Objectives & Deliverables

New Features, New Science

CyVerse strives to create an innovative, comprehensive, generic, and foundational cyberinfrastructure (CI) in support of life science research. CyVerse develops CI that uniquely enables scientists across the diverse fields that comprise life sciences to address Grand Challenge questions in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of CI in research and education.

This page is updated as project teams evaluate deliverables and milestones. Below are the most current deliverables.

Deliverables For Project Year 4 (2021-2022)

[1.1] General O&M: Continue efforts to operate and maintain the infrastructure.
●    Maintain general operations and maintenance
●    Maintain staging environment for pre-release Data Store code
●    Extend user portal to monitor and manage usage

[1.2] Data Store: 
●    Extend ELK stack to obtain consumption metrics and platforms to deposit consumption data
●    Implement failover policies between UArizona and TACC
●    Improve monitoring and reporting on network performance, resource consumption per user, team level
●    Improve usability of Data Store (quality of service, uptime, sharing of resources, safe guards for users) 
●    Manage Data Access (distributed data, edge computing assets, external client access)
[1.3] Atmosphere: 
●    Maintain support for special projects

[1.4.1] Discovery Environment: 
●    Improve DE architecture to support increased volume of jobs
●    Test for quality assurance on DE release
●    Author documentation on DE release
●    Fix various minor bugs
●    Author DE Public API Documentation

[1.4.2] BisQue:
●    Provide improved support for API based access

[1.4.3] Visual Interactive Computing Environment:
●    Implement integration with TAPIs and HPC execution environment

[1.5] APIs: 
●    Develop automated usage monitoring for paid cloud storage
●    Develop automated usage management for paid cloud storage

[2.1] ECP: Continue to nurture extended community partnerships, including:
●    Partner with Legume Federation
●    Partner with Chequamegon Heterogeneous Ecosystem Energy-balance Study Enabled by a High-density Extensive Array of Detectors (CHEESEHEAD19)
●    Support the GenoPhenoEnvo project with data hosting and analyses
●    Support HydroGen project for next generation hydrology modeling

[2.3] Tools and Workflows:
●    Integrate whole genome shotgun (WGS) NCBI submission pipelines in DE (Legume Federation will test).  
●    Integrate tools to support long-read sequencing technologies
●    Integrate tools to support non-coding RNA analysis
●    Deploy tools for RNAseq analysis
●    Deploy tools for metagenomic analysis
●    Deploy tools for genomic analysis
●    Deploy tools for gene functional annotation
●    Integrate tools for ChIP-seq analysis
●    Integrate tools for Single-cell analysis
●    Development of Visual Interactive Computing Environment (VICE)
●    Enable analysis with GPUs in DE
●    Enable machine learning technologies
●    Teach partners to integrate workflows in CyVerse
●    Write peer-reviewed paper on CyVerse
●    Scale up workflows to handling 1000s of SRA entries for lncRNA identification (New NSF grant)

[2.4] Data Commons: 
●    Publish large datasets quarterly for Vertnet biodiversity data
●    Make Genomes 2 Fields data available for phenotype prediction on CyVerse, provide stable identifier
●    Make sorghum high throughput phenotyping datasets public in CyVerse where they can be analyzed
●    Assist with specifying metadata requirements
●    Assist with data publishing through canonical repositories
●    Assist with data organization and formatting for data published through Data Commons
●    Specify requirements for enhanced ontology-based metadata management
●    Enhance metadata entry capabilities via API

[2.5] Documentation and Templates:
●    Develop documentation for using tools and workflows
●    Integrate example data for using tools and workflows
●    Make metadata templates
●    Share and develop best practices with community projects

[2.6] Adoption (LOCs, Confs, Support, Pubs):
●    Provide Letters of Collaboration for researchers
●    Participate at domestic and international conferences (anticipate 2-4 talks/posters per year)
●    Monitor and respond to user tickets -- Limited Support
●    Provide interactive user support via chat (during business hours) -- Limited Support
●    Write and publish manuscripts on Cyverse Platform

[3.0] EOT: 
●    Collaborate on training with CyVerse partners
●    Develop community-driven learning materials on unmet needs (integration of multiple data types, metadata management, and scaling analyses to cloud/HPC)
●    Provide training and support for developers
●    Provide introductory training to the CyVerse platforms
●    Deliver community engagement, collect user feedback, and develop collaborations at conferences and meetings
●    Collaborate with Open Science Training Efforts and Training Missions of CyVerse partners
●    Provide training in basic computing and data management
●    Publish training materials that support virtual learning
●    Deliver in-depth training through CyVerse Learning portal

[4.0] Admin:
●    Execute responsibilities as Principal Investigator
●    Execute responsibilities as Executive Team
●    Execute responsibilities of Project Teams (CI, Science, Training)