6. Software engineering protips
Version everything
Test everything (and automate those tests)
Review everything
Measure everything
Engage users
7. Reproducibility
Don’t rely on a single assembly
Don’t rely on a single source of annotation
Genome sequenced twice at deep (60x) coverage,
variants ID’d; only 94% agreed
8. Web-based tools
Utilize ubiquitous browser
Most are open source, some offer VM distro
APIs and SDKs
integration
extension
programmatic access
9. A few talks of interest
Mario Stanke: comparative gene finding
Lior Pachter: RNA-Seq methods, units
Michael Snyder: integrative “Snyderome”
Sreeram Kannan: RNA-Seq assembly
Rob Patro: Sailfish
Chung-chao Hon: natural antisense transcripts