BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Fast Hands-free Writing by Gaze Direction

We describe a method for text entry based on inverse arithmetic coding that relies on gaze direction and which is faster and more accurate than using an on-screen keyboard. These benefits are derived from two innovations: the writing task is matched to the capabilities of the eye, and a language model is used to make predictable words and phrases easier to write.

Probabilistic inference for fast learning in control

A novel framework is provided for very fast model-based reinforcement learning in continuous state and action spaces. It requires probabilistic models that explicitly characterize their levels of condence. Within the framework, exible, non-parametric models are used to describe the world based on previously collected experience. It demonstrates learning on the cart-pole problem in a setting where very limited prior knowledge about the task has been provided. Learning progressed rapidly, and a good policy found after only a small number of iterations.