Cray Solutions for Healthcare & Life Sciences

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Cray gets you there faster

Whether on-premise or in the cloud, Cray is the shortest path from computation to cure.

Whether you’re in big pharma or at a genomics research center, Cray’s leadership in life sciences enables research without boundaries. Our technology — both on-premise and in the cloud — powers innovation in life science fields including medical imaging, molecular dynamics, healthcare analytics, NGS and cybersecurity.

Ready to ramp up your next-generation sequencing workflows? We’ll help you do genomic analysis up to five times faster than with other systems. Cray systems can handle the world's largest molecular dynamics simulations, scaling nearly linearly up to tens of thousands of nodes. And GPU-based architectures like Cray’s CS-Storm system can provide significant performance benefits for medical imaging applications.

Cray gives you more than speed. We simplify time-to-operation by building key analytics software right into our system architecture. You can improve the productivity of your software development team by a factor of three, even as you explore datasets that are three times larger — or more.

Because Cray builds capability systems, you get speed and flexibility with less computational infrastructure than commodity clusters would require. And Cray systems scale hand in hand with your growing workload.

We leverage 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 data scientists from image and sequence analysis to computational modeling; researchers from analysis tools and machine-learning frameworks to big-graph analytics; and 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.

Roll up your sleeves. We’ll clear the path.

Cray Healthcare & Life Sciences Solutions

Featured Resources

Cray HPC Storage for Life Sciences

High performance computing (HPC) is at the center of modern life sciences research. From genomic sequencing to large-scale genomic analysis to precision medicine, HPC plays a critical role in advancing many life sciences disciplines.

Infographic: Life Sciences Evolution Timeline

Life Sciences Evolution Timeline

eBook: Parallel, Object & NAS Storage Technology Comparison - Life Science Applications

This ebook is designed to help you understand the differences between the different types of storage — parallel, object and network attached storage (NAS) — in order to identify what is best for your budget and the performance you need … today and in the future.

Pinpointing Mutations for Precision Medicine with the Broad Institute

Understanding the human body at the gene level has the potential to revolutionize healthcare, allowing doctors to better understand diseases and more accurately apply treatments.

Power Your Analytics with Supercomputing as a Service from Cray & Markley

Cray's new Supercomputing as a Service is a big data solution with the speed of a supercomputer and the ease of the cloud.

See All Resources

Healthcare & Life Sciences Solutions

Biomedical Imaging to Revolutionize Patient Outcomes

Taking the leap of faith to run code optimized for graphics processing unit (GPU) architectures can provide significant performance benefits for imaging applications, but it can also introduce risks including reduced overall system reliability, upgrade suitability and tedious system manageability. Read more.

Powering NGS Workflows

As the costs of sequencing continue to drop, there has been increasing demand for computing and data storage solutions. Many organizations are struggling to keep up. Regardless of whether you're working with genomic sequences in a research or clinical setting, Cray can help future-proof your lab with an upgradable compute infrastructure capable of managing your entire NGS ecosystem and scaling as your needs change. Read more.

Empowering Healthcare Analytics

In recent years, healthcare organizations have been facing increasing pressure to refocus their businesses away from volume-based drivers toward value-based metrics and improved patient outcomes. This fundamental shift in priorities often leads to broad organizational and operational changes, after which many organizations find their existing infrastructure lacks the analytical capability to support these important changes. Read more.

Breakthrough Molecular Dynamics Performance at Massive Scale

Molecular dynamics, once one of the world's grand challenges, is now seeing broader adoption and application within the life sciences community. As organizations try to run these codes to solve new problems, like pharmaceutical companies tracking rapid processes, they typically find that the molecular dynamics software they're using doesn't run well on commodity clusters. Read more.

Protecting Patients and Their Data

For healthcare organizations, insurance companies, hospitals and other care providers, patient data is a critical asset — and one that often makes these organizations the victims of hackers and other cyber criminals. Read more.

View Bioinformatics Applications
Application
Owner
Description
Application:Abokia BLAST
Owner:Commercial

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.

Application:ABySS
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.

