SeedMe News

Workshop | 2018-08-24

SeedMe workshop: Collaborative data sharing infrastructure for researchers

Date: Aug 24, 2018
Maximum attendees: 25 (20 spots available as of April 26, 2018)
Venue: San Diego Supercomputer Center, UC San Diego. (See directions)
Lodging: The workshop will cover up to two days of stay (arriving Aug 23 and departing Aug 25) at on-campus room and board (dorm style private room, shared common area and bathrooms), meals are included for two days of stay. However, attendees may choose to stay elsewhere and must cover the associated costs on their own. Lodging will be provided for academic non San Diego residents only. Lodging may be requested no later than Jul 31, 2018.
Travel: Attendees must cover travel costs on their own
Food: Light refreshments and lunch will be provided on the workshop day
Contact us: Send email with any queries you may have regarding the workshop to "amit AT"

Registration fee: $50


Workshop abstract

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, these solutions solely focus and rely on hierarchical file and folder organization. While such an organization is pervasively used and quite useful, it relegates information about the context of the data such as description and associated collaborative notes to external systems, dispersing this vital information into different silos not only impedes the flow research activities in near term, but also has an impact on mid and long term retention of knowledge about intermediate steps.

In this workshop, we will introduce and provide hands on experience with tools designed to mitigate this critical gap via the NSF supported SeedMe2 platform. The SeedMe2 platform leverages the familiar hierarchical file and folder organization structure, but extends it with an ability to add data, its description and discussion in one system. It also allows a folder to be shared either privately with collaborators or publically for wider dissemination of information. Users may interact with the system via the web browser, command line utility or via REST API using familiar concepts for each method. The platform will enable users to rapidly share and access transient data and preliminary results with collaborators in consumable form. The workshop aims to provide practical training to customize and utilize this infrastructure and enable attendees to overcome existing gaps in collaboration as well as realize several aspects of research data management.

Note: SeedMe2 platform focuses on data that can be transferred easily on the web with standard tools such as stock Web Browsers. This limits the upload sizes to 2GB per file, however any number of files may be uploaded. Moreover derived products from large scale raw data tends to be small, so this workshop and platform is still highly relevant to large data producing groups. In future the platform will likely support larger size uploads.

Workshop Requirements

  • A laptop computer is required (tablets will not be sufficient for this workshop)
  • Software required for the workshop will be provided later
  • Attendees must be proficient at using web browser and able to make simple edits to text files on a terminal with instructions
  • (Optional) Ability to use command line interface

Who may wish to attend this workshop?

We welcome a broad set of attendees to this workshop with complimentary interests such as

  • Researchers: Interested to set up or use data sharing for project or personal use
  • Research IT/Cyberinfrastructure providers: Provide a predefined or custom data-sharing configuration to your users
  • Scientific application/Gateway developers: Integrate/extend your Application/Science Gateways to provide data sharing capabilities and increase your impact by disseminating exemplar content from your users.
  • Data curators: Create powerful repositories with custom fields to allow easy discovery via search and interactive exploration. Integrate other tools with repository content via powerful web services.

Attendee outcomes

We anticipate by the end of the workshop the attendees will be able to accomplish the following

  1. Gain understanding and working knowledge of SeedMe2 platform and how to leverage it for research data needs
  2. Take away a working research data sharing website with your own branding with
    • Ability to configure and manage site wide data sharing
    • Customized data properties tailored to your project needs
    • Customized website for other uses such as to disseminate project news, publications, etc.
  3. Automation and integration: Learn to use command line and web services tools that could used be used remotely as well as for automation
  4. Deployment options: Learn where such a data infrastructure may be hosted
    • Do-it-yourself: On site
    • Third party vendor
    • Regulatory compliant hosting

Workshop agenda (Tentative)

