an example.
1. Enter the Window menu and open the Preferences option.
2. Find the User Library which is hierarchically located under the Java->Build Path.
3. Make a new User Library with the New button, and put in an expected library name in the pop-up message box, say, JAXB. If you select the System library option, then this Libray would be added to the boot class path.
4. Click the Add JARs... button to add files to the new library. For the Jaxb, I add all the files in the folder of lib.
5.Click OK to make sure the setting. Then, Done!

As the second step, you need to add the created new User library into your project.
1.Enter the Project menu and open the Properties option.
2. Find the Libraries under the Java Build Path.
3. Click Add Library button, then click User Library and Next. Select the one you want to add,say,JAXB.
4.Click OK to make sure the setting.

Having finished these two steps, the expected library is added in your project.
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Wednesday, October 29, 2008

KEGG API or Pathway.xsd?

The first step of my work is to reconstruct the metabolic network.

Previously, we use Perl to extract the enzyme information from the LIGAND database of KEGG as well as the excel sheets of the Ma and Zeng database. (The latter is also based on KEGG, which should be noticed.)

Now I plan to build the whole project on the basis of Java. The first step is using the KEGG API to help reconstruct the organism-specific metabolic networks(graphs).

I can either try to use KEGG API to reconstruct the network or use the pathway.xsd which Samuel did for me before. Which one should I use?

(Sometimes I regretted a little that I gave up Perl and turned to Java. The latter is really a challenge for me, because the history that I was fear of the object-oriented programming can be tracked back to nearly 10 years ago. Anyway, I have started with it. Then don't think too much and do not always worry about the graduation. Learn it step by step, and I must be a good programmer soon.)

1. KEGG API:
Here is the description on the KEGG Java Page.


Here is the steps to get KEGG-API ready.
  1. Download the axis package(Now the latest version is axis-1.4-final).
  2. Download the axisfix.pl to generate the classes for KEGGAPI. This perl file is to fix the KEGGBindingStuf.java generated by axis. Here is the code, very simple. Delete all the text "org.apache.axis.uitls;" and "org.apache.axis.soap;" and if the there is a line who starts with 'package' then add the sentences "import org.apache.axis.utils.*;(enter)" and "import org.apache.axis.soap.*;(enter)" in the file. 


    3. #!/usr/bin/perl -i
    # script to fix KEGGBindingStub.java generated by axis-1_2alpha
    while (<>) {
    s/org\.apache\.axis\.utils\.//;
    s/org\.apache\.axis\.soap\.//;
    print;
    if (/^package/) {
    print "import org.apache.axis.utils.*;\n";
    print "import org.apache.axis.soap.*;\n";
    }
    }


  3. Now the api is ready for use.



However, do remember that KEGG API just provides a web service. If you have no available internet connection, you cannot run your project maybe. Okay, let's see another way, which is to use jaxb and *.xsd to parse the pathway xml files provided by KEGG.


Thank Samuel help me to write pathway.xsd for me. This file is right to parse the KEGG xml files. Follow the steps to make it ready for your project:

1. Download and include the jaxb into the user library
2. Go to jaxb\bin and put pathway.xsd into this folder
3. Under the cmd command line, run xjc pathway.xsd
4. Done.

Yes, the answer is pathway.xsd.
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Sunday, October 26, 2008

Set up the Java Environment for the first time

Technically, this time is not the first time to set the Java environment for me. Long time ago I have ever done it on my note book with the direction from Samuel. Since I haven't touched Java for so long time, I nearly forgot all the necessary steps for the JDK environment setting. Now I need to re-install JDK6 on the sever. With the help of Google, I fininal settled it down. Here is the detailes step by step.(Suppose we've got the JDK installed successfully in this fold: c:\java)
1. Find this location: computer -> properties -> advanced settings -> environment variables (Notice that for the different platform, this setting may locate different.)
2. Create a new System variables named JAVA_HOME, and then value it as "c:\java\jdk1.6.0_10"(the place where the JDK is installed).
3. Add the following to the User variable PATH: "%JAVA_HOME%\bin;%JAVA_HOME%\jre\bin;"
4. Create a new System variable named CLASSPATH and value it as ".;%JAVA_HOME%\lib;%JAVA_HOME%\lib\tools.jar";(Note the first dot and semicolon);
Okay, at the time the command window shows the help information when you run 'javac ' or 'java' without any params instead of the wrong message "javac: Command not found", you win.

