Building data centric website for research projects and research groups

Date and Time: 
Thursday 2018 Apr 5th
CG North Auditorium
Amit Chourasia

Duration: Half day
Level: Beginner (No pre-requisites, minimal familiarity with command line helpful)


  1. Download and install Docker community edition for your operating system
  2. Download begin image, will be used to get started with the tutorial
  3. Download final image, is the fully configured file image for reference
  4. Windows users should also download PuTTY

Data is an integral part of scientific research. With a rapid growth in data collection and generation capability and an increasingly collaborative nature of research activities, data management and data sharing have become central and key to accomplishing research goals. Researchers today have variety of solutions at their disposal from local storage to Cloud based storage. However, most of these solutions focus on hierarchical file and folder organization. While such an organization is pervasively used and quite useful, it relegates information about the data such as description and collaborative notes about the data to external systems. This spread of information into different silos impedes the flow research activities.

In this tutorial, we will introduce and provide hands on experience with the SeedMe2 platform, which provides a web-based data management and data sharing cyberinfrastructure. SeedMe2 provide an ability to collocate Data, its description and discussion in one system as well as an ability to customize and include additional fields that persist besides traditional files and folders. Structured data files with tabular and graph data are presented as light visualizations. The overall goal of the SeedMe2 platform is to make consumable and hot data readily available to team members in usable form.


Who may attend this tutorial?

A broad set of attendees may be interested to attend this workshop, these include:

  • Researchers: Interested to set up or use data sharing for personal or project use
  • Research IT/Cyberinfrastructure providers: Provide a predefined data-sharing configuration to your users
  • Scientific application/Gateway developers: Integrate/extend your Application/Science Gateways provide data sharing capabilities and customize it for your needs


Attendee outcomes

By the end of the workshop the attendees will

  • Gain understanding and working knowledge of collocating data, description and discussions in one system
  • Create a branded research data sharing website
    • Customize data properties
    • Configure and manage site wide data sharing
    • Customize the website further to use for their project or research group
  • Automation and integration: Learn to use command line and web services that could used be used via scripting or programmatically
  • Deployment options: Learn where such a data infrastructure may be hosted
    • Do-it- yourself: On site
    • Third party vendor
    • Regulatory compliant hosting (say for PHI data)


Tutorial agenda

  • Overview of SeedMe2 platform
  • Introduction to Drupal content management system
  • Configuring SeedMe2 data sharing building blocks
  • Using command line to interact with SeedMe2
  • Overview of Single sign-on using CiLogon
  • Customizing and extending your SeedMe2 website
Speaker Description: 

Amit Chourasia is a Sr. Visualization Scientist at the San Diego Supercomputer Center, UC San Diego where he leads the Visualization Group. His work is focused on leading the research, development and application of software tools and techniques for visualization. Result and data sharing are also at a forefront of his interests, to this end he has developed a web based cloud infrastructure to enable this important and at times critical gap in scientific process via the SeedMe project.

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