This example demonstrates a fully-functional walk-through as of the last iPlant/Cartogratree funding cycle.
The SSWAP server is servicing requests, but changes to underlying web services and sites mean that some steps may no longer engage or may return alternative page views.
This page documents how SSWAP semantically integrates data and services across sites.
TreeGenes provisions a public repository for forest tree genetic data recorded from high-throughput genomics projects and has maintained valuable legacy Sanger data for over 15 years. The database provides a foundation for sequence data including genotypes, annotations, sequence assemblies, and genetic maps. TreeGenes houses information for over 1,200 forest tree species, 900,000 sequences, 24,000,000 genotypes, and 19,000 phenotypes.
XSEDE is the National Science Foundation funded Extreme Science and Engineering Discovery Environment.
Here, we show how we start with IDs of contiguous lengths of DNA sequences ("contig" IDs) associated with "copper ion binding" from TreeGenes, gather data from those contigs back to their underlying tree samples, view and select on the samples geospatially, refine a selection of their genomes to those areas functionally associated with copper ion binding, then align those sequences to view their evolutionary relatedness.