István A. Bogdán

Single Ended Pass-Transistor Logic

SPL (Single-rail Pass-transistor Logic) is one of the most promising logic styles for low power circuits. This paper examines some key issues in the implementation of SPL: swing restoration, optimum number of pass-transistor stages between buffers and SPL circuits with two supply voltages. Simulation results based on netlists extracted from layout are presented to compare SPL, CPL and standard CMOS.

Peptide Mass Fingerprinting Using Field-Programmable Gate Arrays

The reconfigurable computing paradigm, which exploits the flexibility and versatility of field-programmable gate arrays (FPGAs), has emerged as a powerful solution for speeding up time-critical algorithms. This paper describes a reconfigurable computing solution for processing raw mass spectrometric data generated by MALDI-TOF instruments. The hardware-implemented algorithms for denoising, baseline correction, peak identification, and deisotoping, running on a Xilinx Virtex-2 FPGA at 180 MHz, generate a mass fingerprint that is over 100 times faster than an equivalent algorithm written in C, running on a Dual 3-GHz Xeon server. The results obtained using the FPGA implementation are virtually identical to those generated by a commercial software package MassLynx.

Reconfigurable computing solution for Peptide Mass Fingerprinting

The paper describes a high-performance rcconfigurable computing solution for real-time peptide mass fingerprinting. The FPGA system can process the raw mass spectrum generated by a MALDI-ToF mass spectrometer and perform a search against the entire MSDB database in 240 ms. This represents an almost 2000 fold speed up compared with an equivalent software implementation in C, running on a single 3 GHz Xeon workstation.

A high-performance reconfigurable computing solution for Peptide mass fingerprinting.

High-throughput, MS-based proteomics studies are generating very large volumes of biologically relevant data. Given the central role of proteomics in emerging fields such as system/synthetic biology and biomarker discovery, the amount of proteomic data is expected to grow at unprecedented rates over the next decades. At the moment, there is pressing need for high-performance computational solutions to accelerate the analysis and interpretation of this data.Performance gains achieved by grid computing in this area are not spectacular, especially given the significant power consumption, maintenance costs and floor space required by large server farms.This paper introduces an alternative, cost-effective high-performance bioinformatics solution for peptide mass fingerprinting based on Field Programmable Gate Array (FPGA) devices. At the heart of this approach stands the concept of mapping algorithms on custom digital hardware that can be programmed to run on FPGA. Specifically in this case, the entire computational flow associated with peptide mass fingerprinting, namely raw mass spectra processing and database searching, has been mapped on custom hardware processors that are programmed to run on a multi-FPGA system coupled with a conventional PC server. The system achieves an almost 2,000-fold speed-up when compared with a conventional implementation of the algorithms in software running on a 3.06 GHz Xeon PC server.