The iPlant Collaborative

Presented by Sheldon McKayCold Spring Harbor Laboratory

What is iPlant?

NSF Cyberinfrastructure for the Biological Sciences: Plant Science Cyberinfrastructure Collaborative   (PSCIC). $10,000,000/yr for five years, with an option for a terminal five year renewal

“The goal of this program is to create a new type of organization – a cyberinfrastructure collaborative for plant science – that will enable new conceptual advances through integrative, computational thinking.”

iPlant is a Virtual Organization

UATACC

CSHL

Example: iPlant Centers and the tree of life grand challenge collaborators

iPlant Cyberinfrastructure

• Universal, accessible, capacious storage

• Access to vast computing power

• Sharing and collaboration

• Scaling Information Visualization

• Ability to integrate community software and practices

Initial focus around grand challenges:

• iPlant Tree of Life (IPTOL):– Build a single tree showing

the evolutionary relationships of all green plant species.

• iPlant Genotype-to-Phenotype (IPG2P)– given the genomic and

environmental information about a given plant, predict its characteristics.

Focus on data integration, not simulation:Plant science is truly data driven.

Still many computational challenges.

Prototype interactive visualization tool, showing 116,000 taxa phylogenetic tree

“The field of genomics is caught in a data deluge. DNA sequencing is becoming faster and cheaper at a pace far outstripping Moore’s law, which describes the rate at which computing gets faster and cheaper. “

“We believe the field of bioinformatics for genetic analysis will be one of the biggest areas of disruptive innovation in life science tools over the next few years,” Isaac Ro, an analyst at Goldman Sachs, wrote in a recent report.

What can iPlant do for you?

iPlant CI serves as basis for custom- tailored applications

iPlant CI serves as basis for custom- tailored applications

Complexity is abstracted behind Application Programming Interfaces

Complexity is abstracted behind Application Programming Interfaces

Resources are virtualized and federated

Resources are virtualized and federated

Public APIsAPI Role

Workflow Domain-aware scientific workflow construction and management

Foundational Expose major CI operations as RESTful web services. File IO, format conversion, Application discovery, Job execution, Auditing, Authentication, Profile discovery

Semantic Web Machine-comprehensible service and data publication and discovery

iPlant Data Store“No matter where you go, there you are (and so is your data)”

Access your data via•Discovery Environment•Mountable file systems•Foundational API•Command line•DropBox-like interface•Web applications•More…

data.iplantcollaborative.org

iPlant Atmosphere

• API-compatible implementation of Amazon EC2/S3 interfaces

• Virtualize the execution environment for applications and services

• Launch and customize your own or pre-configured virtual machines

• CloudBursting desktop application cases

atmosphere.iplantcollaborative.org

The iPlant Discovery Environment

preview.iplantcollaborative.org

The iPlant Discovery EnvironmentMany integrated applications.

You can add more.

Research Education

Students can work with the same data at the same time and with the same tools as

research scientists.

Educational Challenge

• Educational Discovery Environment: simplified workflow for gene annotation and comparison

• Developed with 25 collaborators at 11 institutions – Since 3/2010: 1,400 registered users; 25,000 visits

• Red Line: predict and annotate genes in <150 kb DNA

• Yellow Line: identify homologs in sequenced genomes

• Blue Line: phylogenetics and DNA barcode analysis

DNA Subway

dnasubway.iplantcollaborative.org

Consumer Applications

Public APIs

iPlant Compute Infrastructure

Progress so far…• iPlant’s mission is to build the CI to support plant

biology’s Grand Challenge solutions

• Phase I – Community Input

• Phase II – Building the CI Foundation

• Next Phase – Enabling Plant Science Discovery

– Serve as an incubator for big analysis ideas to generate new projects and funding

– Play an incubator role in partnerships to enable plant sciences in ways that were not previously possible

Where Can I Start?

www.iplantcollaborative.org

iPlant’s Building Blocks

Metadata Data Tools Workflows Viz

Executive Team:Steve GoffDan Stanzione

Staff:Greg AbramSonali AdityaRoger BarthelsonBrad BoyleTodd BryanGordon BurleighJohn CazesMike ConwayKaren CranstonRion DooleyAndy EdmondsDmitry FedorovMichael GattoUtkarsh GaurCornel GhibanMichael GonzalesHariolf HäfeleMatthew HanlonKris Healy

Faculty Advisors & Collaborators:Ali AkogluGreg AndrewsKobus BarnardSue BrownThomas BrutnellMichael DonoghueCasey DunnBrian EnquistDamian GesslerRuth GreneJohn HartmanMatthew HudsonDan KliebensteinJim Leebens-MackDavid LowenthalRobert Martienssen

Students:Peter BaileyJeremy BeaulieuDevi BhattacharyaStorme BriscoeYa-Di ChenJohn DonoghueSteven GregorySneha Jadhav Yekatarina KhartianovaMonica Lent

B.S. Manjunath Nirav Merchant David NealeBrian O’MearaSudha RamDavid SaltMark SchildhauerDoug SoltisPam SoltisEdgar SpaldingAlexis StamatakisAnn StapletonLincoln SteinVal TannenTodd VisionDoreen WareSteve WelchMark Westneat

Zhenyuan LuEric LyonsAaron KubitzNaim MatasciSheldon McKayRobert McLayAngel MercerDave MicklosNathan MillerSteve Mock Martha NarroPraveen NuthulapatiShannon OliverBenoit ParmentierShiran PasternakWilliam PeilJ. Matt PetersonJ.A. Raygoza GarayDennis RobertsPaul Sarando

Anthony HeathBarbara HeathMatthew Helmke Natalie HenriquesUwe HilgertNicole HopkinsEun-Sook JeongLogan JohnsonChris JordanKathleen KennedyMohammed KhalfanB.D. KimSeung-jin KimLars KoersterkSangeeta KuchimanchiKristian KvilekvalAruna LakshmananSue LauterTina LeeAndrew Lenards

Jerry Schneider Bruce SchumakerSriramu SingaramEdwin SkidmoreBrandon SmithMary Margaret Sprinkle Sriram SrinivasanJosh SteinLisa StillwellKris UriePeter Van BurenHans Vasquez-GrossMatthew VaughnLiya WangFusheng WeiJason WilliamsJohn WregglesworthWeijia XuJill Yarmchuk

Amgad Madkour Aniruddha MaratheKurt MichaelsDhanesh PrasadAndrew PredoehlJose SalcedoShalini SasidharanGregory StriemerJason VandeventerKuan Yang

Postdocs:Barbara BanburyJamie EstillBindu JosephChristos NoutsosSolon Pissis Brad RuhfelStephen A. SmithChunlao TangLin WangNorman Wickett