ExpressWeb

The ExpressWeb is an online Tool that will allow you to easily compute clustering on your expression data and provides usefull visualisation tools as heatmaps, graphs and networks . You can import genes annotation from Phytozom or from your own sources and create Toolbox . Using annotation tables (Phytozom, PFAM, GO ... or personal data), you can enrich the results of the clustering.

Before installing Your Expression Database App

ExpressWeb was developped under Codeigniter 3.0.3 framework a PHP framework.

All source code for running ExpressWeb as a standalone web application is provide in this package.

Codeigniter structure is show in fig1.

.
├── application/
├── assets/
├── composer.json
├── contributing.md
├── index.php
├── install/
├── license.txt
├── output/
├── readme.rst
├── system/
└── user_guide/
fig1

application/
├── cache/
├── config/
├── controllers/
├── core/
├── helpers/
├── hooks/
├── index.html
├── language/
├── libraries/
├── logs/
├── models/
├── third_party/
└── views/
fig2

assets/
├── css/
├── img/
├── js/
├── network/
├── scripts/
├── similarity/
├── uploads/
└── users/
fig3

install/
├── annotTester.csv
├── apache_conf/
├── bootstrap.css
├── check_app.sh
├── check_cluster.php
├── config/
├── form.php
├── index.php
├── scripts/
├── sql/
└── submit.php
fig4

Hardware and Software requirements

Cluster environment

ExpressWeb is designed to work on a SGE Cluster architecture.

Web environment

You need an Apache webserver (V 2.2 ) , PHP (>V 5.5 ) and Mysql or MariaDB (V 5.1 )

Third party software

Python: Python 2.7.2                R: version 3.1.2
        Libraries used:                   Libraries used:
            MySQLdb                           RMySQL
            csv                               Hmisc
            json                              RJSONIO
            resource                          dendextend
            math

Third party Data

Data    Description             Source
PFAM    Protein families        ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/database_files/pfamA.txt.gz
        
GO      Gene Ontology           http://geneontology.org/page/downloads

KEGG    Kyoto Encyclopedia of Genes and Genomes    http://www.kegg.jp/

Enzymes KEGG Enzymes            http://rest.kegg.jp/list/enzyme
KO      KEGG Orthology          http://rest.kegg.jp/list/ko
KOG     Eukaryotes Ortholog     ftp://ftp.ncbi.nih.gov/pub/COG/KOG/kog (old !!)

PANTHER Protein ANalysis THrough Evolutionary Relationships     ftp://ftp.pantherdb.org/hmm_classifications/

Installation

All source code (for web interface) are located under application directory (fig2)

assets directory (fig3) contains directories required by our application (network,scripts,similarity,uploads,users)

scripts directory contains scripts used for cluster submission and post-calculations. These scripts will be copied to the cluster in a directory with cluster write access.

install directory contain scripts for installing Expression Database App.

• In apache_conf you will find an example of httpd.conf file
• In sql you will find sql scripts for creating Expression database
• This directory will be renamed after configuration

Download/clone code

1. Create a directory located in your web space (under DocumentRoot ) (ex: /var/www/htm/ExpressWeb)
2. Copy the archive in this directory and Unzip it

OR

1. Clone gitHub repository:
   1.1. cd to your ex: cd /var/www/html/
   1.2. if you want to rename default directory (ExpressWeb) add 'my_directory_name' as last argument

   $ git clone https://github.com/PeroxiBase/ExpressWeb.git  [my_directory_name]
        
   Initialized empty Git repository in /var/www/html/ExpressWeb/.git/
   [ Initialized empty Git repository in /var/www/html/my_directory_name/.git ]
   remote: Counting objects: 2247, done.
   remote: Compressing objects: 100% (1703/1703), done.
   remote: Total 2247 (delta 504), reused 2238 (delta 500), pack-reused 0
   Receiving objects: 100% (2247/2247), 15.31 MiB | 690 KiB/s, done.
   Resolving deltas: 100% (504/504), done.
   
   

Apache configuration

1. Edit your Apache conf file (/etc/httpd/conf/httpd.conf | /etc/apache2/apache2.conf & sites-enabled/)
   1.1. look at install/apache_conf/httpd.conf for example
   1.2. define a new virtual host (website.domain.org) or create an alias (ExpressWeb)
   1.3. reload apache config and open page http://website.domain.org/install/ or http://website.domain.org/ExpressWeb/install
   1.4. you should display the first page of the installer "Before installing Your Expression Database App"

Database settings

Before proceeding to configuration of your local copy of ExpressWeb , you need to create the database on your mysql server.
See README.md in install/sql directory.

Web, directories, third party software and cluster settings

apache_user
By default, apache is run under user apache and group apache.
You may have to run apache under an account allowed to write on the cluster...
This account is used for job submission.
You need to check if apache_user is able to launch a job on your cluster from Apache !!

Site URL
Name of your web site(ex :website.domain.org).
If you defined an Alias in apache config (ex ExpressWeb) give full name:

website.domain.org/ExpressWeb

Web path
Full path of web Site directory as defined in apache conf
<Directory "/var/www/html/ExpressWeb/">

Cluster results Folder
The full path of directory used for storing computed networks and similarity files.
Default under Web Path in /assets/network and /assets/similarity

Admin email
User must request account to access database. Request is send to Admin email for validation purpose.

Cluster Settings

You need to define application and environment variables to submit job on cluster.

Cluster architecture

Cluster Env Path
Root path of cluster manager: /SGE/ogs/

Cluster App Path
Full path of binary command for cluster operation (qsub,qstat,...): /SGE/ogs/bin/linux-x64

Cluster working Folder
The full path to writing directory on cluster. Your cluster job should be able to write in this directory !!
Two directories will be created under this directory:

• files: intermediates results files will be write temporarily in this directory. On success , files are moved to Cluster results Folder
• scripts: scripts in assets/scripts/ will be copied in this directory job submission are done from this directory and all job files and control commands are write/execute from this directory temporary files are deleted on success.

Configuration process

With all these informations , we are able to configure Codeigniter (config,database), configuration scripts for cluster scripts
Path and Directories will be checked. If need we'll try to create missing directories...
A cluster job submission will be launched.
On success, install directory will be renamed and your web site launch!.