Instructors: Amit Chourasia and David Nadeau

  • Welcome and attendee introduction
  • Invited talk on research data management (TBD)
  • Lightning overview of web servers, databases and content management systems
  • Overview of SeedMe2 platform
  • Introduction to Drupal content management system
  • Create your new data sharing website (Hands on)
  • Configure SeedMe2 building blocks (Hands on)
  • Using command line to interact with SeedMe2 (Hands on)
  • Customizing and extending your SeedMe2 website (Hands on)
  • Single sign-on from over 2,200 academic institutions using CiLogon (Demo, so you can do this later)
  • User stories
  • Discussion of best practices for research data

The SeedMe workshop is based upon work supported by the National Science Foundation under Grant No. 1443083. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Location, directions and parking

Address: University of California, San Diego
San Diego Supercomputer Center (SDSC)
10100 Hopkins Drive, La Jolla, CA 92093
Google maps exact location

San Diego Supercomputer Center’s Auditorium E-B212 located on the ground floor of SDSC’s east entrance, just off the driveway on Hopkins Dr, close to the Hopkins Parking Structure, Northwest end of UC San Diego campus.

Local map: Download map with SDSC location, housing, parking, coffee, restaurants

Airport: The San Diego International Airport (SAN) is the closest airport to UC San Diego and SDSC.

Driving: For driving directions see the visitors page on the SDSC website

Taxi / Shuttle
Cab or shuttle Pick-up/Drop-off: 10100 Hopkins Drive, La Jolla, CA 92093

List of few taxi services in San Diego

Public transportation: Surrounding UC San Diego

Presentation | 2017-10-20

Building a data sharing cloud on Drupal 8

Amit Chourasia
Presented at the BADCamp 2017, Berkeley, CA, Oct 20, 2017
Video recording & Slides

Poster | 2017-10-02

SeedMe: Stream Encode Explore and Disseminate My Experiments.

Amit Chourasia, David R. Nadeau, Mona Wong, Dmitry Mishin, and Michael Norman. 2017. SeedMe: Stream Encode Explore and Disseminate My Experiments. To be presented at the Visualization in Practice 2017 workshop at the IEEE Visualization conference 2017.
View slides

Presentation |
2017-08-05 to 2017-08-06

Building a data sharing cloud on Drupal 8

Amit Chourasia & David Nadeau
Presented at the DrupalCampLA 2017, Irvine, CA, Aug 5-6, 2017
View slides

Presentation | 2017-08-04

SeedMe: A Data Sharing Platform for the Research Community

Amit Chourasia
To be presented at the SDSC Summer Institute 2017, La Jolla, CA, Aug 4, 2017

Presentation | 2017-07-12

SeedMe: Data sharing building blocks

Amit Chourasia
Presented at the ARCC 17 workshop collocated with PEARC 17 conference, New Orleans, LA, Jul 12, 2017

Poster | 2017-07-11

SeedMe: Data sharing building blocks

Amit Chourasia, David R. Nadeau and Michael L. Norman
Presented at the PEARC 17 conference, New Orleans, LA, Jul 11, 2017
Download PDF

Poster | 2017-04-13

SeedMe: Data sharing building blocks @ 7th National Data Service Consortium Workshop

Amit Chourasia, David R. Nadeau, John Moreland, Dmitry Mishin and Michael L. Norman
Presented (in absentia) at the 7th National Data Service Consortium Workshop, Chicago, IL, Apr 13, 2017

Presentation | 2017-01-13

Collaborative data sharing with SeedMe @ HIVE project meeting

Presented at the HIV Interaction and Viral Evolution Center (HIVE) project meeting, The Scripps Research Institute, La Jolla, CA, Jan 13, 2017

Presenter: Amit Chourasia, San Diego Supercomputer Center, UC San Diego

Third-party app | 2016-11-10

VisIt visualization software now has better integration with The latest version 2.12.0 ships with a graphical user interface to easily upload, share data and create videos from image sequences.

SeedMe2: Data sharing building block @ 2016 Gateways Conference

Chourasia, Amit; Nadeau, David; Moreland, John; Mishin, Dmitry; Norman, Michael (2017): SeedMe2: Data sharing building blocks. figshare. DOI: