Objectives and Deliverables

New features, more science

In the coming three months, CyVerse's team of developers and scientists will be working on improving and expanding the current cyberinfrastructure as well as developing new, exciting products.

We will release two new sets of services in the new few months: the CyVerse Data Commons and the CyVerse Science APIs. The Data Commons will be an extension of the Data Store that will support data publishing through persistent identifiers (such as DOI and ARK) as well as metadata-driven data discovery and integration. The Science APIs will give developers and bioinformaticians access to an increasing number of CyVerse core and scientific functionalities to develop novel and custom scientific applications using pieces of the CyVerse cyberinfrastructure.

A more detailed list of deliverables by quarter through 2016 is available here.

Cyberinfrastructure development

The Discovery Environment interface will undergo some modifications to improve its usability while the addition of two new major features will further expand its functionality: 1) The ability to export genomes and features to external genome browsers and 2) A more powerful visual workflow editor. The first feature will allow users to access customized views of their genome of interest. The second feature will allow CyVerse users to make use of the TACC high performance computing systems to run computationally intensive analyses outside of their own home institution.

The Atmosphere computational cloud platform will be extended with additional larger virtual machines. The increased allotment will allow CyVerse to set aside a dedicated pool for classes and workshops so that educators will be able to book these resources ahead of time and use them to support their local teaching needs. The Atmosphere user interface will also undergo some usability improvements, including a new way for users to organize and catalogue their virtual machines. Finally, one important change requested by our users is the ability to import and export virtual machines in different formats, including VirtualBox and Amazon Machine Image (AMI).

The BisQue image analysis platform will move towards a more seamless integration with the rest of the cyberinfrastructure by becoming fully compatible with the CyVerse Data Store. This will allow Bisque users to directly use the results of their image analyses in downstream workflows running in the Discovery Environment or Atmosphere. In addition, Bisque users will be able to take advantage of a new core set of image processing functions and more comprehensive documentation for algorithm authoring and integration.

Scientific Tools and Data

CyVerse will offer new scientific tools and workflows through its APIs and through the Discovery Environment. Two notable Apps to be made available are HPC-powered versions of the MAKER genome annotation tool and a user configurable BLAST. Additionally, we will release a new, improved suite of tools for variant analysis that include mrsFAST, Platypus, and a SAMtools based pipeline. Users will be able to perform micro RNA predictions using miRDeep2 and run batch Next Gen Sequencing workflows, while best-of-class Atmosphere virtual machines will be available for visual exploration of Next Gen Sequencing data and for RNA0Seq and genome annotation. Finally, users will have access to the latest Ensembl and Phytozome genome builds and to community-contributed datasets, including a dataset of quantitative traits derived from sorghum root images and libraries of plant repeats and SNAP-derived gene models to use in annotation pipelines.

Education, Outreach and Training

In support of education and training, CyVerse released an improved Learning Center as part of an overall website redesign with links to step-by-step tutorials on how to use the CyVerse cyberinfrastructure and to perform analyses. The DNA Subway educational platform has opened a new "Green Line" to introduce students to RNASeq analyses using real world examples and bioinformatics tools.