Omics Metadata Management Software (OMMS) curation and analysis interface
The OMMS was designed to integrate and implement with open-source bioinformatics tools, such as BLAST, Bowtie 2 and Tophat and/or custom pipelines.
These tools are accessed via the "Analysis Portal" (panel A).
End users select the identifier ("Sequence Run ID") of interest, which is referenced to particular sequence files (panel B and inset).
Following input selection, the desired program is chosen and parameterized (panel C and inset) to launch a run. Output from a given analysis run can be downloaded via the OMMS "Results" portal (not shown).
Required base software
The LAMP bundle (Linux, Apache, MySQL, PHP) was used to develop and test the OMMS; Red Hat Enterprise Linux Workstation release 6.5 (Santiago) was employed in the final stages, and CentOS initially. This distribution of the OMMS has thus been shown to run in diverse Linux environments without extensive cross-platform customization. The yum package management utility was used to install the base software packages (steps A-E below) in our final Linux Red Hat test environment. Development hardware specifications were: Intel Core i7, CPU Q840 @ 1.87 Ghz, 8 Gb RAM. These base software packages MUST be installed and properly configured BEFORE running the OMMS:
- httpd-2.2.15-31 (This is server software from the Apache HTTP Server Project); (http://httpd.apache.org/download.cgi)
- firefox-24.8.0 (This is browser software); (http://www.mozilla.org/en-US/firefox/new/)
- mysql-5.1.73 (This is relational database server software); (http://dev.mysql.com/downloads/mysql/5.1.html)
- php-5.3.3 (cli) (built: July 15, 2014) (This is a server-side scripting language designed for web development); (http://us.php.net/releases/index.php)
- phpMyAdmin-220.127.116.11 (This is php-based tool facilitating MySQL administration over the web); (http://www.phpmyadmin.net/home_page/index.php)
Integrating bioinformatics utilities
For integrated workflows, install and configure the following tools (in accordance with native documentation) AFTER installation of the required base software:
- ncbi-blast-2.2.27+ (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews; and relevant databases)
- bowtie2-2.0.0 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml; and desired indices)
- tophat-2.0.5 (http://ccb.jhu.edu/software/tophat/index.shtml )
- cufflinks-2.0.2 (http://cufflinks.cbcb.umd.edu/)
- samtools-0.1.18 (http://samtools.sourceforge.net/)
- boost_1_51_0 C ++ Libraries (http://www.boost.org/users/history/version_1_51_0.html)
Installing and configuring the OMMS
Nota bene —Linux commands given in parentheses were executed in CentOS release 5.9 (Final) and Red Hat Enterprise Linux Workstation release 6.5 (Santiago). The "$" prompt indicates the standard user mode, while the "#" connotes root-user (super-user). Enter required locations (on the file system) for the OMMS-related bioinformatics databases (detailed below).
- After downloading the OMMS to your Desktop, open a terminal window, su to root, and copy the tar archive to /usr/local/bin from the Desktop (#cp ~/Desktop/OMMS_SUBMIT.tar.gz /usr/local/bin/). The expected OMMS file size is 16MB (#ls -lah).
- Verify that the package is in /usr/local/bin, and extract the OMMS archive (#tar xvzf OMMS_SUBMIT.tar.gz).
- Change directory to OMMS (#cd OMMS), and get a directory listing (#ls -lah) to confirm the contents of the extracted archive; assuming successful extraction, the following items will be present: DBOMMS, installer.sh script, LICENSE, OMMS, README, TestDataSets and uninstaller.sh script.
- Run the installer (#./installer.sh), and either accept or change the defaults, entering the desired directory locations, tailoring according to the partitioning and directory structures of the particular host machine.
- Enter the MySQL directory to access the database DBOMMS. The default location is /var/lib/mysql/.
- Enter the user to access databases in MySQL; the OMMS default is < root >.
- Enter the password for the user to access databases in MySQL; here we suggest entering no password at all, and if desired, returning later for advanced configuring in accordance with MySQL documentation. These configuration data will be stored in #/var/www/html/OMMS/config.inc.
- Enter the localhost; the OMMS default is < localhost >; this information will be stored in #/var/www/html/OMMS/configUser.inc, and ensures that authorized users are actively logged into the software.
- Enter the location for Analysis Directory: on our system: /data1/analysis/ (this location will contain the analysis input and output files; you must manually enter your preferred path at this step).
- Enter the location for Sequences Directory; on our system: /data1/seqs/ (this location will contain the sequence input files; you must manually enter your preferred path at this step).
- Enter the location of BLAST databases; on our system (you must manually enter your preferred path at this step): /usr/bin/blast/db/.
- Enter the location for Bowtie 2 indices; on our system: /usr/bin/bowtie2/index/ (again, details for these, and similar configuration steps can be found in the #/var/www/html/OMMS/configDir.inc file. This configuration information is crucial for the proper functioning of the Analysis and Results portals).
- The OMMS installer will scan for bioinformatics utilities that are to be integrated with the Analysis portal (BLAST, Bowtie 2, TopHat, Cufflinks, etc.).
- Start the Apache (httpd) and MySQL (mysqld) server daemons (# service httpd start; # service mysqld start).
- Start MySQL (# mysql), and list the databases (mysql> show databases;). Use the "DBOMMS" database (mysql> use DBOMMS;). List the tables in this database (mysql> show tables;). Populate the table called "user" in the database DBOMMS for OMMS management and basic security. Either in MySQL enter, "INSERT INTO DBOMMS.user VALUES ("name1", MD5("password1″));" for each user; alternatively, using phpmyadmin, select the following: database – "DBOMMS;" table – "user." To finish, select "Insert," enter a username (e.g., "name1"), and choose the MD5 hash function to enter a password (e.g., "password1").
- Verify that the OMMS web server is running by navigating the Firefox browser to – http://localhost/OMMS.
- The OMMS is now ready for use at http://localhost/OMMS/. Please note that the OMMS can be customized further. Instructions given here are for a quick start generic installation and configuration.
- Verify successful installation of the OMMS by confirming the presence of the OMMS in the default path of the Apache HTTP Server software (#cd /var/www/html/OMMS).
- For further reading, please refer to Perez-Arriaga et al., Bioinformation 11(4):165-172 (2015).
Uninstalling the OMMS
- Verify the presence of the uninstaller script in the OMMS distribution (#ls -lah /usr/local/bin/OMMS/uninstall.sh).
- Run the uninstaller (# ./uninstaller.sh) to remove the OMMS from the file system.