SUMMARY: ProteinPaint BAM track (ppBAM) is designed to assist variant review for cancer research and clinical genomics. With performant server-side computing and rendering, ppBAM supports on-the-fly variant genotyping of thousands of reads using Smith-Waterman alignment. To better visualize support for complex variants, reads are realigned against the mutated reference sequence using ClustalO. ppBAM also supports the BAM slicing API of the NCI Genomic Data Commons (GDC) portal, letting researchers conveniently examine genomic details of vast amounts of cancer sequencing data and reinterpret variant calls. AVAILABILITY AND IMPLEMENTATION: BAM track examples, tutorial, and GDC file access links are available at https://proteinpaint.stjude.org/bam/. Source code is available at https://github.com/stjude/proteinpaint.

Graphic processing unit (GPU)-based general-purpose computing is developing as a viable alternative to CPU-based computing in many domains. Today’s tools for GPU analysis include simulators like GPGPU-Sim, Multi2Sim, and Barra. While useful for modeling first-order effects, these tools do not provide a detailed view of GPU microarchitecture and physical design. Further, as GPGPU research evolves, design ideas and modifications demand detailed estimates of impact on overall area and power. Fueled by this need, we introduce MIAOW (Many-core Integrated Accelerator Of Wisconsin), an open-source RTL implementation of the AMD Southern Islands GPGPU ISA, capable of running unmodified OpenCL-based applications. We present our design motivated by our goals to create a realistic, flexible, OpenCL-compatible GPGPU, capable of emulating a full system. We first explore if MIAOW is realistic and then use four case studies to show that MIAOW enables the following: physical design perspective to “traditional” microarchitecture, new types of research exploration, and validation/calibration of simulator-based characterization of hardware. The findings and ideas are contributions in their own right, in addition to MIAOW’s utility as a tool for others’ research.