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Life Sciences


Few industries have experienced more dramatic growth during the last decade than life sciences. The life sciences are highly research and development intensive, from design and testing through clinical trials and process automation. The extensive use of computer simulations used today by the life sciences market can easily stress the upper limits of any computing solution.

Like other computationally intense industries, the life sciences industry uses a mix of computing technologies. With the added pressures from significant regulatory, compliance, cost and time constraints, life sciences companies and research institutions are confronted with an array of challenges, including:

  • Align costly and scarce resources to the most promising research
  • Match computing resources to business priorities
  • Maximize end-user productivity
  • Protect intellectual property
  • Control the growing complexity of systems and applications

Meeting these demanding goals requires technical computing and high productivity software systems. Investments in technical computing don't just save time and money. They enable life sciences researchers and companies to investigate more drug design options. They expedite new medical devices and pharmaceuticals, bringing them to market sooner and safer. They ensure that bioinformatics and computational chemistry applications are continually improved.

AccelerEyes' software provides a variety of benefits to address the challenges of the industry all while saving time and money, improving productivity, accelerating results, and decreasing time-to-market.


Example Applications

ArrayFire can help educate students and support research in many application areas including:

  • Bioinformatics
  • Image Processing
  • Computational Chemistry
  • Math and Statistics
  • Manufacturing
  • Biostatistics
  • Biochemical Modeling
  • And much more...

Parallelized Gene Predictors
University of Quebec
Speedup: 43X



Authors: University of Quebec
Speedup: 43X

Computerized approaches to studying the human genome are challenged by the exploding amount of data, which doubles roughly every 6 months. In order to deal with this burgeoning datasets, demands for faster processing power continue to arise. This work focuses on predicting genes using frequency analysis with FFTs and with an equivalent technique known as Goertzel's algorithm. In these applications, the emphasis of this paper is to propose tools to geneticists and molecular biologists for the prediction or identification of new genes using existing complementary strategies. The criteria for these tools are speed, reliability, accuracy and ease of use, thus requiring little training.

Last Updated: 26 Jun 2012

Pathology advances with GPUs
Northeastern University
Speedup: 100X+



Pathology advances with GPUs

Authors: Laboratory for Spectral Diagnosis at Northeastern University
Speedup: 100X+

One element of the hyperspectral image analysis workflow that requires more than a traditional desktop workstation or personal computer is Hierarchical Cluster analysis (HCA). HCA requires a large amount of data space and substantial computation time (~11 hours) for typical datasets using a single processor personal computer. Rather than following the traditional approach of moving to a lower level programming language like C or C++ and complex parallel programming paradigms such as OpenMP or the Massage Passing Interface (MPI), the lab utilized graphics processing units, or GPUs, and AccelerEyes software. The solution allowed the lab to dramatically increase the performance of the analysis while substantially decreasing the amount of calendar time to reach the desired results.

Last Updated: 27 May 2010

Hepatitis C Virus - mutation modeling
Centers for Disease Control and Prevention
Speedup: ~20X


hepatitis C

Hepatitis C Virus - mutation modeling

Authors: CDC Research and Development Team
Speedup: ~20X

This case study provides a look at biological research regarding coordinated mutations of the Hepatitis C Virus (HCV). AccelerEyes provided collaborative R&D resources and greatly improved the speed of this HCV research with the use of parallelization, reducing the computing time from 40 days to less than 1 day. Most importantly, the conclusion of the case study illustrates the the relative price-performance of personal supercomputers that leverage AccelerEyes software provide a compelling solution versus other architectures and approaches.

Last Updated: 10 Sep 2010

Accelerating the SPM package for Neuroimaging
Georgia Institute of Technology
Speedup: 3.5X


fmri image analysis

fMRI with SPM in Neuroimaging

Authors: Georgia Institute of Technology
Speedup: 3.5X

The Georgia Tech team explores the value of AccelerEyes software and GPUs for fMRI workflows within the popular SPM - Statistical Parametric Mapping software widely used in neuroscience research.

 

Last Updated: 8 Mar 2010

Medical Image Compression
Indian Institute of Technology, Roorkee, India
Speedup: 38X


skull image

Medical Image Compression

Authors: Jaideep Singh, Ipseeta Aruni, R. Balasubramanian - IIT - Roorkee, India
Speedup: 38x

This study presents the acceleration of Haar wavelet-based image compression algorithm for medical imaging on the Graphics Processing Unit (GPU) using AccelerEyes software. Due to bandwidth and image size constraints of medical imaging systems, image compression plays a vital role in reducing the bit rate of transmission or storage. Wavelet-based image compression provides the most promising approach for high quality image compression.

Last Updated: 23 June 2010

Brain Displacement
Spencer Technologies
Speedup: 12X


Brain visualization

Brain Displacement

Authors: Spencer Technologies
Speedup: 12X

Spencer describes how AccelerEyes software facilitates the development of fast algorithms enabling observation of brain displacement across depth with sampling density that far surpasses previous benchmarks.

 

Last Updated: 23 Jan 2010

Multidimensional Scaling for Genomics
Leibniz Institute of Plant Genetics and Crop Plant Research
Speedup: 20X - 35X


Gene Expression visualization

Multidimensional Scaling for Genomics

Authors: Leibniz Institute of Plant Genetics and Crop Plant Research
Speedup: 20 to 35X

Multidimensional scaling (MDS) is a general computing technique to turn a distance matrix into a set of reconstructed points with pair-wise relationships approximating the original distances by points located in a usually low-dimensional space. AccelerEyes software is used to enhance execution of the HiT-MDS procedure and delivers considerable performance improvement.

 

Last Updated: 26 Jun 2009

Drug Delivery Model
Georgia Institute of Technology
Speedup: 70X


Cell simulation visualization for Drug
                                   Discovery

Drug Delivery Model

Authors: Georgia Institute of Technology
Speedup: 70X

In this work, the researchers simulate the delivery of a novel nanoparticle chemotherapy drug to cancerous tissue. Simulation allows scientists to predict experimental outcomes and thus reduce the cost of development and time to clinical relevance. The simulation model includes blood vessels, tumor cells, and healthy cells and an engine to calculate the spatial distributions of both drug and oxygen. AccelerEyes software is used to speed up the diffusion calculations for the drug and oxygen within the tissue.

 

Last Updated: 09 Nov 2008

Biomedical Infrared Spectroscopy
University of Manchester and Nofima Mat, Norway
Speedup: Hours of runtime reduction


cancer cell image

Biomedical Infrared Spectroscopy

Authors: University of Manchester and Nofima Mat, Norway
Speedup: Hours of runtime reduction

The authors present an iterative algorithm that applies full Mie scattering theory and avoids noise accumulation in their iterative algorithm by integrating a curve-fitting step. AccelerEyes software along with NVIDIA GPUs are leveraged to reduce the time added by the curve-fitting step.

Last Updated: 20 May 2010