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Deliverables by Quarter

Q3-2017

Science APIs

Integrate with CyVerse Search API. Adopt CyVerse common usage logging framework. Integrate ADAMA API publishing framework from Araport.org. Develop integration with cloud-based messaging systems like Amazon SNS. Integrate with CyVerse persistent identifier service. Develop command-line and SDK tooling to let users work with metadata. Integrate End-of Day workflow system with Common Workflow Language (CWL). Support streaming HTTP websockets. Develop support for Box.com storage. Develop support for Dropbox storage. Develop support for automatic command line generation in apps service. Implement Functions-as-a-Service via Reactors API. Implement Agave- and Data Store-integrated JupyterHub. Develop tutorials illustrating use of all CyVerse APIs together. Develop reconfigurable Agave desktop clients. Develop campus HPC system enrollment tutorials. Develop Agave-to-Go tutorial and training material. Develop support for Singularity containers. Integrate with BioConda. Develop "publish from Github" model for apps. Implement interactive landing page for browser-based access to API URLs.

Discovery Environment

Implement services for managing groups, projects, and tags. Implement interfaces to coordinate, manage, and analyze data, tasks, and results. Develop provenance UI.

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 initatied 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. Develop support for bulk metadata operations. Enhance metadata annotation features. Improve continuous integration /deployment to support rapid releases. Release version 0.6.0.

Spatial Data Infrastructure

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.

Atmosphere

Sharing of projects to other users. Implementation of rules engine for allocations and quotas. Develop DOI issuance for VMs. Develop mechanisms to publish VMs to document repositories. Develop Python-based Atmosphere Command Line Interface. Implement services for managing groups, projects, and tags. Implement interfaces to coordinate, manage, and analyze data, tasks, and results. Develop automatic search and indexing via CyVerse Search. Develop Atmosphere for persistent hosting. Implement localization integration.

Data Store

Support content indexing. Write rules and policy to support data preservation and archiving. Automate verification of backups and replicas. Optimize general subset request performance. Develop functions to enhance data discoverablilty. Implement services for managing groups. Script deployment and upgrades of data store services. Make diagnostic information searchable. Implement internal documentation maintenance policies and procedures.

Data Commons

Develop support for landing page for data sets for DOIs. Request existing data sets to include minimum metadata. Implement services for managing groups. Implement omnibar and faceted search across all data collections.

DNA Subway

Enable users to combine distributed annotations into a navigable ‘master’ project. Develop a proof of concept workflow based on dockerized apps available through Agave/AWS (Green Line). Assemble QIIME pipeline in containers.

SciApps

Enable interactive workflow diagram for metadata retrievement. Support chaining Agave Apps running at TACC. Add usage statistics. Delpoy Shiny app for Ballgown. Implement tool to autobuild track hubs for biodalliance.

Scientific Workflows

Deploy NanoOK. Deploy Interproscan 5.20. Deploy gffreader to link Hisat2 and tophat2 to rnaQuast. Deploy vcf-validator tool on SciApps. Develop and deploy algorithms for identifying methylated regions using PacBio sequencing. Deploy ChIP seq workflow - BWA,SAMTools,Picard,HOMER,BEDTools. Deploy Trinotate 3.0.2 in the DE. Deploy KOBAS 3.0 in the DE. Deploy GOseq 1.26.0 in the DE. Deploy ontologizer 2.0 in the DE. Deploy custom script to combine outputs from DESeq2/EdgeR to input into annotation tools. Integrate InterProScan tool on Sciapps. R shiny app in DE for genome annotaiton evaluation. R shiny app in DE for differetnial expression analysis pacakges Ballgown, Sleuth & DESeq2. 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. Develop rapid quality assessment for drone data from ag field phenotyping. Deploy BIEN species range modelling on Jetstream. Develop GIS and Spatial Data Analysis on Jetstream. Develop sUAS field data pipeline to DataStore.

Data

Host a dataset containing raw and processed results and other data for a manuscript on Sorghum encode project. Host the EpiDB livestock community genomic and traits data. Host the SeedAdapt data set. Host Genomes to Fields (G2F) field data. Develop metadata template for ENCODE like projects. Develop plant phenotyping metadata thesaurus.

Education, Outreach, and Training

Maintain EOT workshop and webinar schedule. Continue implementation of the Campus Helpers program.

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.