Create a platform that will allow iReceptor Plus users to run comparison and analysis pipelines on query results
Develop a tool integration mechanism for integrating advanced analysis tools into AIRR-seq analysis platforms such as the iReceptor Gateway, VDJServer, and ImmuneDB. Both iReceptor and VDJServer make use of the Tapis Science-as-a-Service platform (developed at the Texas Advance Compute Centre, University of Texas at Austin) to manage the staging of AIRR-seq data to computational analysis platforms and the management of analysis jobs on that data. Tapis provides an application specification (tool description) that defines tool inputs and parameters. We will enhance the Tapis APIs to provide complete tool descriptions (e.g., add description of tool outputs), while also incorporating standardization efforts. We will provide a tool ecosystem that provides many shared services that eliminate duplication of effort while providing greater functionality for all tools. These shared services include: (1) Tool descriptions defining inputs, parameters, and outputs that ensure tool execution is fully transparent and reproducible; (2) Automatic compilation and deployment of tool applications on multiple HPC platforms using container specification (e.g., Bootstrap Definition File for Singularity, http://singularity.lbl.gov; Dockerfile for Docker, http://www.docker.com); (3) Provenance, versioning, and publishing of tools across release cycles by encapsulating application assets with associated metadata; (4) Automatic metadata capture for tool and workflow executions; (5) Open APIs to data, tools, metadata, workflows, and visualizations; (6) User interface and programmatic access automatically generated from tool descriptions; and (7) Automatic parallelization and scalability that performs map/reduce operations. Open APIs will allow tools to act more like interoperable services, and all tools will be able to find, access, and reuse any data or metadata available within the ecosystem. Develop documentation and processes for integrating these tools into the iReceptor platforms. Implement tool integration for tools identified in Task 4.1.