In the last years, bioinformatics and, more generally speaking,
computational biology have crossed the borders of universities and
basic-research institutes to enter in the palette of tools used in
pharmaceutical and biotechnological industries. Such a migration
implies also that bioinformatics and computational biology (BCB) tools
should respond to industrial requirements such as high-throughput data
processing, standardized performance, cost efficacy, and reusability.
The recently approved FP7-EU project PharMEA (Multi-Electrode Array
technology-based platform for industrial pharmacology and toxicology
drug screening), in which REDS participates actively, constitutes a
good example of this new tendency towards industrialized BCB data
processing and management. At the same time, there is an increasing
interest for developing high-performance reconfigurable computing
(HPRC) solutions, applied in particular to accelerate scientific
computing tasks offering a very competitive performance-to-cost ratio
(usually measured in mega-operations per watt). Besides the intended
computational speed-up, other advantages of HPRC with respect to
processor-based solutions are lower power consumption for similar
computational performance and less space required. The main current
drawback is that some hardware-specific programming skills are required
to implement algorithms on HPRC platforms. To palliate this, a number
of solutions and initiatives are emerging to facilitate porting
algorithms from common programming environments (e.g., C language or
Matlab) to HPRC platforms. A good example is the HES-SO project
Math2Mat, which REDS participates to. The goal of this project is to
develop a tool for automatically translating Matlab code into a
hardware description language.
PreBio is a self-contained project conceived as the first stage
of a longer-term research goal, the HiperBio facility, which will be a
HPRC set of tools oriented specifically towards the development of
algorithms and solutions for BCB applications. With HiperBio-1 we will
explore and establish the technological and methodological bases of
HiperBio. To do this, we will use a top-down approach based on the
implementation of two selected applications that will allow us to
identify and implement a number of basic functional blocks. Goals 1.To
establish a basic computational facility for rapid-prototyping and
implementation of algorithms for bioinformatics and computational
biology (BCB). 2.To implement two selected, industrially relevant, BCB
solutions as a proof of the concept. 3.To constitute, based on the
developed solutions, a set of hardware-oriented computational “blocks”
that will serve as the basic bricks for implementing further advanced
BCB solutions. 4.Establish and measure a number of criteria allowing to
evaluate a computer-aided hardware development environment and to
compare it against the traditional, human-driven, design flow.