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Deliverables by Quarter

Q2-2017

Science APIs

Rewrite job and data scheduling to enhance concurrency and resiliency. Develop web-based application and systems manager. Develop support for Agave to adopt Jetstream Cloud for hosting environment. Develop support for Common Workflow Language. Support streaming HTTP websockets. Add support for Jetstream to CyVerse SDK. Add support to SDK for new XSEDE and TACC HPC. Implement Jupyter Notebooks service connected to APIs. Add self-updating capability to CyVerse SDK. Add support for DE APIs to CyVerse SDK. Add support for Jetstream to CyVerse SDK. Develop microsites tutorial. Add status check command to CyVerse SDK connected to CyVerse status.io. Develop support for commercial cloud compute providers. Develop Groups API.

Discovery Environment

Allow the DE to launch JetStream virtual machines and run jobs on it. Develop NCBI Genome submission pipeline.

BisQue

Begin developing interface allowing user annotation of public images.

SDI

Begin integration of SDI with CyVerse Search platform; adopt projects and groups interface.

Atmosphere

Develop automatic search and indexing via CyVerse Search. Develop bare-metal provisioning.

Data Store

Write rules and policy to support data preservation and archiving. Develop data sub-setting for genomics data. Perform routine maintenance of systems.

Data Commons

Develop support for landing page for data sets for DOIs. Deploy submission pipeline to NCBI Genome Assembly. Develop landing pages for data collections.

DNA Subway

Deploy “Green Line” through Agave hosted on CUNY or other clusters. Enable users to partition genome into projects. Enable users to assign genome segments to individual annotators. Enable users to add or refine annotation on assigned genome segments. Develop a proof of concept workflow based on dockerized apps available through Agave/AWS (Green Line).

SciApps

Adding SciApps as a CyVerse service, and CyVerse authentication. Support chaining any Agave Apps by pulling data from DataStore (UA) to CSHL. Deploy Desq2 differential expression tool. Implement tool to autobuild track hubs for biodalliance. Build ChIP-Seq workflow on CyVerse.

Scientific Workflows

Deploy MultiQC in the DE for advanced visualization of read files. Deploy Blastp 2.2.29. Add GO to Blastp-Uniprot. Deploy Blastp_a_subset_of_uniprot.

Data

Host a dataset containing raw and processed results and other data for a manuscript on Sorghum encode project.

Datasets

Develop metadata template for ENCODE-like projects. Develop guidelines for genome sequence quality assessment.

Education, Outreach, and Training

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

Support

Continue effort toward 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.