SeedMe Platform for Sharing Research Results

Your results from disk to device

Stream Encode Explore and Disseminate My Experiments

SeedMe name inspired by Seed : proliferate and grow

National Science FoundationThis material is based upon work supported by the National Science

Foundation under Grant No. OCI-1235505

AcknowledgementsKristen Levy, Mahidhar Tatineni, Michael Dwyer, Tom Hutton, & Doug Weimer, SDSC

Apple Inc. : Provided test hardware/software on loan during conceptualization phase

TeamAmit Chourasia

Mona WongDavid Nadeau

Andrew FerbertMichael Norman

Presentation Overview

• Situate context & define problem• Introduce SeedMe• Sample use cases• Sample end user interaction• Q & A

Computation Cycle

Compute/IngestPost ProcessAnalyze

Monitor?

Validate?

Abstract?

Monitoring

Validation

Derived Products

Abstraction

Direct Access Direct Web Sharing

Not All Members

Have Access----

Need Exact Location +

Permissions

Inflexible Security Policy

Derived Products(Preliminary Results)(Transient Content)

Many customers

WebpageEmail

Download + SendScattered ResultsCan’t share larger contentManual

Download + UploadHandle Privacy Significant time commitmentManual

Cloud Drive

Download + UploadCannot describe contentManual

Sharing Derived Products(Many customers)

Compute Anticipate React

Waterworld (1995)

Accessibility Irony1993

“NCSA Mosaic, or simply Mosaic, is the web browser credited with popularizing the World Wide Web.”

Mosaic (Web browser), Wikipediahttp://en.wikipedia.org/wiki/Mosaic_(web_browser)

1990“The web was originally conceived and developed to meet the demand for automatic information-sharing between scientists in universities and institutes around the world.”

The birth of the web. CERNhttp://home.web.cern.ch/topics/birth-web

Mission Dashboard at NASA – JPL Voyager space crafts have been sharing

information since 1977

2007Mobile devices can share content instantly

2014Computation simulations cannot share information with us

• No place to push information (no infrastructure)• Lack of easy tools

Pitfalls in sharing derived content

Download Upload

Download (Round Trip + 1)

Video Encoding

Complexity

Missing Easy Automation

How To Describe &

Discuss Content

Replication &

Scalability

Why not use existing tools?

Your results from disk to device

SeedMe offers you to• Seamlessly seed (upload) your research content• Share and access your content• Generate dashboards for your simulation or expt.• Describe your content (everything is not a file)• Discuss your work, right next to your content

SeedMe Collection

Ticker(Text)

Ephemeral

Sequences(Image set)

Videos(video)

Files(Catch all)

Meta Data(Title, Description, Tags, Key Value Pairs, Credits, License)

Privacy + Collaborators(Public, Group, Private) + (emails)

Plots(Image)

SeedMe: How it Works

SeedMe User Interactions

• Create Collection ( CLI, API, Web Browser)

• Update Collection ( CLI, API, Web Browser)

• View Collection (Web Browser only)

Hardware

Software

MySQL

Drupal

Apache

Gearman Scheduler

Web nodes Storage

Video encoding

nodes

Responsive Web Output

Desktops

Phones

Tablets

IngestionHTTPSWeb

Browser REST

SeedMe Architecture

Network Switch 20 gbe20 gbe

SeedMe Processing

Ingestion (Atomic or Recurring)

Instant Processing

(Text, Images)

NotificationResponsive

Content Access

Batch Processing

(Videos)

Use Case: Sequence to VideoSequences of images are generated by

Visualizations Confocal scans Time lapse recording

Requirements Frame rate High Quality

EncodingUniversal playbackAutomation

seedme.cmd -t “Seq Collection” \ # Collection title

-sp "sample/sequences/steam" \ # Seq Path

-st "sequence title" \ # Seq Title

-sd "Desc of sequence" \ # Seq Description

-sr "5" \ # Seq frame Rate

-se # Trigger Seq Encode

Command line example, but you can upload content simply via Web Browser

Use Case: Create DashboardsResults from simulations, instruments, analysis

Files Plots SequencesVideos

Requirements Managed SharingUniversal accessAutomation

seedme.cmd -t “Quick Start” \ # Collection title

-privacy group \ # Privacy

-email nobody@sdsc.edu \ # Share

-notify \ # Notify (not automatic)

-pp "sample/plots/node.png" \ # Plot Path -sp "sample/sequences/steam" \ # Seq Path

-vp "sample/videos/air.mp4" \ # Video Path

-fp "sample/files/doc.pdf” # File Path

Command line example, but you can upload content simply via Web Browser

Use Case: MonitorComputation state

Progress %Progress parametersLast file created

Requirements SharingUniversal accessAutomation

seedme.cmd -t “Progress Tracking” \ # Create new Collection

seedme.cmd -update 29643 \ # Update collection ID

-tic "step 1" \ # Ticker Text

-tic "step 2" \ # Ticker Text

-fp "sample/files/doc.pdf” # File Path

Command line example, but you can upload content simply via Web Browser

Use Case: Share & Reuse

Disseminate

Share and reuse content IPython notebook

State files from vis tools

R scriptsMatlab scripts

Applications Exploring :‘Save to SeedMe’

Kepler Workflow

VisIt softwareYT software

Integrate SeedMe Python Module or write your own REST client

Demo: Web Browser

Types of Collections: My Shared Publichttp://www.seedme.org/collections

You may Add, Edit and Notify collaborators

Add a new collectionhttps://www.seedme.org/collections/add

View a collection with monitoring infohttps://www.seedme.org/collection/14924

View a collection with variety of contenthttps://www.seedme.org/collection/16567

seedme.cmd -title "SeedMe Quick Start"

seedme.cmd -update 29643 \ # Update-fp "sample/files/doc.pdf" \ # File Path-pp "sample/plots/node.png" \ # Plot Path-sp "sample/sequences/steam" \ # Seq Dir

Path

-vp "sample/videos/air.mp4" \ # Video Path

seedme.cmd -update 29643 \ -privacy group \ -email abc@sdsc.edu \ -email xyz@sdsc.edu

seedme.cmd -update 29643 -notify

Demo: Command Line InteractionCreate a new

collection

Add image seq.+ create video

from it

Setup sharing

Notify Group

Getting Started

Interaction• Web Browser• Standalone executable

(command line)• Python module with API

(demo.py)• Curl

Information• Quick Start Guide• Use Cases• Documentation• Tips for C, Fortran codes• Blog

Signup / Share http://www.seedme.org

Contact Usamit sdsc.edu

https://www.seedme.org/contact

Twitter@SeedmeOrg