J. Li, S. Ranka, S. Sahni
We develop cache efficient, multicore, and GPU algorithms for RNA folding using Nussinov’s equations. Our cache efficient algorithm provides a speedup between 1.6 and 3.0 relative to a naive straightforward single core code. The multicore version of the cache efficient single core algorithm provides a speedup, relative to the naive single core algorithm, between 7.5 […]
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Harry A Stern, David H Mathews
BACKGROUND: RNA performs many diverse functions in the cell in addition to its role as a messenger of genetic information. These functions depend on its ability to fold to a unique three-dimensional structure determined by the sequence. The conformation of RNA is in part determined by its secondary structure, or the particular set of contacts […]
Thierry Coppey
Dynamic programming is an algorithmic technique to solve problems that follow the Bellman’s principle: optimal solutions depends on optimal sub-problem solutions. The core idea behind dynamic programming is to memoize intermediate results into matrices to avoid multiple computations. Solving a dynamic programming problem consists of two phases: filling one or more matrices with intermediate solutions […]
Sean O. Settle
Field programmable gate arrays (FPGAs) provide reconfigurable computing fabrics that can be tailored to a wide range of time and power sensitive applications. Traditionally, programming FPGAs required an expertise in complex hardware description languages (HDLs) or proprietary high-level synthesis (HLS) tools. Recently, Altera released the worlds first OpenCL conformant SDK for FPGAs. OpenCL is an […]
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Konstantin Berlin, Nail A. Gumerov, Ramani Duraiswami, David Fushman
Small Angle Scattering (SAS) of X-rays or neutrons is an experimental technique that provides valuable structural information for biological macromolecules under physiological conditions and with no limitation on the molecular size. In order to refine molecular structure against experimental SAS data, ab initio prediction of the scattering profile must be recomputed hundreds of thousands of […]
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Matthias Alexander Lee
The aim of this project is to explore the possible application of Graphics Processors (GPUs) to accelerate and speed up sequence alignment by Fourier-space cross-correlation. Aligning signals using cross-correlations is a well studied approach in the world of signal processing, but has found relatively little reception in the realm of computational genomics. As long as […]
Balaji Venkatachalam, Yelena Frid, Dan Gusfield
The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n^3) time using dynamic programming. Four-Russians is a technique that will reduce the running time for certain dynamic programming algorithms by a factor after a preprocessing step where solutions to all […]
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Andrew J. Proctor, Tyson J. Lipscomb, Anqi Zou, Joshua A. Anderson, Samuel S. Cho
Molecular dynamics (MD) simulations provide a molecular-resolution physical description of the folding and assembly processes, but the size and the timescales of simulations are limited because the underlying algorithm is computationally demanding. We recently introduced a parallel neighbor list algorithm that was specifically optimized for MD simulations on GPUs. In our present study, we analyze […]
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Bhardwaj Aditi, Bhardwaj Rohatash K., Shishir K. Gangwar
Parallel processing is a form of computation in which many calculations are carried out simultaneously, operating on the principle that large problems can often be divided into smaller ones, which are then solved concurrently. Parallelism has been employed for many years, mainly in high-performance computing. As power consumption by Computer has become a concern in […]
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Tyson J. Lipscomb
Protein and RNA biomolecular folding and assembly problems have important applications because misfolding events are associated with diseases like Alzheimer’s and Parkinson’s. However, simulating biologically relevant sized biomolecules on timescales that correspond to biological functions is an extraordinary challenge due to computational bottlenecks that are mainly involved in force calculations. We briefly review the molecular […]
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Guoqing Lei, Yong Dou, Wen Wan, Fei Xia, Rongchun Li, Meng Ma, Dan Zou
BACKGROUND: Prediction of ribonucleic acid (RNA) secondary structure remains one of the most important research areas in bioinformatics. The Zuker algorithm is one of the most popular methods of free energy minimization for RNA secondary structure prediction. Thus far, few studies have been reported on the acceleration of the Zuker algorithm on general-purpose processors or […]
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Jean-Stephane Varre, Bertil Schmidt, Stephane Janot, Mathieu Giraud
Mining the increasing amount of genomic data requires having very efficient tools. Increasing the efficiency can be obtained with better algorithms, but one could also take advantage of the hardware itself to reduce the application runtimes. Since a few years, issues with heat dissipation prevent the processors from having higher frequencies. One of the answers […]
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Free GPU computing nodes at hgpu.org

Registered users can now run their OpenCL application at hgpu.org. We provide 1 minute of computer time per each run on two nodes with two AMD and one nVidia graphics processing units, correspondingly. There are no restrictions on the number of starts.

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Node 1
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  • RAM: 12GB
  • OS: OpenSUSE 11.4
  • SDK: AMD APP SDK 2.8
Node 2
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  • CPU: Intel Core i7-2600 @ 3.4GHz
  • RAM: 16GB
  • OS: OpenSUSE 12.2
  • SDK: nVidia CUDA Toolkit 5.0.35, AMD APP SDK 2.8

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