The iPlant CollaborativeCyberinfrastructure

akaDevelopment of Public Cyberinfrastructure to Support Plant Science

Nirav MerchantUniversity of Arizona

PowerPoint Does Rocket Science--and Better Techniques for Technical ReportsEssay by Edward Tufte

What is iPlant?• iPlant’s mission is to build the CI to support plant

biology’s Grand Challenge solutions

• Grand Challenges were not defined in advance, but identified through engagement with the community

• A virtual organization with Grand Challenge teams relying on national cyberinfrastructure

• Long term focus on sustainable food supply, climate change, biofuels, ecological stability, etc

• Hundreds of participants globally… Working group members at >50 US institutions, USDA, DOE, etc.

Brief History

• Formally approved by National Science Board – 12/2007

• Funding by NSF – February 1st, 2008

• iPlant Kickoff Conference at CSHL – April 2008o ~200 participants

Grand Challenge Workshops – Sept-Dec 2008 CI workshop – Jan 2009 Grand Challenge White Paper Review – March 2009 Project Recommendations – March 2009 Project Kickoffs – May 2009 & August 2009 First Release of Discovery Environments – April 2010

The paradigm shift

Classic paradigm: You produce data, analyze, interpret (end to end)

Conventional paradigm: Consortium/centers produce data and you consume it

New Paradigm: Consortium/centers have produced data and creating “cyber infrastructure” to tackle the “grand challenge”

GC Projects Recommended by the iPlant Board of Directors March 2009Initial Projects:

Plant Tree of Life – iPToL – May ‘09+Taxonomic Intelligence+ APWeb2+ Social Networking Website

Genotype to Phenotype – iPG2P – Aug ‘09+ Image Analysis Platform

iPlant Tree of Life Working Groups Trait Evolution, Brian Omeara

– Post-tree analysis and mapping of ancestral traits

Tree Reconciliation, Todd Vision– Large-scale reconciliation of gene trees, co-evolving parasites, etc.,

with species trees

Big Trees, Alexandros Stamatakis– HPC Phylogenetic inference with 500K taxa

Tree Visualization Michael Sanderson; Karen Cranston– Cross cutting group for the viz needs of all

Data Integration, Val Tannen, Bill Piel– Cross cutting group for the data integration needs of all

Data Assembly, Doug Soltis, Pam Soltis, Michael Donoghue– Community and network building, data assembly

iPlant Genotype to Phenotype Working Groups

• NextGen Sequencing– Establishing an informatics pipeline that will allow the plant community to process

NextGen sequence data• Statistical Inference

– Developing a platform using advanced computational approaches to statistically link genotype to phenotype

• Modeling Tools– Developing a framework to support tools for the construction, simulation and analysis

of computational models of plant function at various scales of resolution and fidelity• Visual Analytics

– Generating, adapting, and integrating visualization tools capable of displaying diverse types of data from laboratory, field, in silico analyses and simulations

• Data Integration– Investigating and applying methods for describing and unifying data sets into virtual

systems that support iPG2P activities

What is Cyberinfrastructure?(Originally about TeraGrid)

And More!:

- Viz

- Facilities

- Data collections

…

It’s a Grid!

It’s Storage!

It’s a Common Software Environ!

It’s a Network!They are

HPC Centers!

It’s Apps and

Support!

It was six men of Indostan,To learning much inclined,

Who went to see the elephant,(Though all of them were blind),

That each by observationMight satisfy his mind.

WWW.TERAGRID.ORG

The iPlant Cyberinfrastructure

Physical Infrastructure

ComputeStorage

Persistent Virtual Machines

TeraGridOpen Science Grid

UA/ASU/TACC

iPlant Middleware

Job Submission Workflow Management Service/Data APIsiRODS, Grid Technologies, Condor, RESTful Services

iPlant Discovery Environments

Grand Challenge Workflows, iPlant InterfacesThird Party Tools, iPlant-built Tools, Community Contributed Tools and Data!

Build a CI that’s robust, leverages national infrastructure, and can grow through community contribution!

User

Open Source Philosophy, Commercial Quality Process

• iPlant is open in every sense of the word:– Open access to source– Open API to build a community of contributors– Open standards adopted wherever possible– Open access to data (where users so choose).

• iPlant code design, implementation, and quality control will be based in best industrial practice

Portfolio of Activities• Maintaining a balance of “past, present, future”

strategies– “Past”: make services, systems, and support available to

existing bioinformatics projects, either to enhance them or simply make critical tools more widely available.

