Heathcare & Life Sciences

Cray Solutions for Healthcare and Life Sciences

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Advances in affordable sequencing and high-resolution imaging are producing extremely large, varied and complex data sets at ever-higher levels of sample specificity and sensitivity. Combine this with novel analytical methods and new computational tools to explore and collaborate on these data in minutes and at scale, and the stage is set for faster drug discovery, precision disease treatment, improved patient outcomes and more-efficient healthcare.

Cray has leveraged 40 years of dominance in HPC and supercomputing to build a platform that enables all the core components for precision medicine, with the power to take your data scientists from image and sequence analysis to computational modeling; your researchers from analysis tools and machine-learning frameworks to big-graph analytics; and your clinicians from big data store to connectors, query engines and productivity tools. All while minimizing the impact on your IT environment, and protecting your data and your patients.

Areas in which we collaborate with healthcare and life sciences organizations include:

Medical Imaging

  • Analyzing medical images at scale
  • Enabling computational pathology
  • Cryo-electron microscopy

Simulation for Life Sciences

  • Improve the resolution of molecular dynamics

Next-Generation Sequencing for Healthcare & Life Sciences

  • Assemble a large plant or human genome de novo in minutes
  • Find statistically significant variants in 10,000+ genomes
  • Leverage big data technologies to contextualize NGS results

Cybersecurity for Healthcare

  • Protect patients and their data from cyberattacks

Featured Resources

Cray Announces Agile Analytics Platform

The Broad Institute says Cray's new Urika-GX platform “highlights the potential to accelerate delivery of genomic insights to researchers who are making breakthroughs in the fight against disease.”

Enabling Scientific Breakthroughs at the Petascale

If you think the requirements for enterprise storage systems are growing at a dizzying pace, try these numbers on for size...

Cray Storage Solutions for Life Sciences

Genomics, structural biology, informatics, drug discovery, materials science and other life sciences benefit from Cray’s expert solutions. 

See All Resources

View Bioinformatics Applications
Application:Abokia BLAST

AbokiaBLAST is a parallel implementation of NCBI BLAST created by the inventors of the open-source mpiBLAST project. AbokiaBLAST inherits the super-scalable architecture from mpiBLAST but is re-factored and re-engineered to offer production quality. With intelligent task parallelization and I/O optimization, AbokiaBLAST enables users to massively accelerate large-scale BLAST search on clusters or supercomputers with a single command.

Owner:Open Source

ABySS is a de novo, parallel, paired-end sequence assembler designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

Owner:Open Source

ALLPATHS-LG is a short-read assembler that works on both small and large (mammalian size) genomes.

Owner:Open Source

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences and help identify members of gene families.

Owner:Open Source

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at more than 25 million 35bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end.

Owner:Open Source

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the other two are for longer sequences ranging from 70bp to 1Mbp.

Owner:Open Source

ClustalW is a general-purpose multiple alignment program for DNA or proteins. ClustalX is a graphical user interface for the ClustalW multiple-sequence alignment program.

Owner:Open Source

De novo short reads assembler

Owner:Open Source

The EULER-SR assembly package contains a suite of programs for correcting errors in short reads and assembling them.

Owner:Open Source

FASTA is a more sensitive derivative of the FASTP program that can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence database by translating the DNA database as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences.

Owner:Open Source

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

Owner:Open Source

Sequence assembler and sequence mapping for whole genome shotgun and EST/RNASeq sequencing data

Owner:Open Source

MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and amino acid sequences, restriction sites and standard binary data.

Owner:Open Source

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. 

Application:NCBI BLAST
Owner:Open Source

Genomics/protein analytics, integer/character manipulation intensive, query and database required, shared-memory parallelization


Tool designed for mapping  short reads onto a reference genome from Illumina, Ion Torrent and 454 NGS platforms

Application:Phred Phrap Consed
Owner:Commercial (Univ. Wash.)

Phred is a base calling software with quality estimation; Phrap performs shotgun sequence assembly; and Consed is a sequence assembly editor companion to Phrap. Also available are Swat and CrossMatch, sequence alignment tools; and Phrapview, a graphical tool that provides a "global" view of the Phrap assembly, complementary to the "local" view provided by the Consed.

Owner:Open Source

Parallel genome assemblies for parallel DNA sequencing

Owner:IO Informatics
The Sentient Knowledge Explorer uses the power of semantic technologies to easily integrate data from virtually any source into coherent, unified knowledge bases.
Owner:Open Source

SeqAn is an open-source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data.