Application:ALLPATHS-LG
Owner:Open Source

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

Application:BLAST
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.

Application:Bowtie
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.

Application:BWA
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.

Application:ClustalW
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.

Application:Edena
Owner:Open Source

De novo short reads assembler

Application:EULER-SR
Owner:Open Source

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

Application:FASTA
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.

Application:HMMER
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).

Application:MIRA2
Owner:Open Source

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

Application:MrBayes
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.

Application:MUMmer
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

Application:Novoalign
Owner:Commercial

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.

Application:RAY
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.
Application:SeqAn
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.

Application:SHARCGS
Owner:Open Source

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

Application:SHRiMP
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.

Application:SOAP
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).

Application: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. 

Application:SSAKE
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.

Application:Trinity
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.

Application:VCAKE
Owner:Open Source

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

Application:Velvet
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
Application
Owner
Description
Application:AutoDock
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.

Application:DOCK6
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.

Application:FlexX
Owner:Commercial (BioSolveIT)

Predicts protein-ligand interactions.

Application:GLIDE
Owner:Commercial (Schrödinger)

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

Application:GOLD
Owner:Open Source

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

Application:ICM
Owner:Commercial (molsoft)

A desktop-modeling environment for molecular structure and function.

Application:LigandFit
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.

Application:ROCS
Owner:Commercial (OpenEye)

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

View Materials Science Applications
Application
Owner
Description
Application:ABINIT
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.

Application:BigDFT
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.

Application:CASTEP
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.

Application:CP2K
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.

Application:CPMD
Owner:Open Source

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

Application:DMol3
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.

Application:LAMMPS
Owner:Open Source

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

Application:SIESTA
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.

Application:VASP
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
Application
Owner
Description
Application:Mascot
Owner:Commercial (Matrix Science)

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

Application:OMSSA
Owner:Open Source

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

Application:ProteinProspector
Owner:Open Source

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

Application:SEQUEST
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.

Application:X!Tandem
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
Application
Owner
Description
Application:ACEMD
Owner:Acellera

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

Application:AMBER
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.

Application:CHARMM
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.

Application:DESMOND
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.

Application:GAMESS
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.

Application:Gaussian
Owner:Commercial (Gaussian)

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

Application:GROMACS
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.

Application:Jaguar
Owner: Commercial (Schrödinger)

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

Application:LAMMPS
Owner:Open Source

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

Application:MOLPRO
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.

Application:NAMD
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.

Application:NWChem
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.

Application:Q-Chem
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.

Application:MPACK
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

Application:Terachem
Owner:Commercial (PetaChem)

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

Briefs & White Papers

Cray HPC Storage for Life Sciences

High performance computing (HPC) is at the center of modern life sciences research. From genomic sequencing to large-scale genomic analysis to precision medicine, HPC plays a critical role in advancing many life sciences disciplines.

Infographic: Life Sciences Evolution Timeline

Life Sciences Evolution Timeline

eBook: Parallel, Object & NAS Storage Technology Comparison - Life Science Applications

This ebook is designed to help you understand the differences between the different types of storage — parallel, object and network attached storage (NAS) — in order to identify what is best for your budget and the performance you need … today and in the future.

Hail Powers Precision Medicine on the Urika-GX Platform

The Cray Urika-GX platform’s large RAM capacity and best-in-class Aries interconnect can be transformative in the HTS ecosystem and help users realize significant performance gains.

Pinpointing Mutations for Precision Medicine with the Broad Institute

Understanding the human body at the gene level has the potential to revolutionize healthcare, allowing doctors to better understand diseases and more accurately apply treatments.

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.

Videos & Webinars

Power Your Analytics with Supercomputing as a Service from Cray & Markley

Cray's new Supercomputing as a Service is a big data solution with the speed of a supercomputer and the ease of the cloud.

Large-Scale Variant Analysis at the Broad Institute with Hail

In this webinar, learn how Hail can boost the production of your informatics workflows and accelerate your journey from computation to cure.

Blog

Cray Blog - Life Sciences

Commentary and insight from Cray’s top experts and customers