Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization

November 3rd, 2014

Abstract:

The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.

(Cazzaniga P., Nobile M.S., Besozzi D., Bellini M., Mauri G.: “Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization”. BioMed Research International, vol. 2014. [DOI])

cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems

March 26th, 2014

Abstract:

Tau-leaping is a stochastic simulation algorithm that efficiently reconstructs the temporal evolution of biological systems, modeled according to the stochastic formulation of chemical kinetics. The analysis of dynamical properties of these systems in physiological and perturbed conditions usually requires the execution of a large number of simulations, leading to high computational costs. Since each simulation can be executed independently from the others, a massive parallelization of tau-leaping can bring to relevant reductions of the overall running time. The emerging field of General Purpose Graphic Processing Units (GPGPU) provides power-efficient high-performance computing at a relatively low cost. In this work we introduce cuTauLeaping, a stochastic simulator of biological systems that makes use of GPGPU computing to execute multiple parallel tau-leaping simulations, by fully exploiting the Nvidia’s Fermi GPU architecture. We show how a considerable computational speedup is achieved on GPU by partitioning the execution of tau-leaping into multiple separated phases, and we describe how to avoid some implementation pitfalls related to the scarcity of memory resources on the GPU streaming multiprocessors. Our results show that cuTauLeaping largely outperforms the CPU-based tau-leaping implementation when the number of parallel simulations increases, with a break-even directly depending on the size of the biological system and on the complexity of its emergent dynamics. In particular, cuTauLeaping is exploited to investigate the probability distribution of bistable states in the Schlögl model, and to carry out a bidimensional parameter sweep analysis to study the oscillatory regimes in the Ras/cAMP/PKA pathway in S. cerevisiae.

(Nobile M.S., Cazzaniga P., Besozzi D., Pescini D., Mauri G.: “cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems”. PLoS ONE 9(3): e91963. [DOI])

cupSODA: a CUDA-Powered Simulator of Mass-action Kinetics

October 19th, 2013

Abstract:

The computational investigation of a biological system often requires the execution of a large number of simulations to analyze its dynamics, and to derive useful knowledge on its behavior under physiological and perturbed conditions. This analysis usually turns out into very high computational costs when simulations are run on central processing units (CPUs), therefore demanding a shift to the use of high-performance processors. In this work we present a simulator of biological systems, called cupSODA, which exploits the higher memory bandwidth and computational capability of graphics processing units (GPUs). This software allows to execute parallel simulations of the dynamics of biological systems, by first deriving a set of ordinary differential equations from reaction-based mechanistic models defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm LSODA. We show that cupSODA can achieve a 112× speedup on GPUs with respect to equivalent executions of LSODA on CPUs.

(Nobile M.S., Besozzi D., Cazzaniga P., Mauri G., Pescini D.: “cupSODA: a CUDA-Powered Simulator of Mass-action Kinetics”,  In 12th International Conference on Parallel Computing Technologies (PaCT), Lecture Notes in Computer Science, volume 7979, pp. 344-357, 2013. [DOI])

A GPU-Based Multi-Swarm PSO Method for Parameter Estimation in Stochastic Biological Systems Exploiting Discrete-Time Target Series

August 1st, 2012

Abstract:

Parameter estimation (PE) of biological systems is one of the most challenging problems in Systems Biology. Here we present a PE method that integrates particle swarm optimization (PSO) to estimate the value of kinetic constants, and a stochastic simulation algorithm to reconstruct the dynamics of the system. The fitness of candidate solutions, corresponding to vectors of reaction constants, is defined as the point-to-point distance between a simulated dynamics and a set of experimental measures, carried out using discrete-time sampling and various initial conditions. A multi-swarm PSO topology with different modalities of particles migration is used to account for the different laboratory conditions in which the experimental data are usually sampled. The whole method has been specifically designed and entirely executed on the GPU to provide a reduction of computational costs. We show the effectiveness of our method and discuss its performances on an enzymatic kinetics and a prokaryotic gene expression network.

(M. Nobile, D. Besozzi, P. Cazzaniga, G. Mauri and D. Pescini: “A GPU-based multi-swarm PSO method for parameter estimation in stochastic biological systems exploiting discrete-time target series”,  in M. Giacobini, L. Vanneschi, W. Bush, editors, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Springer, vol. 7246 of LNCS. pp. 74-85, 2012. [DOI])

Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems

June 26th, 2011

Abstract:

This paper describes the approach and the speedup obtained in performing Smith-Waterman database searches on heterogeneous platforms comprising of multi core CPU and multi GPU systems. Most of the advanced and optimized Smith-Waterman algorithm versions have demonstrated remarkable speedup over NCBI BLAST versions, viz., SWPS3 based on x86 SSE2 instructions and CUDASW++ v2.0 CUDA implementation on GPU. This work proposes a hybrid Smith-Waterman algorithm that integrates the state-of-the art CPU and GPU solutions for accelerating Smith-Waterman algorithm in which GPU acts as a co-processor and shares the workload with the CPU enabling us to realize remarkable performance of over 70 GCUPS resulting from simultaneous CPU-GPU execution. In this work, both CPU and GPU are graded equally in performance for Smith-Waterman rather than previous approaches of porting the computationally intensive portions onto the GPUs or a naive multi-core CPU approach.

