1 iPlant: Cyberinfrastructure for Plant Sciences (and Beyond) Your Name Here 1.

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iPlant:Cyberinfrastructure for Plant Sciences

(and Beyond)

Your Name Here

One Big Problem...

•Transfer•Storage•Analysis•Visualization•Metadata Mark-up•Search and Discover•Share/Collaborate•Publish

High-throughput Data Acquisition

In 11 Days•Generates 4TB of raw data•600,000,000,000 bases of DNA sequence•(200 human genomes)

•$70K for~30 camera sets•~200 movies of plants undergoing a dynamic growth process•“Only” 4GB a day

High-throughput Phenotyping(Watching Grass Grow)

Big Data in EcologyGlobal Multidimensional Data

GGGTGCCCAAAAGCCCGGTTTGTTAGCCCCTTTCCGATTCCCTCACCCAATCTCATTAAAAGCAAGCCCAGCAGGCCCTGCCTTAACCTGTCCCCAGACAGCCAGCCCTCACCAGGCCGCTGGCATTACTCAATGCTCCGCCACGAAGCAAGCTCTCCCGAATACGACAGATGCGGAAGTGGCTCAAGAAGTCGGAGGAATCAAGTAGTTGGAAAACTGTATGCACGAGGGGACATGAGTCTTCTGGGAATTGGCAACATTGGCAGAAAATAAAGGGGAATACAAGGGGGGTAGGAATCCACTTTGTTAGGTGTAGCTATACTCACGTAAGTAGTCGGCCTAACCTTCGGTTCCCGTAACCAAGTTGTTCTTTCTCACTCCTGATTGACTTTTGATTACTGAATCCATACTTTTTTACTTTTTTTGAATTTGAAGTGTGGGGAAAAGGGCGCCCTCTACTTCTACTTCTAACTACAGGCGAAAAGCTGGCATTGCAAGCAAATAGAGAGCCCCCGCCCGTTTGAGTCGTTGCGAGCCGGAAAGCGTACCAGCGGTTTGAGTCGCGAAAGGGCCGCTTGCTTAATTATATTATAATATAATATATATAATCTTCTATCTCTATCTATCAACAATAAAATCAGAAGAAAGTAAAAAAAATATAAAAAAGAAAATCATTTTTTGTATCCAATTTTGCATTCCTGGGAAGAGGAAGAAGCAGATAGAGCAAAGGCCTCCTCTTTCCGTCCGCTCTTCCCGAAGTGAGCGAATTGCATGTAGAGATCCGTAGGGGCTTATAGTTTAATTGGTTGAAACGTACCGCTCATAACGGTGATATTGTAGGTTCGAGCCCTACTAAGCCTACCACCCCCTTCTCTTCACCCGATACAAGGCAGTCGAAGTCCCCGCCACCCTGCAGATCTCAATCTAGCGACGGCACCTAGAACCACACTGCTGCCGCTGCCCGAAGGGCACGCCTCCTACGCTCTTGCAGCATGCCCCCTTCGGGGCAGATGTTACTATACTAAAAAAGAAGGCCCTCGCTAAGCGCTGGTTCTATCCCGGCCAAGCAACCAAGGTGGGAATAGTGAACGAAAGAGAAGGACATTGTTCAGAGTGAAACTGAACCCCCTTGATCAATCCTGTAAGAACGAAGACTTCACCAATCGACCAATGGGCCTTTCCTTGTAGGCGGCGAAGGGCAGGTGAACACTCTTCCCTTGGAACCTGCGCATAATGAAATATAACATTTTTTACTTCCATGGTCATACTATATTTATCTTTATATTGCGAATGAGTCTGGACCATCTCCTATTGTAGTATCAAAATGAATATGACTTTACTTTGAAGTTTAGCCCTCTTTCAACAGTATGACAACCTTCCCAATCACTCGGTTCAATCCTTACCTGAGGATGACAAGGCTTGGCTGATAGGCCGAGGACGAAGCATGCACCTTCGCTTAACCTTCGATGTTGTCATCACGCTGCCTTTCGCATGTCGGGCCTATACACGCTCGTCAAGTTACACCTTAACTGCTTTCTCAACGCGCGGCTCTTATAGATAACCCTTCCTTATCAATCAAATAAGCATTTGTGAGTTGAGATTCCTTCCCTATGTTTCAAAGCTAGCTTCTCTAGCTATACTGTGTGACCCACCTCCTCCCTTCGCTCTCTTGCTAGAGCTGGTTCTAAGCCTACCTTTTCCTTCCCCACCCTCTGTCTGACCAACCTCTGACTTCGATAATGACCTATAAACAATTATTCCAAGTGAAACGATAAGCATGTTGGCTTAGACCTTATCTTACCAGACAAGACATTGATGTCTGCCCGAACATCGAAATGAATCTTTCATATGCGGATTTTCACTTCCCCTCATTAAGCTAGCTAGCGCAAGTGTCAGAAAGGATGAATGCATTCCGAGATCGAATTAGCCCCTTACATCTTAGAACATTTTATACAAGGAATGTGTGTGACCTCTCTGATAGTAAGAGCGCACTAACGGAAAGAGAAATTGTTATAAGGAAAGAGAACACACTAGGGTAGAGTGGAAAGGGAACAGGAAAAAACTTTAGTCGACTAACTCTAGTATTCATGCTAGAACAGAGCTCCCGAAATAAAATATATCAATTATAGCGCTTCATCACTTGAAATAGGATCTTGCCTACGGCCCTAGTACTTTACTTTAGTCGATCGACATCTCATTAGCAAACAAACATAGAAGAGTCAGCTTCCTCAGTCTTGGTTATCGAGTTATCTTACCTGACAGGGTCGGCTAGGTGAGTTTGATTCCATTCCCGTGGCAAAAGGAAAAGAGCTTGATATCCGGGCTTCTATCGGTGAAGAAATGTTATGCCCACGGTTCCGTACTAAAGAATGAGCCAACAGCTATCTCCTTAGCTTCTTAAGGCACTCTTTTTCTGTTTAGTTATTGGTAATCCATCCGAGTGATCTATCTTATCGATAAAGAAATTCTCTCCCCTTACCGATCTTGTTATGCCTCCCGCGGTACATACAAAGGAACCTTCTATCCCATCGGTTAATCAAAGAAATTAGGTGCTCCTACGCCTGAAGTTATCGGTGAAGGCTTCCCCTCCATTTGATCTGTAGGATATCGAGTTTTCTTACCGCCTCTATCGGCTATGGGATATGCAATTCTCTTCTCTGACTTAACACAGAGCAAAGTAGACTGATTTCGCGCTAGTGCTAGTACACGAGTAGACCGCTTTCACCTAGCTATTGCTCACTAACAGAACCTTCTCGTACTGGAGAAAAGAACTTGAGCTCTGCTTCGAGGAACTAGCAGTCGAAGGGTGACGATTTCTGATCACTGGATTCAAGAGCTTTTAGGGTGTTCGGAACAGTTATTAGTAGAAGATAAGACTTTCTCGGCTTGTTTACTAAGTCTCTGATTCGAATAAGCGACTCGGAACTCTGTTCGCGGTTAGCTGAGAATGTTCTTGCTTCTTGCCAGTTAGATTAGCTTGAAAGGGAATGAGTGAGTCGAAAGTATGACAACGGGCATAGATAGAGGAGTTCCTGATCCCGGTACTAGGGCGAATGGCATAACTGCTTCTTTCTCTTTTTACGGGTAGAATCCGCTATAGTTGAGGAAGCCCAGAGATGAGGATAAAATCTCTTGTTTAAGAAGCAACTCATGTTTCAGG GGGTGCCCAAAAGCCCGGTTTGTTAGCCCCTTTCCGATTCCCTCACCCAATCTCATTAAAAGCAAGCCCAGCAGGCCCTGCCTTAACCTGTCCCCAGACAGCCAGCCCTCACCAGGCCGCTGGCATTACTCAATGCTCCGCCACGAAGCAAGCTCTCCCGAATACGACAGATGCGGAAGTGGCTCAAGAAGTCGGAGGAATCAAGTAGTTGGAAAACTGTATGCACGAGGGGACATGAGTCTTCTGGGAATTGGCAACATTGGCAGAAAATAAAGGGGAATACAAGGGGGGTAGGAATCCACTTTGTTAGGTGTAGCTATACTCACGTAAGTAGTCGGCCTAACCTTCGGTTCCCGTAACCAAGTTGTTCTTTCTCACTCCTGATTGACTTTTGATTACTGAATCCATACTTTTTTACTTTTTTTGAATTTGAAGTGTGGGGAAAAGGGCGCCCTCTACTTCTACTTCTAACTACAGGCGAAAAGCTGGCATTGCAAGCAAATAGAGAGCCCCCGCCCGTTTGAGTCGTTGCGAGCCGGAAAGCGTACCAGCGGTTTGAGTCGCGAAAGGGCCGCTTGCTTAATTATATTATAATATAATATATATAATCTTCTATCTCTATCTATCAACAATAAAATCAGAAGAAAGTAAAAAAAATATAAAAAAGAAAATCATTTTTTGTATCCAATTTTGCATTCCTGGGAAGAGGAAGAAGCAGATAGAGCAAAGGCCTCCTCTTTCCGTCCGCTCTTCCCGAAGTGAGCGAATTGCATGTAGAGATCCGTAGGGGCTTATAGTTTAATTGGTTGAAACGTACCGCTCATAACGGTGATATTGTAGGTTCGAGCCCTACTAAGCCTACCACCCCCTTCTCTTCACCCGATACAAGGCAGTCGAAGTCCCCGCCACCCTGCAGATCTCAATCTAGCGACGGCACCTAGAACCACACTGCTGCCGCTGCCCGAAGGGCACGCCTCCTACGCTCTTGCAGCATGCCCCCTTCGGGGCAGATGTTACTATACTAAAAAAGAAGGCCCTCGCTAAGCGCTGGTTCTATCCCGGCCAAGCAACCAAGGTGGGAATAGTGAACGAAAGAGAAGGACATTGTTCAGAGTGAAACTGAACCCCCTTGATCAATCCTGTAAGAACGAAGACTTCACCAATCGACCAATGGGCCTTTCCTTGTAGGCGGCGAAGGGCAGGTGAACACTCTTCCCTTGGAACCTGCGCATAATGAAATATAACATTTTTTACTTCCATGGTCATACTATATTTATCTTTATATTGCGAATGAGTCTGGACCATCTCCTATTGTAGTATCAAAATGAATATGACTTTACTTTGAAGTTTAGCCCTCTTTCAACAGTATGACAACCTTCCCAATCACTCGGTTCAATCCTTACCTGAGGATGACAAGGCTTGGCTGATAGGCCGAGGACGAAGCATGCACCTTCGCTTAACCTTCGATGTTGTCATCACGCTGCCTTTCGCATGTCGGGCCTATACACGCTCGTCAAGTTACACCTTAACTGCTTTCTCAACGCGCGGCTCTTATAGATAACCCTTCCTTATCAATCAAATAAGCATTTGTGAGTTGAGATTCCTTCCCTATGTTTCAAAGCTAGCTTCTCTAGCTATACTGTGTGACCCACCTCCTCCCTTCGCTCTCTTGCTAGAGCTGGTTCTAAGCCTACCTTTTCCTTCCCCACCCTCTGTCTGACCAACCTCTGACTTCGATAATGACCTATAAACAATTATTCCAAGTGAAACGATAAGCATGTTGGCTTAGACCTTATCTTACCAGACAAGACATTGATGTCTGCCCGAACATCGAAATGAATCTTTCATATGCGGATTTTCACTTCCCCTCATTAAGCTAGCTAGCGCAAGTGTCAGAAAGGATGAATGCATTCCGAGATCGAATTAGCCCCTTACATCTTAGAACATTTTATACAAGGAATGTGTGTGACCTCTCTGATAGTAAGAGCGCACTAACGGAAAGAGAAATTGTTATAAGGAAAGAGAACACACTAGGGTAGAGTGGAAAGGGAACAGGAAAAAACTTTAGTCGACTAACTCTAGTATTCATGCTAGAACAGAGCTCCCGAAATAAAATATATCAATTATAGCGCTTCATCACTTGAAATAGGATCTTGCCTACGGCCCTAGTACTTTACTTTAGTCGATCGACATCTCATTAGCAAACAAACATAGAAGAGTCAGCTTCCTCAGTCTTGGTTATCGAGTTATCTTACCTGACAGGGTCGGCTAGGTGAGTTTGATTCCATTCCCGTGGCAAAAGGAAAAGAGCTTGATATCCGGGCTTCTATCGGTGAAGAAATGTTATGCCCACGGTTCCGTACTAAAGAATGAGCCAACAGCTATCTCCTTAGCTTCTTAAGGCACTCTTTTTCTGTTTAGTTATTGGTAATCCATCCGAGTGATCTATCTTATCGATAAAGAAATTCTCTCCCCTTACCGATCTTGTTATGCCTCCCGCGGTACATACAAAGGAACCTTCTATCCCATCGGTTAATCAAAGAAATTAGGTGCTCCTACGCCTGAAGTTATCGGTGAAGGCTTCCCCTCCATTTGATCTGTAGGATATCGAGTTTTCTTACCGCCTCTATCGGCTATGGGATATGCAATTCTCTTCTCTGACTTAACACAGAGCAAAGTAGACTGATTTCGCGCTAGTGCTAGTACACGAGTAGACCGCTTTCACCTAGCTATTGCTCACTAACAGAACCTTCTCGTACTGGAGAAAAGAACTTGAGCTCTGCTTCGAGGAACTAGCAGTCGAAGGGTGACGATTTCTGATCACTGGATTCAAGAGCTTTTAGGGTGTTCGGAACAGTTATTAGTAGAAGATAAGACTTTCTCGGCTTGTTTACTAAGTCTCTGATTCGAATAAGCGACTCGGAACTCTGTTCGCGGTTAGCTGAGAATGTTCTTGCTTCTTGCCAGTTAGATTAGCTTGAAAGGGAATGAGTGAGTCGAAAGTATGACAACGGGCATAGATAGAGGAGTTCCTGATCCCGGTACTAGGGCGAATGGCATAACTGCTTCTTTCTCTTTTTACGGGTAGAATCCGCTATAGTTGAGGAAGCCCAGAGATGAGGATAAAATCTCTTGTTTAAGAAGCAACTCATGTTTCAGG

