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

Regenerative polymeric bus architecture for board-level optical interconnects

A scalable multi-channel optical regenerative bus architecture based on the use of polymer waveguides is presented for the first time. The architecture offers high-speed interconnection between electrical cards allowing regenerative bus extension with multiple segments and therefore connection of an arbitrary number of cards onto the bus. In a proof-ofprinciple demonstration, a 4-channel 3-card polymeric bus module is designed and fabricated on standard FR4 substrates. Low insertion losses (≤ -15 dB) and low crosstalk values (< -30 dB) are achieved for the fabricated samples while better than ± 6 μm -1 dB alignment tolerances are obtained. 10 Gb/s data communication with a bit-error-rate (BER) lower than 10-12 is demonstrated for the first time between card interfaces on two different bus modules using a prototype 3R regenerator. © 2012 Optical Society of America.

Polymer waveguide-based backplanes for board-level optical interconnects

Optical interconnects are increasingly considered for use in high-performance electronic systems. Multimode polymer waveguides are a promising technology for the formation of optical backplane as they enable cost-effective integration of optical links onto standard printed circuit boards. In this paper, two different types of polymer waveguide-based optical backplanes are presented. The first one implements a passive shuffle architecture enabling non-blocking on-board optical interconnection between different cards/modules, while the second one deploys a regenerative bus architecture allowing the interconnection of an arbitrary number of electrical cards over a common optical bus. The polymer materials and the multimode waveguide components used to form the optical backplanes are presented, while details of the interconnection architectures and design of the backplanes are described. Proof-of-principle demonstrators fabricated onto low-cost FR4 substrates, including a 10-card 1 Tb/s-capacity passive shuffle router and 4-channel 3-card polymeric bus modules, are reported and their optical performance characteristics are presented. Low-loss, low-crosstalk on-board interconnection is achieved and error-free (BER10 12) 10 Gb/s communication between different card/module interfaces is demonstrated in both polymeric backplane systems. © 2012 IEEE.

A polymer waveguide-based 40 Gb/s optical bus backplane for board-level optical interconnects

Optical interconnects are increasingly considered for use in high-performance electronic systems. Multimode polymer waveguides are a promising technology for the formation of optical backplanes as they enable cost-effective integration of optical links onto standard printed circuit boards. In this paper, we present a 40 Gb/s optical backplane demonstrator based on the use of polymer multimode waveguides and a regenerative shared bus architecture. The system allows bus extension by cascading multiple polymeric bus modules through 3R regenerator units enabling the connection of an arbitrary number of electrical cards onto the bus. The proof-ofprinciple demonstrator reported here is formed with low-cost, commercially-available active devices and electronic components mounted on conventional FR4 substrates and achieves error-free 4×10 Gb/s optical interconnection between any two card interfaces on the bus. © 2013 IEEE.

A 40 Gb/s optical bus for optical backplane interconnections

Optical technologies have received large interest in recent years for use in board-level interconnects. Polymer multimode waveguides in particular, constitute a promising technology for high-capacity optical backplanes as they can be cost-effectively integrated onto conventional printed circuit boards (PCBs). This paper presents the first optical backplane demonstrator based on the use of PCB-integrated polymer multimode waveguides and a regenerative shared bus architecture. The backplane demonstrator is formed with commercially-available low-cost electronic and photonic components onto conventional FR4 substrates and comprises two opto-electronic (OE) bus modules interconnected via a prototype regenerator unit. The system enables interconnection between the connected cards over four optical channels, each operating at 10 Gb/s. Bus extension is achieved by cascading OE bus modules via 3R regenerator units, overcoming therefore the inherent limitation of optical bus topologies in the maximum number of cards that can be connected to the bus. Details of the design, fabrication, and assembly of the different parts of this optical bus backplane are presented and related optical and data transmission characterisation studies are reported. The optical layer of the OE bus modules comprises a four-channel three-card waveguide layout that is compatible with VCSEL/PD arrays and ribbon fibres. All on-board optical paths exhibit insertion losses below 13 dB and intra-channel crosstalk lower than -29 dB. The robustness of the signal distribution from the bus inputs to all respective bus output ports in the presence of input misalignment is demonstrated, while 1 dB input alignment tolerances of approximately ±10 μm are obtained. The electrical layer of the OE bus modules comprises the essential driving circuitry for 1×4 VCSEL and PD arrays and the corresponding control and power regulation circuits. The interface between the optical and electrical layers of the bus modules is achieved with simple OE connectors that enable end-fired optical coupling into and out of the on-board polymer waveguides. The backplane demonstrator achieves error-free (BER < 10-12) 10 Gb/s data transmission over each optical channel, enabling therefore, an aggregate interconnection capacity of 40 Gb/s between any connected cards. © 1983-2012 IEEE.