1. iPlant Collaborative Tools and Services Workshop iPlant Collaborative Tools and Services Workshop Overview of the iPlant Discovery Environment

2. Human Resource Bottleneck Rapidly advancing computational methods Inefficient dependence on the resident computer guru Need to liberate & empower bench scientists and bioinformaticians alike

3. Overview of the iPlant Discovery Environment Scalable platform for powerful computing, data, and application resources The DE provides: Web-based GUI High-performance computing iPlant data store Virtually limitless apps Analysis history (provenance)

4. Data Store

5. Open-Source Applications

6. >300 Open Source Applications & Counting… 6 6 Next-Gen Sequence Transcriptome Profiling Tuxedo Suite ChiP-Seq Chromatra (L&T) MACS PeakRanger Assembly Trinity ABySS Newbler SCARF SOAPdenovo Evaluation tools Aligners SOAP BLAT BWA QC & Processing FASTX FASTQC Variant detection SAMtools mpileup & bcftools VCF utilities Utilities SAMTools NCBI SRA Tool Kit BEDtools suite EMBOSS suite Next-Gen Sequence Transcriptome Profiling Tuxedo Suite ChiP-Seq Chromatra (L&T) MACS PeakRanger Assembly Trinity ABySS Newbler SCARF SOAPdenovo Evaluation tools Aligners SOAP BLAT BWA QC & Processing FASTX FASTQC Variant detection SAMtools mpileup & bcftools VCF utilities Utilities SAMTools NCBI SRA Tool Kit BEDtools suite EMBOSS suite Functional Analysis Ontologizer EMBOSS transeq EMBOSS checktrans PAGE Bayesian BiClustering EBI InterProScan (web service) GeneMania Query Runner eFP Batch Retrieve Functional Analysis Ontologizer EMBOSS transeq EMBOSS checktrans PAGE Bayesian BiClustering EBI InterProScan (web service) GeneMania Query Runner eFP Batch Retrieve QTL & GWAS TASSEL suite GBS workflow QTL Cartographer suite FaST-LMM Qxpac AntEpiSeeker Random Jungle Structure PGDSpider QTL & GWAS TASSEL suite GBS workflow QTL Cartographer suite FaST-LMM Qxpac AntEpiSeeker Random Jungle Structure PGDSpider Metagenomics MetaGeneMark MetaPhyler-SR FragGeneScan KronaTools ktlmportText MetPhlan SequenceLOGO Metagenomics MetaGeneMark MetaPhyler-SR FragGeneScan KronaTools ktlmportText MetPhlan SequenceLOGO Phylogenetics Tree Building DNANJ FastTree2 Ninja RAxML PROML PROTNJ DNAML DNAPARS PhyML Comparative Methods DACE CONTRAST Disparity Through Time CACE Evolutionary Models Ornstein-Uhlenbeck models PAML Molecular Dating w/ Penalized Likelihood Community Ecology Picante Utilitiies Subset Reference Tree TreeView Lopper Phylogenetics Tree Building DNANJ FastTree2 Ninja RAxML PROML PROTNJ DNAML DNAPARS PhyML Comparative Methods DACE CONTRAST Disparity Through Time CACE Evolutionary Models Ornstein-Uhlenbeck models PAML Molecular Dating w/ Penalized Likelihood Community Ecology Picante Utilitiies Subset Reference Tree TreeView Lopper Motif Identification DREME SequenceLOGO Motif Identification DREME SequenceLOGO RNA Prediction Infernal suite EvoFold TargetSpy miRanda PITA RNA Prediction Infernal suite EvoFold TargetSpy miRanda PITA

7. Job Monitoring (Analyses)

8. Discovery Environment Hands-on Lab

9. Discovery Environment Lab Navigate the components of the DE Access and manipulate data (upload, download, move, etc.) Start and complete an analysis Track your analysis and see your results By the end of this module you should be able to:

10. Goal: Create a multiple sequence alignment. Task 1: Download a file from the community data folder. Task 2: Upload the file to your personal data store. Task 3: Find and select the multiple sequence aligner MUSCLE and run the app. Task 4: Monitor the progress of your analysis and save parameters. Task 5: View your results. Download an input FASTA Upload FASTA to data store Create multiple Alignment with MUSCLE Monitor analysis progress Locate and view results Discovery Environment Lab

11. 1 1 4 4 3 3 2 2 1.Access to help, notifications, login/out 2.Access to data (files, results, etc.) 3.Analysis history 4.Bioinformatics apps (directory and integration) Discovery Environment Lab

12. Please login to the Discovery Environment. Follow along with the instructor Or Follow along with the handouts on your own Discovery Environment Lab

13. What happens when we need more? Rich platform for bioinformatics ~300 apps (and counting) Data co-localized with analysis Easy to use interface, with access to support More than just RNA-seq (phylogenetics GWAS, QTLs, and more Easy to integrate and customize your own tools

14. SOME AREAS NOT COVERED

15. 15 Integrating Your Own Tools

16. 16 Build A Custom Workflow

17. Market Place for Tool Development & Sharing Integrate existing open-source tools Optimize to advanced resources at XSEDE Create new tools and share Create synergy with existing tools Customize already-integrated tools Build reproducible pipelines to share with colleagues and collaborators

18. Discovery Environment Lab What’s coming next? 1.6 Release (March) Managing data links Managing collaborators Relaunching an application with parameters Sharing data with collaborators