Owner:Open Source

Short-read assembler based on robust contig extension for genome sequencing

Owner:Open Source

SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next-generation sequencing machines in mind, as well as Applied Biosystems' colourspace genomic representation.

Owner:Open Source

SOAP provides a full solution to next generation sequencing data analysis. It consists of a new alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder (SOAPindel), a structural variation scanner (SOAPsv) and a de novo short reads assembler (SOAPdenovo).

Owner:Open Source

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina GA short reads. 

Owner:Open Source

SSAKE is a de novo assembler for short DNA sequence reads. It is designed to help leverage the information from short-sequence reads by assembling them into contigs and scaffolds that can be used to characterize novel sequencing targets.

Owner:Open Source

A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules — Inchworm, Chrysalis and Butterfly — applied sequentially to process large volumes of RNA-seq reads.

Owner:Open Source

VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error.

Owner:Open Source

Velvet performs de novo short read assembly using de Bruijn graphs. It can be used for Solexa and 454 sequencing data assembly.

View Drug Discovery Applications
Owner:Open Source

AutoDock is a suite of automated docking tools that predicts how small molecules, such as substrates or drug candidates, bind to a receptor of known 3-D structure.

Owner:Commercial (UCSF )

DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

Owner:Commercial (BioSolveIT)

Predicts protein-ligand interactions.

Owner:Commercial (Schrödinger)

A complete solution for ligand-receptor docking, from virtual screening of millions of compounds to binding mode predictions.

Owner:Open Source

Gold calculates the docking modes of small molecules into protein binding sites.

Owner:Commercial (molsoft)

A desktop-modeling environment for molecular structure and function.

Owner:Commercial (Accelrys )

Code for docking ligands into protein active sites. The method employs a cavity detection algorithm for detecting invaginations in the protein as candidate active site regions.

Owner:Commercial (OpenEye)

ROCS is a virtual screening tool that can identifies potentially active compounds by shape comparison.

View Materials Science Applications
Owner:Open Source

Main program helps users find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within density functional theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on density-functional perturbation theory, and many more properties.

Owner:Open Source

BigDFT is a DFT massively parallel electronic structure code (GPL license) using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh. GTH or HGH pseudopotentials are used to remove the core electrons. With a Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions.

Owner:Commercial (Accelrys )

CASTEP is a code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of material properties including energetics, structure at the atomic level, vibrational properties and electronic response properties. Offers a wide range of spectroscopic features that link directly to experiment, such as infrared and Raman spectroscopies, NMR and core level spectra.

Owner:Open Source

CP2K performs atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as density functional theory using a mixed Gaussian and plane waves approach (GPW) and classical pair and many-body potentials.

Owner:Open Source

The CPMD code is a parallelized plane wave/pseudopotential implementation of density functional theory, particularly designed for ab-initio molecular dynamics.

Owner:Commercial (Accelrys )

DMol3 is a commercial (and academic) software package that uses density functional theory with a numerical radial function basis set to calculate the electronic properties of molecules, clusters, surfaces and crystalline solid materials from first principles. It can either use gas phase boundary conditions or 3-D periodic boundary conditions for solids or simulations of lower dimensional periodicity.

Owner:Open Source

Large-scale atomic/molecular massively parallel simulator (LAMMPS) is a classical molecular dynamics code.

Owner:Open Source (commercial version from Nanotec)

SIESTA is both a method and its computer program implementation for performing electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA uses strictly localized basis sets and linear-scaling algorithms that can be applied to suitable systems. The code can be used for a wide range of applications, from quick exploratory calculations to simulations that match other approaches, such as plane-wave and all-electron methods.

Owner:Commercial (Univ. of Vienna)

VASP performs ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.

View Proteomics Applications
Owner:Commercial (Matrix Science)

Mascot is a mass spectral search algorithm that uses mass spectrometry data to identify proteins from primary sequence databases.

Owner:Open Source

Mass spectrometry software used for data acquisition, analysis or representation.

Owner:Open Source

Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments.

Owner:Open Source

SEQUEST correlates uninterpreted tandem mass spectra of peptides with amino acid sequences from protein and nucleotide databases. It will determine the amino acid sequence and thus the protein(s) and organism(s) that correspond to the mass spectrum being analyzed.

