QBiC Portal (qPortal) - Software and Portlets

qPortal is a web-based science gateway providing users with an intuitive way to create (qWizard), manage, and analyze quantitative biological data (qNavigator). The portal comprises a backend consisting of databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. We provide a one-stop-shop solution for biomedical projects, providing up to date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query existing metadata for statistics and future re-analysis on high-performance computing systems via coupling of workflow management systems.

 

Availability

The source code of the portlets which are part of qPortal can be found in our github repository.

The direct links of the main portlets are the following:

 

Instructions

The prerequisite for using the before mentioned portlets is a running portal instance like Liferay and the biological data management system openBIS.

Detailed information on how to the use the provided portlets can be found in the corresponding repositories.

  • You also need openBIS to store and manage metadata.
    • Since our software uses a number of specific ‘controlled vocabularies’ (e.g. different species and tissue types) as well as our own data model (all stored in openBIS), you need the “master-data” script which you can use to transfer the data model to your own instance. You can import it from the command line like this: ./register-master-data.sh -s http://localhost:8888/openbis/openbis -f /local/master-data.py
    • Additionally, we are using a number of core plugins in openBIS, that allow creation of new experiments/samples and the query of meta information from the portal. The latest version can be found in our repository. Most important for getting started are the 'reporting-plugins’. They belong into the following folder of your openBIS installation: /path/to/openbis/servers/core-plugins/QBIC/1/dss/ 
  • We are using a MySQL database to store some additional metadata like project investigators and their affiliations as well as longer project descriptions. The database schema can be imported into your database using the following command: mysql -u root -p < qbic_usermanagement_db.sql
  • Settings: you need a config file on your Liferay instance storing connection info to the different parts of the portal. This is done in the qbic-ext.properties file in our case, which should be stored here: /path/to/liferay/qbic-ext.properties
  • User management: Our software connects to openBIS using the admin account. For user management to work, the users logging into Liferay need to have their own openBIS account with the same screen name. The admin account then fetches the workspaces with projects they are allowed to see (see openBIS documentation). In our case, both are connected to an LDAP system, so the accounts are the same by default.
  • An additional 'labeling methods' file is needed for qWizard.
  • If you plan to use imaging data you also need to install an OMERO server. Our imaging infrastructure has been tested (and is currently integrating) OMERO 4.6. Instructions on the server setup can be obtained from the official OMERO installation guide.

 

Workflows

The workflows which are available through qPortal are stored in our repository as well.