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IPPS
2010
IEEE
15 years 2 months ago
pFANGS: Parallel high speed sequence mapping for Next Generation 454-roche Sequencing reads
Millions of DNA sequences (reads) are generated by Next Generation Sequencing machines everyday. There is a need for high performance algorithms to map these sequences to the refer...
Sanchit Misra, Ramanathan Narayanan, Wei-keng Liao...
IPPS
2010
IEEE
15 years 2 months ago
Exploring parallelism in short sequence mapping using Burrows-Wheeler Transform
Next-generation high throughput sequencing instruments are capable of generating hundreds of millions of reads in a single run. Mapping those reads to a reference genome is an ext...
Doruk Bozdag, Ayat Hatem, Ümit V. Çata...
IPPS
2010
IEEE
15 years 2 months ago
Dynamic analysis of the relay cache-coherence protocol for distributed transactional memory
Transactional memory is an alternative programming model for managing contention in accessing shared in-memory data objects. Distributed transactional memory (TM) promises to alle...
Bo Zhang, Binoy Ravindran
IPPS
2010
IEEE
15 years 2 months ago
Improving the performance of Uintah: A large-scale adaptive meshing computational framework
Abstract--Uintah is a highly parallel and adaptive multiphysics framework created by the Center for Simulation of Accidental Fires and Explosions in Utah. Uintah, which is built up...
Justin Luitjens, Martin Berzins
IPPS
2010
IEEE
15 years 2 months ago
MMT: Exploiting fine-grained parallelism in dynamic memory management
Dynamic memory management is one of the most expensive but ubiquitous operations in many C/C++ applications. Additional features such as security checks, while desirable, further w...
Devesh Tiwari, Sanghoon Lee, James Tuck, Yan Solih...
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