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SeedMe News

Workshop | 2018-08-24

SeedMe workshop: Collaborative data sharing infrastructure for researchers

Date: Aug 24, 2018
Maximum attendees: 25
Venue: San Diego Supercomputer Center, UC San Diego. (See directions)
Lodging: The workshop will cover up to two days of stay (Aug 23-25) 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 non San Diego residents only.
Travel: Attendees must cover travel costs on their own
Food: Light refreshments and lunch will be provided on the workshop day
Contact us: Post any queries you may have regarding the workshop here

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.

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 edit text files
  • (Optional) Ability to use command line interface

Who may wish to attend this workshop?

We welcome a broad set of attendees to attend 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 data-sharing configuration to your users
  • Scientific application/Gateway developers: Integrate/extend your Application/Science Gateways provide data sharing capabilities and further customization for your needs
  • Data curators: Create powerful repositories that include descriptions, and allow easy discovery via search and interactive exploration

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 in your research work
  2. Take away a working research data sharing website with your own branding
    • Customize data properties
    • Configure and manage site wide data sharing
    • Customize the website further to use for their project or research group
  3. Automation and integration: Learn to use command line and web services tools that could used be used 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
  • Overview of SeedMe2 platform
  • Overview of content management systems, webservers and databases
  • Introduction to Drupal content management systems
  • Invited talk on research data management (TBD)
  • Create your new data sharing website (Hands on)
  • Configure SeedMe2 building blocks (Hands on)
  • Using command line to interact with SeedMe2 (Hands on)
  • Single sign-on from many academic institutions using CiLogon (Demo, so you can do this later)
  • Customizing and extending your SeedMe2 website (Hands on)
  • User stories
    • Dr. Alexey Arefiev, UC San Diego
    • TBD
  • Best practices

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 | 2016-11-03

Demo: SeedMe.org - Share data and visualization @ 2016 Gateways Conference

To be presented at the Gateways 2016 Conference, San Diego, CA, Nov 2, 2016

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

Tutorial | 2016-11-02

Tutorial: Data sharing via SeedMe @ 2016 Gateways Conference

To be presented at the Gateways 2016 Conference, San Diego, CA, Nov 2, 2016

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

Poster |
2016-09-11 to 2016-09-13

SeedMe: Data sharing building blocks

Amit Chourasia, David R. Nadeau, John Moreland, Dmitry Mishin and Michael L. Norman
Presented at the SCEC 2016 annual meeting. Palm Spring, CA, Sep 11-14, 2016.

Tutorial | 2016-08-03

Data sharing tutorial @ 2016 SDSC summer institute

Introduction to Scientific Visualization and Data Sharing. Presented at the 2016 SDSC summer institute, San Diego, CA, Aug 3, 2016

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

Paper | 2016-07-21

SeedMe: A scientific data sharing and collaboration platform.

Amit Chourasia, Mona Wong, Dmitry Mishin, David R. Nadeau, and Michael Norman. 2016. SeedMe: A scientific data sharing and collaboration platform. In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale (XSEDE16). ACM, New York, NY, USA, , Article 48 , 6 pages. DOI=10.1145/2949550.2949590

Preprint PDF

Poster | 2016-07-20

SeedMe: Data sharing building blocks

Amit Chourasia, David R. Nadeau, John Moreland, Dmitry Mishin and Michael L. Norman
Presented at the XSEDE 2016 conference. Miami, FL Jul 17-21, 2016.
Download poster

Tutorial | 2016-07-18

Data sharing tutorial @ XSEDE 2016

Introduction to Scientific Visualization and Data Sharing. Presented at the XSEDE 2016 Conference, Miami, FL, Jul 17-21 2016

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

Webinar | 2016-06-21

SeedMe platform: Enabling scriptable data sharing @ XSEDE ECSS Symposium

Webinar | 2016-06-21

Overview of SeedMe @ XSEDE Campus Champions Teleconference

In this talk we introduce the SeedMe platform which provides a web-based cyberinfrastructure to enable easy sharing and streaming of transient data and preliminary results directly from computing resources to a variety of platforms, from mobile devices to workstations. The SeedMe platform is open to all researchers and provides web browser based as well scriptable tools for easy integration with ad hoc computation workflows.

Release | 2016-06-09

SeedMe has been upgraded to version 1.4, with several new improvements:

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