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 quarterly as project teams evaluate deliverables and milestones. Below are the most current deliverables.

Deliverables For Q4 2017

[1.2] APIs: Integrate with CyVerse Search API; Develop web-based application and systems manager; Develop support for Agave to adopt Jetstream Cloud for hosting environment; Develop support for Common Workflow Language; Integrate End-of-Day workflow system into "Reactions" API; Develop support for Globus Online transfers and storage; Implement Functions-as-a-Service via Reactors API; Implement Agave- and Data Store-integrated JupyterHub; Add support for Jetstream to CyVerse SDK; Add support to SDK for new XSEDE and TACC HPC; Add support for Atmosphere to SDK; Add support for Jetstream to CyVerse SDK; Develop real-time analytics tutorial; Create Heroku buildpack for Agave-to-Go; Develop support for Singularity containers; Integrate with BioConda.

[1.3] DE: Develop ontology-based metadata management.

[1.4] BisQue: Refine compatibility with CyVerse Data Store; Integrate with Atmosphere/Docker for algorithm development; Develop support for offloading computation via CyVerse Science APIs; Implement QA testing on BisQue releases; Develop support for file rename, move, delete actions initiated from the BisQue interface by users to be reflected in iRODS; Improve support for user-integrated algorithms in BisQue; Develop support for machine learning algorithms; Enhance metadata annotation features; Improve continuous integration /deployment to support rapid releases; Release version 0.6.0.

[1.5] SDI: Perform requirements analysis for SDI; Populate SDI application with environmental layers data; Integrate SDI with CyVerse Search platform; Test for quality assurance on SDI releases; Write documentation for SDI releases; Expose publicly shared spatial data for discovery via CSW; Integrate GeoNode with CyVerse SSO; Deploy CyVerse-operated GeoNode server; Create and release templates for user-created spatial data web apps; Establish and configure connections with hydrology data sets; Adopt projects and groups interface; Contribute fixes and enhancements back to GeoNode project.

[1.6] Atmosphere: Sharing of projects to other users; Develop synchronization between block storage volumes; Develop support for on-demand compute clusters; Develop Python-based Atmosphere Command Line Interface; Develop automatic search and indexing via CyVerse Search; Develop Atmosphere for persistent hosting; Migrate to OpenStack Mitaka.

[1.7] Data Store: Write rules and policy to support data preservation and archiving; Develop functions to enhance data discoverablity; Implement data organization policies and procedures; Perform routine maintenance of systems.

[1.8] Data Commons: Implement services for managing groups.

[1.9] DNA Subway: Move apps to Stampede containers.

[1.10] SciApps: Create SciApps Guide.

[2.1] Workflows: Deploy standalone NCBI BioProject registration pipeline; Deploy standalone NCBI BioSample registration pipeline; Deploy NCBI TSA system in DE; Deploy Trinity-2.4.0; Deploy READemption-2.4.3; Deploy BWA 0.7.10 app in DE; Deploy Picard 2.7.0 app in DE; Deploy BEDTools 2.26.0 app in DE; Deploy HOMER app in DE; Maize TE annotation workflow image on JetStream Cloud; Deploy RSEM on SciApps; Update Kallisto App in DE with Pseudo bam output; Ballgown App in DE with time series option; Deploy Circos app in DE; Develop and deploy validate workflow for genotype-phenotype method comparisons (Atmo images and Stampede apps); Develop rapid quality assessment for drone data from ag field phenotyping; Develop GIS and Spatial Data Analysis on Jetstream; Develop Singularity Containers for GIS on Atmo and JS; Deploy AISO (Annotation of Image Segments with Ontologies) tool integrated into Bisque (ECS).

[2.2] Data: Host a dataset containing raw and processed results and other data for a manuscript on Sorghum encode project; Host the SeedAdapt data set; Host a dataset containing raw and processed results and other data for a manuscript on Oryza Genome Evolution Project; Host Genomes to Fields (G2F) field data.

[3.0] EOT: Hold SC workshop in Tucson, AZ; Attend Cotton Inc. Cotton Breeders Tour; Hold workshop on Bioinformatics tools for Plant Genomics, CSH, NY; Hold webinar: Data Store; Hold webinar: Leveraging CyVerse for Large-scale Spatial Analysis. Maintain EOT workshop and webinar schedule. Continue implementation of the Campus Helpers program.

[4.0] Support: Continue effort towards identifying and completing Community Support, ECS, and Powered by CyVerse projects. Continue user support and consulting services. Continue operational support for physical and software infrastructure.