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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 

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

OpenCGA Configuration


OpenCGA
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.

Consequence 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"
                },

				.		
				.
				.
			]
		},
		.	
		.
	]
};
Population 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]"
                },
				.	
				.
				.
			]
		},
		.	
		.
	]
};
Protein 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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