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All the configuration settings are in config.js file.

CellBase Configuration

The host and version of CellBase are configured in the section below 

Code Block
languagejs
titleCellBase
var cellbase = {
    hosts: ["bioinfodev.hpc.cam.ac.uk/cellbase-4.5.0-beta"],
    version: "v4"
};

OpenCGA Configuration

The below section in config.js allows to do the following:

  • OpenCGA Host and version can be configured.
  • There is a section called projects which allows to browse public projects without any login.  
  • Cookies section is useful when the application expects users to login and their cookie names that store the actual user name and session ID can be configured here. 

Code Block
languagejs
titleOpenCGA
var opencga = {
    host: "bioinfodev.hpc.cam.ac.uk/opencga-1.0.0-rc3",
    version: "v1",
    projects: [
         {
             name: "Project A",
             alias: "proj_a",
             studies : [
                 {
                     name: "Study 1",
                     alias: "std_1"
                 }
             ]
         }
    ],
    cookies: {
        userName: "iva_userId",
        sessionId: "iva_sid"
    }
};

The above section in config.js allows to do the following:

  • OpenCGA Host and version can be configured.
  • There is a section called projects which allows to browse public projects without any login.  
  • Cookies section is useful when the application expects users to login and their cookie names that store the actual user name and session ID can be configured here. 

    Visual Settings

    Consequence Type, Population frequency and Protein Substitution Scores which can be found in config.js are enabled to have colors in web application. They can be modified to your needs.

    Code Block
    languagejs
    titleConsequence Type
    var consequenceTypes = {
        // This is the impact color. It allows to customise both the impact categories and desired colors
        color: {
            high: "red",
            moderate: "orange",
            low: "blue",
            modifier: "green"
        },
        /* 'Title' is optional. if there is no title provided then 'name' is going to be used.
         There are two more optional properties - 'checked' and 'color'. They can be set to display them default in web application.
         Similarly 'description' is optional as well.
         */
        categories: [
            {
                id: "",
                name: "",
                title: "Intergenic",
                description: "",
                terms: [
                    {
                        id: "SO:0001631",
                        name: "upstream_gene_variant",
                        title: "upstream gene variant",
                        description: "A sequence variant located 5' of a gene",
                        impact: "modifier"
                    },
    
    				.		
    				.
    				.
    			]
    		},
    		.	
    		.
    	]
    };


    Code Block
    titlePopulation Frequency
    var populationFrequencies = {
        color: {
            veryRare: "red",
            rare: "yellow",
            average: "orange",
            common: "blue"
        },
        studies: [
            {
                id: "1kG_phase3",
                title: "1000 Genomes",
                populations: [
                    {
                        id: "ALL",
                        title: "All populations [ALL]",
                        active: true
                    },
                    {
                        id: "EUR",
                        title: "European [EUR]"
                    },
    				.	
    				.
    				.
    			]
    		},
    		.	
    		.
    	]
    };


    Code Block
    titleProtein Substitution Score
    var proteinSubstitutionScores = {
        // This is to show the predictions in respective colors
        sift: {
            deleterious: "red",
            tolerated: "green"
        },
        polyphen: {
            probablyDamaging: "red",
            possiblyDamaging: "orange",
            benign: "green",
            unknown: "black"
        }
    };


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