Can-VD README.
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Description of the Can-VD stack Can-VD uses a Linux, Apache, MySQL, PHP stack.
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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/
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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
- 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 */;