– “Present” build the best bioinformatics software tools that today’s technologies can provide.

– “Future” track emerging technologies, and where appropriate stimulate research into the creation and use of those technologies.

Portfolio of Activities• In a nutshell:

– 12 Working groups in the two grand challenges, each of which is defining requirements for DE development.

Each group not only has discussions that leads to final projects, but they also spawn prototyping efforts, tech eval projects, tool support projects, etc.

– Services group: provide cycles, storage, hosting, etc. to users.

– A comprehensive technology evaluation program to find, borrow, or build relevant technologies, headlined by the semantic web effort.

– A number of ancillary projects related to grand challenges, i.e. APWEB, high throughput image analysis

– The Core development/integration effort.

Systems and Services

• Provide access for problems like these on large scale systems

• Provide the storage infrastructure for biological data (again, in support of existing projects)

• Provide cloud style VM infrastructure for service hosting.

iPlant : Connecting Users, Ideas and Resources

The core foundation component comprises of :

Data layerRegistry and Integration layerCompute and Analysis layerInteraction and Collaboration layer

iPlant: Using proven technologies

• Data layer:providing access to raw and ingested data sets including high throughput data transfers

• iRODS• GridFTP , Aspera• Dspace (DuraSpace), OpenArchive initiative• Content Distribution Networks (CDN)• High performance storage @ TACC (Lustre)• MySQL and Postgres database clusters• Connection to established data sources (NCBI, TAIR,

Gramene)• Connection to DataOne, DataNet initiatives• Cloud style storage (similar to Amazon S3 and Walrus)

iPlant: Using proven technologies

• Registry and Integration Layer:Connecting services, data and meta data elements with semantic understanding

• Meta data catalog management • Provenance tracking (W7 model)• Integrated Registry and Service discovery servers• Data Client and Data Provider Ontology

development Kit• Semantic Architecture (OWL based SSWAP)

iPlant: Using proven technologies• Compute and Analysis Layer:

Connecting tasks with scalable platforms and algorithms

• Virtualization (Xen clusters)• High Performance Computing at TACC and TeraGrid• Grid (Condor, BOINC, Gearman)• Cloud (Eucalyptus, Nimbus)• Reconfigurable Hardware (GP GPU, FPGA)• Checkpoint & Restart (DMTCP)• Scaling and parallelizing code (MPI)• Workflow engines (DAGman, Pegasus, Kepler)

iPlant: Using proven technologies

• Interaction and Collaboration layer:Providing end user access to unified services and data, from API to large scale visualization

• Google Web Toolkit (GWT driven front end)• Messaging bus (Java Mule, RabbitMQ, XMPP/Jabber)• RESTful web services (web API access)• Single sign-on/identity management (Shibboleth. Oauth ?)• Transparent HPC integration (TeraGrid science gateway and TACC

resources• Integration with desktop applications (via web services)• Collaboration platforms (openmeeting, webex wiki, mailman)• Shared analysis (shared workflows, desktop view)• Sharing data (DOI, persistent URL, CDN, social networks)• Large scale visualization (Large Tree, Paraview, SAGE)

Storage Services• We have also begun offering storage to a

number of projects connected to the grand challenges in some way, as well as iPlant internal.– IRODS interface– Corral at TACC, a local storage array at UA

• Data arriving now for 1KP project, Gates C3/C4 project.

Cloud Services

• iPlant is now offering “cloud” style hosting services.

• Dynamically launch virtual servers hosted by iPlant.

• Still in prototype

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SaaS: Software as a Service(e.g. Clustering/Assembly is a service)

IaaS: Infrastructure as a Service (get computer time with a credit card and with a Web interface like EC2)

PaaS: Platform as a ServiceIaaS plus core software capabilities on which you build SaaS

(e.g. Hadoop/MapReduce is a Platform)

Cyberinfrastructure Is “Research as a Service”

Arrival of “As a Service” models

http://salsahpc.indiana.edu

What do working groups want ?• Wiki• Shared storage• WebEX• CMS• Google apps• Machine for prototyping/development• Change management s/w (git/svn)• Access to compute grid/cluster

What iPlant wants

• Ability to integrate single sign on (sso) with all services we offer (api, cloud, grid, irods etc)

• Leverage credentials from users home institutions

• Lower the barrier to access while still being secure

• Emphasis on ease of access to “research as a service”

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Phases of a project

• Enthusiasm

• Disillusionment

• Panic

• Search for the guilty

• Punishment of the innocent

• Praise and honor for the non-participants

Karla Jennings