1. CyVerse Tools and Services
Jason Williams – Education, Outreach, Training Lead
Cold Spring Harbor Laboratory
@JasonWilliamsNY

2. Transforming science through data-driven discovery
CyVerse vision
Transforming science through data-driven discovery
More than 40K users, PBs of data, and hundreds of publications, courses, and discoveries

3. CyVerse evolution iPlant 2013 CyVerse 2016 Cyberinfrastructure for
Life Sciences
funding renewal
CyVerse 2016
Transforming Science Through Data-Driven Discovery
iPlant 2008
Empowering a
New Plant Biology
2017
2006
public launch
2010
2015

4. CyVerse growth: user accounts

5. CyVerse growth: publications/acknowledgements

6. Community-focused cyberinfrastructure
Platforms, tools, datasets Storage and compute Training and support

7. CyVerse is built for data
Microbial Plant Animal Biomedical Ecological
Sequence Images Other datatypes

8. CyVerse product stack Ease of Use Flexibility Ready to use Platforms
Foundational Capabilities
Established CI Components
Extensible Services

9. Data Store Initial 100 GB allocation – TB allocations available
The resources you need to share and manage data with your lab, colleagues and community
Initial 100 GB allocation – TB allocations available
Automatic data backup
Easy upload /download and sharing
Focus here is on genomics data, but not restricted to genomics data

10. Data lifecycle support
Discovery
Upload
Data Commons Repository (DCR), Elasticsearch
Discovery Environment, iCommands, Cyberduck
Metadata
Add, delete, copy; metadata templates; bulk metadata
Publication
Analysis
Data Commons Repository (DCR), NCBI-SRA
Discovery Environment, Atmosphere, Agave API, BisQue, DNA Subway
Sharing
Community Data folders, Data Commons, quick share links

11. Discovery Environment
Hundreds of bioinformatics Apps in an easy-to-use interface
A platform that can run almost any bioinformatics application
Seamlessly integrated with data and high performance computing
User extensible – add your own applications
Focus here is on genomics data, but not restricted to genomics data

12. Sequence Read Processing
Example Workflows
Sequence Read Processing
Data Publication
HTProcess
SRA Submission
Data Commons
Assembly
Genome
Transcriptome
Variation Analysis
Assembly Analysis
Genome Annotation
Association
Association Pipeline
Validate Pipeline
RNA-Seq
Methylation
Discovery Environment
Agave API
Atmosphere

13. Atmosphere Simple: Access to hundreds of virtual machine images
Cloud computing for the life sciences
Simple: Access to hundreds of virtual machine images
Flexible: Fully customize your software setup
Powerful: Integrated with CyVerse computing and data resources
Focus here is on genomics data, but not restricted to genomics data

14. On-demand Cloud CyVerse Cloud Atmosphere Instance (virtual machine)
(Disk + CPU + Memory) + (Image)
CyVerse Cloud
Atmosphere Instance
(virtual machine)

15. Science APIs Science-as-a-service platform
Fully customize CyVerse resources
Science-as-a-service platform
Define your own compute, and storage resources (local and CyVerse)
Build your own app store of scientific codes and workflows
Focus here is on genomics data, but not restricted to genomics data

16. API-enabled federation
RENCI
CSHL
NASA
Powered by
CyVerse
Arizona
TACC

17. DNA Subway Commonly used bioinformatics tools in streamlined workflows
Educational workflows for Genomes, DNA Barcoding, RNA-Seq
Commonly used bioinformatics tools in streamlined workflows
Teach important concepts in biology and bioinformatics
Inquiry-based experiments for novel discovery and publication of data
Focus here is on genomics data, but not restricted to genomics data

18. Support for Course-Based Research Experiences

19. Bisque Secure image storage, analysis, and data management
Image analysis, management, and metadata
Secure image storage, analysis, and data management
Integrate existing applications or create new ones
Custom visualization and image handling routines and APIs
Focus here is on genomics data, but not restricted to genomics data

20. Image and GxE-driven collaboration

21. Looking ahead Future Funding: Division of Biological Infrastructure
$100 Million, 10-year investment
Year 9 of 10 (end date Sept 30, 2018)
Future Funding:
“The NSF BIO Directorate and NSF leadership are pleased with the progress
of the project, and will be inviting an application for continued funding to support advances in life science research.”
Discussions with Other Agencies and Foundations

22. Future-focused mission goals
Enable data-driven discovery:
Enable “deep” data integration and analysis
Support sophisticated data expeditions defined by users or user groups
Foster interoperability across computational resources and platforms:
Deliver CyVerse as a self contained platform to public and private sector entities
Encourage ”Powered by CyVerse
Align with other resources: Amazon, Google, NIH Commons, many other federal projects.
Train the next generation of data scientists:
Develop a sophisticated workforce for academia and industry

23. Looking ahead Transitioning to Stampede 2
This summer, high-performance computing (HPC) systems utilized by CyVerse applications will transition to Stampede2
Improved speed, memory, and overall performance
Longer wait times on these jobs till early fall

24. Looking ahead Improved user support
Live chat feature to help you when you are stuck
Project-based interfaces to help you organize data, analyses, and collaborators for a more collaborative experience.

25. Looking ahead All new CyVerse Learning Center
Improved, easier to navigate guides and tutorials
Organized through GitHub and Read-the-Docs – Easier to contribute to our documentation or make your own

26. Looking ahead Introducing SciApps
Streamlined workflows for the most common analyses needs
Extensible compute in an easy-to-navigate interface

27. CyVerse is a collaborative virtual organization
CyVerse Institutions
CyVerse is a collaborative virtual organization
CyVerse UK