Transforming genomes of information into knowledge

Biologist

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•Transfer•Storage•Analysis•Visualization•Metadata Mark-up•Search and Discover•Share/Collaborate•Publish

Cyberinfrastructure for Plant Sciences(and Beyond):

ScalableCapable

Extensible

Cyberinfrastructure for Plant Sciences(and Beyond):

ScalableCapable

Extensible

Cyberinfrastructure Philosophy

• iPlant’s CI uses the pillars of CIF21

–High Performance Computing

–Data and Data Analysis

–Virtual Organization (VO)

–Learning and Workforce

• iPlant is a shining example of a VO for CI creation, delivery and support.

What is Cyberinfrastructure?Connecting Scientists and Computation

• Experimental Verifiability, Reproducibility, and Provenance• User Identity Management (Collaborative trust)• Connections Between Resources• Multiple Access Levels• Facilitate Collaborations

Democratizing Supercomputing for ResearchLiberating High-Throughput Data Acquisition

• Integrate• Software• Data

• Scalable • Data Management • Computing Resources

EndUsers

ComputationalUsers

iPlant Layered Services and Access

TeraGridXSEDE

iPlant Discovery Environment

Managing and Integrating: Data, Tools, Analysis

Tool Integration and Publication

iPlant Data StoreFree Your Data

Different Users, Different Access Needs:

One Data Store

Different Users, Different Access Needs:

One Data Store

iPlant Data StoreFree Your DataWebDAV DE

i-commands iDrop

APIiPlant Data Store

Desktop FolderDiscovery EnvironmentCommand Line (HPT)

i-Drop (HPT)API

iPlant Data StoreDesktop Folder

Discovery EnvironmentCommand Line (HPT)

i-Drop (HPT)API

Atmosphere: Servers and Software on Demand

Use Your iPlant Credentials

http://atmosphere.iplantcollaborative.org

Atmospherehttp://atmosphere.iplantcollaborative.org

AtmospherePlus VNC

AtmosphereNew Images

Dear iPlant staff,

I have a running instance that has a few mainstream genome assemblers and gene prediction pipeline installed. The details are as below. Would you please create an image from this running instance? I'd like to talk about this during the upcoming iPlant workshop at PAG. Thanks ~1.Username: tanghaibao2.IP Address of the instance: 128.196.142.173.Name of the Image: TwigToGenome4.Description of the Image: This image includes three genome assemblers, a gene annotation pipeline and several visualization tools. The VM image is intended for researchers who start with raw reads, and follow a standard pipeline of preparation, assembly, annotation and visualization for genomic data.5.List installed software: CABOG (v7.0-prerelease)/ALLPATHS-LG (v40173)/SOAPdenovo (v1.05) installed in /usr/local/packages and symlinked in /usr/local/bin; MAKER (v2.11) in /opt/maker; SNAP/BLAST/REPEATMASKER/EXONERATE installed as part of MAKER; GENEMARK(v2.8a)/AUGUSTUS(v2.5.5) installed in /usr/local/packages and symlinked in /usr/local/bin; Python modules in /usr/lib/python26/site-packages (on default search path of python26). The image is built on top of image "New NGS viewers".6.Unmount EBS Volumes: I had vol-9B430876 mounted in /data/ during testing. Currently unmounted.7.iPlant-managed System Files: n/a8.Image Tags: assembly, annotation, visualization, pipeline, twig to genome, jcvi, allpaths, soapdenovo, cabog, maker9.Do you want the visibility of the image to be private, public, or select users?: Publicly visible.--Haibao Tang, Ph. D.Senior Bioinformatics EngineerJ. Craig Venter Institute9704 Medical Center Dr. Rockville, MD, 20850Office Phone: 301-795-7841; Fax: 301-795-7070