(J. Singh and I. Aruni: “Accelerating Smith-Waterman on Heterogeneous CPU-GPU Systems”, Proceedings of Bioinformatics and Biomedical Engineering (iCBBE), May 2011. [DOI])

CfP: High performance computational systems biology

April 13th, 2011

The High performance computational systems Biology (www.hibi.it) special session of CMSB 2011 (http://contraintes.inria.fr/CMSB11/) establishes a forum to link researchers in the areas of parallel computing and computational systems biology. Experts from around the world will present their current work, discuss profound challenges, new ideas, results, applications and their experience relating to key aspects of high performance computing in biology. Topics of interest include: Workload partitioning strategies, Parallel stochastic simulation, Biological and Numerical parallel computing, Parallel and distributed architectures, General-Purpose Computation on Graphics Hardware, Emerging processing architecture (Cell processors, FPGA, PlayStation3, etc.),
Parallel model checking techniques, Parallel parameter estimation, Parallel sensitivity analysis, Parallel algorithms for biological network analysis, Application of concurrency theory to biology, Parallel visualization algorithms, Web-services and Internet computing for e-Science, Grid/Could/P2P/High performance computing for biology, Multicore and Cluster computing for biology, Tools and applications.

The call for papers is now open, please refer to www.hibi.it for details.

OpenMM 2.0 Now Available to Accelerate Molecular Dynamics on NVIDIA and ATI GPUs

July 18th, 2010

Simbios, the NIH Center for Biomedical Computation at Stanford University, is excited to announce the release of OPENMM 2.0.

OPENMM was designed to enhance the performance of almost any molecular dynamics simulation package (MD package) by allowing the code to be executed on high performance computer architectures, in particular Graphics Processing Units (GPUs). Most molecular dynamics packages can be modified to call OPENMM, resulting in significant acceleration on such high performance architectures, without changing the way users interact with the MD package. Read the rest of this entry »

HiBi 2010 deadline extension to July 1

June 18th, 2010

In response to the large number of requests from the community, the organizing committee of HiBi 2010 extend the deadline for paper and abstract submission from Monday June 21 to Thursday July 1, 2010.

The HiBi workshop establishes a forum to link researchers in the areas of parallel computing and computational systems biology. One of the main limitations in managing models of biological systems comes from the fundamental difference between the high parallelism evident in biochemical reactions and the sequential environments employed for the analysis of these reactions. Such limitations affect all varieties of continuous, deterministic, discrete and stochastic models; undermining the applicability of simulation techniques and analysis of biological models. The goal of HiBi is therefore to bring together researchers in the fields of high performance computing and computational systems biology. Experts from around the world will present their current work, discuss profound challenges, new ideas, results, applications and their experience relating to key aspects of high performance computing in biology.

CfP: High performance computational systems Biology

February 8th, 2010

The HiBi workshop establishes a forum to link researchers in the areas of parallel computing and computational systems biology. One of the main limitations in managing models of biological systems comes from the fundamental difference between the high parallelism evident in biochemical reactions and the sequential environments employed for the analysis of these reactions. Such limitations affect all varieties of continuous, deterministic, discrete and stochastic models; undermining the applicability of simulation techniques and analysis of biological models. The goal of HiBi is therefore to bring together researchers in the fields of high performance computing and computational systems biology. Experts from around the world will present their current work, discuss
profound challenges, new ideas, results, applications and their experience relating to key aspects of high performance computing in biology.

Topics of interest include, but are not limited to:

  • Parallel stochastic simulation
  • Biological and Numerical parallel computing
  • Parallel and distributed architectures
  • Emerging processing architecture: Cell processors, GPUs, mixed CPU-FPGA, etc.
  • Parallel model checking techniques
  • Parallel parameter estimation
  • Parallel algorithms for biological analysis
  • Application of concurrency theory to biology
  • Parallel visualization algorithms
  • Web-services and Internet computing for e-Science
  • Tools and applications

More Information: http://www.cosbi.eu/hibi2010/

Cellular Level Agent Based Modelling on the Graphics Processing Unit

November 25th, 2009

Abstract:

Cellular-level agent based modelling is reliant on either sequential processing environments or expensive and largely unavailable PC grids. The GPU offers an alternative architecture for such systems, however the steep learning curve associated with the GPU’s data parallel architecture has previously limited the uptake of this emerging technology. In this paper we demonstrate a template driven agent architecture which provides a mapping of XML model specifications and C language scripting to optimised Compute Unified Device Architecture (CUDA) for the GPU. Our work is validated though the implementation of a Keratinocyte model using limited range message communication with non-linear time simulation steps to resolve intercellular forces. The performance gain achieved over existing modelling techniques reduces simulation times from hours to seconds. The improvement of simulation performance allows us to present a real-time visualisation technique which was previously unobtainable.

(Richmond Paul, Coakley Simon, Romano Daniela (2009), Cellular Level Agent Based Modelling on the Graphics Processing Unit, (Best Student Paper) Proc. of HiBi09 – High Performance Computational Systems Biology, 14-16 October 2009, Trento, Italy)