Getting Started

What is GenIECMS?

The Genome Integrative Explorer Content Management System (GenIE-CMS) is dedicative in-house CMS to facilitate external groups in setting up their own web resource for searching, visualizing, editing, sharing and reproducing their genomic and transcriptomic data while using project raw data(GFF3,FASTA,FASTQ) as an input.

GenIE-CMS will support cutting-edge genomic science, providing easily accessible, reproducible, and shareable science. The increasingly large size of many datasets is a particularly challenging aspect of current and future genomics based research; it is often difficult to move large datasets between servers due to constraints of time and finance. It is also important to keep the experimental datasets private among the group members until the project goals are accomplished or until after publication. In other words, it must provide a high level of security to ensure that the genomic web resource remains private without requiring the moving of data to unknown remote servers. Therefore, a locally hosted GenIE-CMS installation represents a more secure, less expensive and time consuming resource to implement.

In Addition, Researchers who are not specialized in bioinformatics or have limited computers skills are not currently able to gain maximal insight from the biological data typically produced by genomics projects. In order to overcome this limitation, GenIE-CMS will provide an ideal gateway with simple graphical user interfaces to those who have limited skills in bioinformatics.

Web resources such as Phytozome(Goodst et al., 2012) , iPlant( Goff. et al.,2011), TAIR (Rhee et al., 2003) and PLAZA (Proost et al., 2011). These collections of tools and services have been sources of inspiration to be and have contributed my desire to develop the GenIE-CMS as well as, and importantly, developing an understanding of their limitations to end users. None of these resources allow users to easily setup their own web resource without submitting their data to the resource developers and making them publicly available.

GenIECMS’s folder structure

├── GenIECMS 
│   ├── data
│   ├── docs   
│   ├── genie_files   
│   ├── index.php   
│   ├── js   
│   ├── LICENSE   
│   ├── plugins   
│   ├── README.md   
│   ├── scripts   
│   └── themes

Database design

Creating a new database

Due to increasing number of species in PlantGenIE we use standard naming convention to easily identify and maintain the databases. For example: [website name]_[species name]_[version number]

https://github.com/irusri/GenIECMS/blob/master/docs/images/genie_databases.png?raw=true

Log into the MySQL server and create a database.

#Create a database:
CREATE DATABASE new_database;

You can download the empty database here. Then load the database into the newly created database using following commands.

git show HEAD~1:scripts/dump.sql > dump.sql
mysql -u newuser -p newpassword new_database < dump.sql

Log into the MySQL server to create user and grant permissions.

#Create MySQL user:
CREATE USER newuser@'localhost' IDENTIFIED BY 'newpassword';

#User permissions:
GRANT SELECT ON new_database.* TO newuser@'localhost';
GRANT INSERT,UPDATE,DELETE ON new_database.genebaskets TO newuser@'localhost';
GRANT INSERT,UPDATE,DELETE ON new_database.defaultgenebaskets TO newuser@'localhost';

newuser, newpassword and new_database should be included in the plugins/settings.php similar to following example.

//Define the databasename names
$db_species_array=array("new_database"=>"new genome",...
//Define the databasename and background colours
$db_species_color_array=array("new_database"=>"#86c0a6",....
//Define the username, password and host here
$db_url=  array ('genelist'=>'mysqli://newuser:newpassword@localhost/'.$selected_database); 
//Define the base url with trailing slash
$GLOBALS["base_url"]='http://localhost:3000/';

Loading tables

Following database diagram shows the initial genie database architecture. It will be used with basic GenIECMS tools such as GeneList, gene information pages, autocomlete search and BLAST.

https://raw.githubusercontent.com/irusri/GenIECMS/master/docs/images/GenIE-CMS_V4.png

We have to to follow the data loading instructions in order to load data into the database tables.

Configuring genome database

All configuration settings in GenIECMS need to be added into /GenIECMS/plugins/settings.php file. You need to update /GenIECMS/plugins/settings.php file with your available details. You can find everything about the integration plugins and how to load data in the plugins section.

Plugins/Modules

Analysis, expression or genomic tools can be integreated into a CMS as external plugins. Detailed plugin development guidelines will be available under the plugins section. GenIE-CMS will contain JBrowse, GeneList, gene information pages and BLAST as standard default plugins. All additional tools(exImage, exNet, Enrichment) can be integrated as external plugins to the GenIE-CMS.