/** -------------------------------- **/
The following I would say something about how to set Ultraedit for Java.
1. Run UltraEdit, then go to "Advanced" in the menu, and then "Tool configuration"

2. Create a shortcut for "javac"
Command: Menu Item Name -> javac; Command Line-> C:\jdk1.6.0_10\bin\javac "%f" ; Working directory -> %p;
Options: Program Type : Dos program; Save all files first;
Output: Output to the List Box; Capture Output;

3. Create a shortcut for "java -no params"
Command: Menu Item Name -> java -no params; Command Line-> C:\jdk1.6.0_10\bin\java "%n" ; Working directory -> %p;
Options: Program Type : Dos program; Save all files first;
Output: Output to the List Box; Capture Output;

4.3. Create a shortcut for "java -params"
Command: Menu Item Name -> java -params; Command Line-> C:\jdk1.6.0_10\bin\java "%n%modified%"; Working directory -> %p;
Options: Program Type : Dos program; Save all files first;
Output: Output to the List Box; Capture Output;

Okay, it is finished. It seems to be good. Let's try it.
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The puzzle of Rope

Obviously, in order to grasp a new programming language as a tool faster, a bunch of exercises are necessary and helpful. Okay, let's start from now on. Today comes the first one, the puzzle of Rope.

[Q] There are two ropes with different length. Both of them can be burned up in one hour exactly. However, their combustion rate are not always the same. Some parts of them are burned faster while others slower. Now in case you are given two such ropes as well as plenty of matches, with these stuff try to get a algorithm to count the exact interval of 45 minutes.

[My design]
Here is my diagram:

It works well and I have a better understanding on the use of interface(I used to design a interface between the Rope class and the App one. But since it is so simple I do not really use it.) . But I am not satisfied my low efficiency on it. Such a tiny puzzle costs me more than one day, since I also went shopping and cooking during this period. It is not good to scatter the attention when studying, I have to acknowledge it :S. I believe in myself that I can do it faster and better next time.

[PS] Something useful from the internet.
Shihab's Blog: Use System.currentTimeMillis() instead of Date or Calendar
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Saturday, October 25, 2008

A new departure

I'd like to take this blog as the new departure of mine, not only of the study but also of the life.

This blog would contain at least five parts: the Java Learning, the Paper Reading, the English Learning, the Thoughts on Research and Photography as well.

The part of Java Learning would show my path of Java, from the basic to the advanced. After several months, before my graduation, I am sure I must be able to write Java projects very fluently. I'd like to record every tiny experience or acquisition here, not only to deepen the memory but also to facilitate the look-up when I met some problems in the study.

The part of Paper Reading is planned to record the daily paper reading. In order to collect enough knowledge and have the current research situation, I need to read a lot of paper continuously. In this case, the record is very important.

The part of English Learning is set up to keep the improvement on the English learning. In order to write it a lot in English, I need to pile up lots of words, phrases and sentences. Gather the good ones bit by bit and write down them here, I hope I could grasp this language as good as my mother tongue sooner.

The part of Thoughs on Research is to help myself get the useful thoughts systematiclly. Now it is nearly on the topics of Network Comparison, Phylogenetic analysis as well as Biological networks in which Metabolic network is more interested in.

Finally, Photography is to show my exercises on this topic. I can do it better than Samuel someday, I know it.

Okay, let's go ahead.
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