Ecosystems
One school of thought toward aiding in reproducibility is that of creating complete software and data ecosystems. By enforcing a complete stack, these services ensure software interoperability, make data integration easier, provide an easy means of reproducing pipelines, and lower the barrier of entry in terms of computational skills. Detractors would point out that closed stacks hinder cutting edge research, reliance on centralized services risks obsolesence, private services might not be trustworthy data stewards, and virtualization solutions hinder software remixability. Regardless, complete ecosystems have gained considerable traction in some niches, particularly services like galaxy.
Complete Software Ecosystems
- Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor try to support and enables reproducible reasearch through the use of vignettes.
- Biostars - A Q&A portal for bioinformatics.
- Docker - Software executable environment and delivery: software versioning, provenance, packaging, IO metadata. If docker containers will also be delivered with a vignette, like the one enforced by the Bioconductor, then it can become a powerful ecosystem.
- Bio-Linux - Biology-targeted linux distro
- Galaxy - Fully integrated pipelining, data hosting, compute resources on many diff HPC platforms
Cloud based ecosystems
-BaseSpace -DNANexus -Synapse -GeneStack -batlab - Cross-platform automated software testing -Cytoscape