Dear iPlant staff,

I have a running instance that has a few mainstream genome assemblers and gene prediction pipeline installed. The details are as below. Would you please create an image from this running instance? I'd like to talk about this during the upcoming iPlant workshop at PAG. Thanks ~1.Username: tanghaibao2.IP Address of the instance: 128.196.142.173.Name of the Image: TwigToGenome4.Description of the Image: This image includes three genome assemblers, a gene annotation pipeline and several visualization tools. The VM image is intended for researchers who start with raw reads, and follow a standard pipeline of preparation, assembly, annotation and visualization for genomic data.5.List installed software: CABOG (v7.0-prerelease)/ALLPATHS-LG (v40173)/SOAPdenovo (v1.05) installed in /usr/local/packages and symlinked in /usr/local/bin; MAKER (v2.11) in /opt/maker; SNAP/BLAST/REPEATMASKER/EXONERATE installed as part of MAKER; GENEMARK(v2.8a)/AUGUSTUS(v2.5.5) installed in /usr/local/packages and symlinked in /usr/local/bin; Python modules in /usr/lib/python26/site-packages (on default search path of python26). The image is built on top of image "New NGS viewers".6.Unmount EBS Volumes: I had vol-9B430876 mounted in /data/ during testing. Currently unmounted.7.iPlant-managed System Files: n/a8.Image Tags: assembly, annotation, visualization, pipeline, twig to genome, jcvi, allpaths, soapdenovo, cabog, maker9.Do you want the visibility of the image to be private, public, or select users?: Publicly visible.--Haibao Tang, Ph. D.Senior Bioinformatics EngineerJ. Craig Venter Institute9704 Medical Center Dr. Rockville, MD, 20850Office Phone: 301-795-7841; Fax: 301-795-7070

How to get access:www.iplantcollaborative.org

iPlant APIsResources

Cyberinfrastructure for Life SciencesScalableCapable

Extensible

Cyberinfrastructure for Life SciencesScalableCapable

Extensible

iPlant’s Building Blocks

Metadata Data Tools Workflows Viz

Staff:Greg AbramSonali AdityaRoger BarthelsonBrad BoyleTodd BryanGordon BurleighJohn CazesMike ConwayKaren CranstonRion DoodeyAndy EdmondsDmitry FedorovMichael GattoUtkarsh GaurCornel GhibanMichael GonzalesHariolf HäfeleMatthew Hanlon

iPlant’s Building Blocks

Metadata Data Tools Workflows Viz

Executive Team:Steve GoffDan Stanzione

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 Gregory Yekatarina KhartianovaMonica Lent Amgad Madkour

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

Andrew LenardsZhenyuan LuEric LyonsNaim MatasciSheldon McKayRobert McLayAngel MercerDave MicklosNathan MillerSteve Mock Martha NarroPraveen NuthulapatiShannon OliverShiran PasternakWilliam PeilTitus PurdinJ.A. Raygoza GarayDennis RobertsJerry Schneider

Anthony HeathBarbara HeathMatthew Helmke Natalie HenriquesUwe HilgertNicole HopkinsEun-Sook JeongLogan JohnsonChris JordanB.D. KimKathleen KennedyMohammed KhalfanSeung-jin KimLars KoersterkSangeeta KuchimanchiKristian KvilekvalAruna LakshmananSue LauterTina Lee

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

Aniruddha MaratheKurt MichaelsDhanesh PrasadAndrew PredoehlJose SalcedoShalini SasidharanGregory StriemerJason VandeventerKuan Yang

Postdocs:Barbara BanburyJamie EstillBindu JosephChristos Noutsos Brad RuhfelStephen A. SmithChunlao TangLin WangLiya WangNorman Wickett

Comments• Emphasize:–Scalable

–Extensible

• Getting introduction–Quick start guide

–wiki

– forums

• Last slide: link to resources

• Emphasize what CI gets us

• Dress up the list of stuff slides–Less words, more animation/images

• More bullet points for other people to know the walk away message–Work with Dan

1 iPlant: Cyberinfrastructure for Plant Sciences (and Beyond) Your Name Here 1.

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