nrnb / gsoc2014alex

Can-VD README.

1. Description of the Can-VD stack Can-VD uses a Linux, Apache, MySQL, PHP stack.

2. Setting up the Can-VD stack A. Installing the stack: sudo apt-get install apache2 mysql-common mysql-client mysql-server php5 php5-mysql B. Set 'PSSWD' in the file /var/www/admin/upload_text.php, line 23, to the server's MySQL password. C. Set 'PASSWORD' in the file /var/www/common.php, line 14, to the server's MySQL password (and / or username). D. Run sudo chmod -R 775 on the /var/www/proteins/ and /var/www/pwms/ directories if they are changed or moved. E. Run sudo chown -v www-data -R /var/www/admin/upload/

3. Can-VD code

A quick introduction to the important source code files of Can-VD: index.php - HTML/PHP for the front landing page. generate_stats.php - HTML/PHP for generating database statistics. logout.php - Logs the administrator user out of the portal. PDOext.class.php - An extension of PHP's PDO class, gives a few basic extra functions. jquery.tooltip.css/js - CSS and JS files for the tooltip extension. search.php - runs and handles searches for network data. site.js - some javascript which is primarily used on the front page. styles.css - the custom styles for Can-VD. common.php - Settings and configuration common to all PHP files. ./tables/ - PHP files for the generation of the browsing tables on the main page. ./admin/ - PHP files for the administration panel. ./variants/index.php - PHP/HTML for the variant search page. ./variants/details.php - PHP/HTML for the variant details page. /variants/variant_load.php - AJAX PHP for loading variant search results. ./network/index.php - PHP/HTML for display of the network page. Called by search.php. ./network/download.php - Handles network downloads.

APPENDIX

1. Structure of the Can-VD database The following MySQL code will generate the structure of the database:

SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO"; SET time_zone = "+00:00";

/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT /; /!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS /; /!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION /; /!40101 SET NAMES utf8 */;

CREATE DATABASE IF NOT EXISTS canvd DEFAULT CHARACTER SET latin1 COLLATE latin1_swedish_ci; USE canvd;

CREATE TABLE IF NOT EXISTS admin ( username varchar(255) NOT NULL, password varchar(255) NOT NULL ) ENGINE=InnoDB DEFAULT CHARSET=latin1;

CREATE TABLE IF NOT EXISTS announcements ( id int(11) NOT NULL AUTO_INCREMENT, date varchar(255) NOT NULL, title text NOT NULL, body text NOT NULL, show int(11) NOT NULL DEFAULT '1', show_homepage int(11) NOT NULL DEFAULT '1', PRIMARY KEY (id) ) ENGINE=InnoDB DEFAULT CHARSET=latin1 AUTO_INCREMENT=17 ;

CREATE TABLE IF NOT EXISTS tissue_table_browser ( id int(11) NOT NULL AUTO_INCREMENT, Tissue varchar(255) NOT NULL, variants int(11) NOT NULL, proteins int(11) NOT NULL, gain int(11) NOT NULL, loss int(11) NOT NULL, PRIMARY KEY (id) ) ENGINE=InnoDB DEFAULT CHARSET=latin1 AUTO_INCREMENT=44 ;

CREATE TABLE IF NOT EXISTS T_Domain ( Domain varchar(255) DEFAULT NULL, Type varchar(255) DEFAULT NULL, Isoform varchar(255) DEFAULT NULL, GeneName varchar(255) DEFAULT NULL, EnsGID varchar(255) DEFAULT NULL, EnsPID varchar(255) DEFAULT NULL, ProteinLength varchar(255) DEFAULT NULL, DomainStartPos varchar(255) DEFAULT NULL, DomainEndPos varchar(255) DEFAULT NULL, DomainSequence text, OtherEnsemblGenes text, OtherEnsemblProteins text, OriginalID varchar(255) DEFAULT NULL, Ac_Geneart varchar(255) DEFAULT NULL, Purification varchar(255) DEFAULT NULL, ELISAForPhageDisplay varchar(255) DEFAULT NULL, PCR varchar(255) DEFAULT NULL, Position varchar(255) DEFAULT NULL, Specificity varchar(255) DEFAULT NULL, UniquePep varchar(255) DEFAULT NULL, Note varchar(255) DEFAULT NULL, EnsTID varchar(255) DEFAULT NULL, KEY Domain (Domain), KEY GeneName (GeneName), KEY Domain_2 (Domain) ) ENGINE=InnoDB DEFAULT CHARSET=utf8;