Owner:Open Source

X! Tandem can match tandem mass spectra with peptide sequences. It generates theoretical spectra for peptide sequences using information about intensity associated with amino acids. These spectra are compared with experimental data to generate an expectation value as a threshold score.

View Structural Biology Applications

ACEMD is a heavily optimized molecular dynamics engine specially designed to run on NVIDIA GPUs.

Owner:Open Source

Assisted model building with energy refinement (AMBER) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs), and a package of molecular simulation programs which includes source code and demos.

Owner:Commercial (Accelrys )

CHARMM (Chemistry at HARvard Molecular Mechanics) is the academic version of the CHARMM simulation program available through Harvard. CHARMM uses empirical energy functions to describe the forces on atoms in molecules.

Owner:D.E. Shaw Research

DESMOND performs high-speed molecular dynamics simulations of biological systems on conventional commodity clusters. The code uses novel parallel algorithms and numerical techniques and can run on platforms containing a large number of processors, or on a single computer.

Owner:Open Source

General atomic and molecular electronic structure system (GAMESS) is a general ab initio quantum chemistry package. It can compute wave functions ranging from RHF, ROHF, UHF, GVB and MCSCF, with CI and MP2 energy corrections available for some of these.

Owner:Commercial (Gaussian)

Gaussian 09 provides electronic structure modeling, and is licensed for a wide variety of computer systems.

Owner:Open Source

GROMACS performs molecular dynamics, simulating the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules such as proteins, lipids and nucleic acids that have complicated bonded interactions, but is also being used for research on nonbiological systems, such as polymers.

Owner: Commercial (Schrödinger)

Jaguar is an ab initio package for both gas and solution phase simulations, with particular strength in treating metal containing systems.

Owner:Open Source

Large-scale atomic/molecular massively parallel simulator (LAMMPS) is a classical molecular dynamics code.

Owner:Commercial (University College Cardiff Consultants Ltd.)

Molpro is a complete system of ab initio programs for molecular electronic structure calculations. The emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods.

Owner:Open Source

NAMD is a parallel molecular dynamics code designed for simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms.

Owner:Open Source

NWChem provides many methods to compute the properties of molecular and periodic systems by using standard quantum mechanical descriptions of the electronic wave function or density. NWChem can perform classical molecular dynamics and free energy simulations. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations.

Owner:Commercial (Q-Chem)

Q-Chem is a comprehensive ab initio quantum chemistry package. Its capabilities range from DFT/HF calculations to post-HF correlation methods.

Owner:Open Source

MPACK is a Fortran program package that involves scattering problems of two octet baryons by the quark-model interactions, fss2 and FSS (fssG.f), and their applications to the Faddeev calculations for the triton (triton.f) and the hypertriton (hypt.f

Owner:Commercial (PetaChem)

TeraChem is general-purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system.

Case Studies

Applying Big Data Analysis Techniques to Simulated DNA Data

Researchers from the Centre for Biomolecular Sciences at the University of Nottingham along with the Edinburgh-based Cray Centre of Excellence team have been carrying out a pioneering study applying big data analysis techniques to simulation-generated DNA data.

The Pawsey Centre’s Cray XC40 Supercomputer “Magnus” Gives Researchers a Big Advantage in Fight Against Lung Disease

Chronic respiratory diseases interrupt the airways and other lung structures, affecting hundreds of millions of people worldwide. Researchers created a first-ever 3D model of the lung using “Magnus,” Pawsey Supercomputing Centre’s Cray XC40 supercomputer, with the goal of improved delivery of aerosolized medications.

Enabling Scientific Breakthroughs at the Petascale

If you think the requirements for enterprise storage systems are growing at a dizzying pace, try these numbers on for size...

Boron Nitride and the Nanoribbons of Tomorrow

Materials modeling on ORNL’S "Jaguar" shows big future for boron nitride

ORNL and Purdue Explore Technology at the Nanoscale

A team led by Gerhard Klimeck of Purdue University has broken the petascale barrier while addressing a relatively old problem in the young field of computer chip design.

Application, Solution and Technology Briefs

Removing Bottlenecks to Large-Scale Genetic and Genomic Data Analysis with DISSECT and the Cray XC Supercomputer

Genomic and genetic research have a big data problem. The field is producing ever-increasing amounts of data. But a lack of sufficiently scalable computational tools prevents researchers from analyzing it adequately. The situation leaves the massive opportunities inherent in this data untapped.

