SciApps

SciApps provides a cloud-based workflow platform for analysis, distribution, and management of MaizeCODE functional genomics data, including RNA-Seq, ChIP-Seq, RAMPAGE, and small RNA sequencing from maize strains B73, NC350, W22, and TIL11.

Key Features:

• Publicly Accessible Scientific Workflows: Reproducible and shareable workflows encapsulate analyses for MaizeCODE functional genomic datasets.
• RESTful API for Batch Processing: A RESTful API supports batch processing of data and metadata to manage large volumes of experiments.
• Cataloging of Experiments as Workflows: Each MaizeCODE experiment is cataloged as a reproducible workflow linked to its metadata.
• Integrated JBrowse Genome Browser Tracks: Genome browser tracks in JBrowse are linked to workflows and metadata for visualization of genomic data.
• Flexible Integration Platform: The platform supports incorporation of new analysis tools, workflows, and genomic datasets from multiple projects.
• Metadata-Driven Cloud Computation: Comprehensive metadata and a ready-to-compute cloud infrastructure enable remote execution of analyses.

Scientific Applications:

• Functional Element Annotation in Maize: Identification and analysis of functional genomic elements across tissues and strains using RNA-Seq, ChIP-Seq, RAMPAGE, and small RNA sequencing.
• Reproducible Distribution of MaizeCODE Data: Sharing raw data and analytical results as executable workflows to enable reproducible research.
• Scalable Batch Analyses: Large-scale batch processing and metadata-driven management of MaizeCODE experiments via the RESTful API and cloud compute.
• Genomic Data Visualization: Generation and linking of JBrowse tracks to support visual interpretation of experimental results and genomic features.

Methodology:

Uses reproducible, shareable workflows; exposes a RESTful API for batch processing of data and metadata; links workflows and metadata to JBrowse genome browser tracks; executes analyses on a ready-to-compute cloud infrastructure.