CREATE TABLE IF NOT EXISTS T_Ensembl ( EnsPID varchar(255) DEFAULT NULL, EnsTID varchar(255) DEFAULT NULL, EnsGID varchar(255) DEFAULT NULL, Version varchar(255) DEFAULT NULL, GeneName varchar(255) DEFAULT NULL, Description varchar(255) DEFAULT NULL, Sequence text, KEY GeneName (GeneName), KEY Description (Description), KEY EnsPID (EnsPID) ) ENGINE=InnoDB DEFAULT CHARSET=utf8;

CREATE TABLE IF NOT EXISTS T_Interaction ( IID varchar(255) DEFAULT NULL, PWM varchar(255) DEFAULT NULL, Domain_EnsPID varchar(255) DEFAULT NULL, Interaction_EnsPID varchar(255) DEFAULT NULL, Start varchar(255) DEFAULT NULL, End varchar(255) DEFAULT NULL, Score varchar(255) DEFAULT NULL, Type varchar(255) DEFAULT NULL, KEY IID (IID), KEY Domain_EnsPID (Domain_EnsPID), KEY Interaction_EnsPID (Interaction_EnsPID) ) ENGINE=InnoDB DEFAULT CHARSET=utf8;

CREATE TABLE IF NOT EXISTS T_Interactions_Eval ( IID int(11) DEFAULT NULL, Gene_expression double DEFAULT NULL, Protein_expression double DEFAULT NULL, Disorder double DEFAULT NULL, Surface_accessibility double DEFAULT NULL, Peptide_conservation double DEFAULT NULL, Molecular_function double DEFAULT NULL, Biological_process double DEFAULT NULL, Localization double DEFAULT NULL, Sequence_signature double DEFAULT NULL, Avg double DEFAULT NULL, KEY IID (IID) ) ENGINE=InnoDB DEFAULT CHARSET=utf8;

CREATE TABLE IF NOT EXISTS T_Interaction_MT ( IID varchar(255) DEFAULT NULL, WT varchar(255) DEFAULT NULL, MT varchar(255) DEFAULT NULL, KmerNo varchar(255) DEFAULT NULL, WTscore varchar(255) DEFAULT NULL, MTscore varchar(255) DEFAULT NULL, VID varchar(255) DEFAULT NULL, Int_EnsPID varchar(255) DEFAULT NULL, Mut_Syntax varchar(255) DEFAULT NULL, DeltaScore varchar(255) DEFAULT NULL, LOG2 varchar(255) DEFAULT NULL, Eval varchar(255) DEFAULT NULL, PWM varchar(255) DEFAULT NULL, KEY IID (IID), KEY IID_2 (IID), KEY Int_EnsPID (Int_EnsPID), KEY Int_EnsPID_2 (Int_EnsPID), KEY Mut_Syntax (Mut_Syntax), KEY Int_EnsPID_3 (Int_EnsPID), KEY Eval (Eval) ) ENGINE=InnoDB DEFAULT CHARSET=utf8;

CREATE TABLE IF NOT EXISTS T_Mutations ( ID varchar(255) NOT NULL DEFAULT '', MUTATION_ID varchar(255) DEFAULT NULL, mut_description varchar(255) DEFAULT NULL, mut_syntax_cds varchar(255) DEFAULT NULL, mut_syntax_aa varchar(255) DEFAULT NULL, GRCh37 start varchar(255) DEFAULT NULL, GRCh37 stop varchar(255) DEFAULT NULL, mut_nt varchar(255) DEFAULT NULL, mut_aa varchar(255) DEFAULT NULL, examined_samples varchar(255) DEFAULT NULL, tumour_site varchar(255) DEFAULT NULL, mutated_samples varchar(255) DEFAULT NULL, Mutation_Source_ID varchar(255) DEFAULT NULL, gene name varchar(255) DEFAULT NULL, EnsTID varchar(255) DEFAULT NULL, EnsPID varchar(255) DEFAULT NULL, EnsGID varchar(255) DEFAULT NULL, Source varchar(255) DEFAULT NULL, PRIMARY KEY (ID), UNIQUE KEY ID (ID), KEY EnsPID (EnsPID), KEY tumour_site (tumour_site), KEY ID_2 (ID), KEY Source (Source), KEY gene name (gene name), KEY mut_description (mut_description) ) ENGINE=MyISAM DEFAULT CHARSET=utf8;

CREATE TABLE IF NOT EXISTS T_PWM ( PWM varchar(255) DEFAULT NULL, APlus varchar(255) DEFAULT NULL, AMinus varchar(255) DEFAULT NULL, Domain varchar(255) DEFAULT NULL, KEY PWM (PWM) ) ENGINE=InnoDB DEFAULT CHARSET=utf8;

/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT /; /!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS /; /!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;