Cray Helps Optimize De Novo Assembler Application Trinity for Use on Massively Parallel Supercomputers

To fully realize the benefits of the Cray XC30 system for NGS, Cray is actively collaborating with leading researchers to improve the performance of NGS workflows.

Cray Demonstrates Top-Level Performance and Scalability on Very Large Datasets with Velvet

Velvet is a de novo genomic assembler designed for short reads generated by NGS sequencers.

Cray Helps Tune Ray De Novo Genomic Assembler Software

Ray is a highly parallel computer software developed at the Université Laval that performs de novo genome assemblies with next-generation DNA sequencing data.

Cray Storage Solutions for Life Sciences

Built on open systems, Cray’s scalable storage solutions address life science’s data- and I/O-intensive workflows and get results faster.

Tuning NAMD on the Cray XK6 "Titan" Supercomputer

With Cray support, the NAMD developers are optimizing their code on each new iteration of Cray hardware, achieving scaling to hundreds of thousands of cores.

Speed Your Time to Results Using Galaxy on a Cray System

Galaxy is a widely used web-based platform for data integration and analysis in the life sciences.

Customer Solutions

PDC Center for High Performance Computing: Milner Marches On

The Cray XC30 system Milner, which is named in recognition of significant work in neuropsychology that was done by Brenda Milner and her then husband Peter in the 1950s, is part of a high performance computing platform for research in neuroinformatics and was funded by an infrastructure grant from the Swedish Research Council (VR).

The Problem with Cellulosic Ethanol

At Oak Ridge National Laboratory, simulation provides a close-up look at the molecule that complicates next-generation biofuels.

Supercomputers Simulate the Molecular Machines That Replicate and Repair DNA

Researchers used "Jaguar," at Oak Ridge National Laboratory, to elucidate the mechanism by which accessory proteins, called sliding clamps, are loaded onto DNA strands and coordinate enzymes that enable gene repair or replication.

Early Molecular Dynamics Research Blazes through Titan’s New GPUs

A look at the transition from CPUs to GPUs when the Oak Ridge Leadership Computing Facility upgraded its Cray "Jaguar" system to the new "Titan." 

Beagle: The CI Supercomputer for Biomedical Simulations & Data Analysis at the University of Chicago

The official website for "Beagle," a Cray XE6 system used primarily for biomedical research at the University of Chicago's Computation Institute.

Computation Institute, University of Chicago, Beagle Newsletter

The Beagle Cray system is one of the fastest supercomputers in the world that is devoted to life sciences.

Technical Papers

Genomic Applications on Cray Supercomputers: Next Generation Sequencing Workflow

A team of Cray and university researchers discusses its work with Ray, a parallel shortread de novo assembler code. They also present a configuration for an NGS workflow based on a Cray supercomputing system and the Cray Sonexion storage solution. 

Human Analysts at Superhuman Scales

Ray, a scalable genome assembler, addresses big data problems by using optimal resources and producing one correct and conservative timely solution.

Videos & Webinars

Bio-IT World Breakfast: A dialogue with Dr. George Church

Join us for breakfast at the Renaissance Hotel in the Caspian Room from 8:30 to 10:00 a.m. on April 5th.

Webcast Replay: Population Genetics Examples with Apache Spark

Emerging big data analytics techniques hold the promise of accelerating scientific data processing, lowering the cost and complexity of data management and providing new capabilities for genomic interpretation.

Unprecedented Speed: Lumenogix and Cray for Next-Generation Data Sequencing

Dave Anstey, global head of life sciences at Cray Inc., and Boris Umylny, director of bioinformatics services at the National Center for Genome Resources, talk about processing NGS data with unprecedented speed

Why Scientific Innovation Outpaces Infrastructure

Dave Anstey, global head of life sciences at Cray Inc., talks about scientific innovation and how it relates to computer infrastructure.

Accelerating NGS Workflows with Hadoop and Spark

Learn how to accelerate NGS workflows to enable scientific breakthroughs across a wide variety of fields including cancer research, clinical genomics and precision medicine.

Personalized Medicine: Technology Needs to Be Ready

Carlos Sosa, high performance computing architect at Cray Inc., says personalized medicine is on the way, but HPC technology must be more robust to answer questions quickly for patients and doctors.

Leveraging a Cray Supercomputer for Parallel De Novo Transcriptome Assembly Using Trinity

By the Broad Institute, a unique, collaborative community pioneering a new model of biomedical science.


Cray Blog - Life Sciences

Commentary and insight from Cray’s top experts and customers