UVA School of Medicine

Research Computing

Enabling scientific breakthroughs at scale with advanced computing

/tag/ivy

  • Ivy Secure Environment

    Ivy Ivy is a secure computing environment for researchers consisting of virtual machines (Linux and Windows) and Domino Data Lab. Researchers can use Ivy to process and store sensitive data with the confidence that the environment is secure and meets HIPAA requirements. Overview Ivy consists of two separate computing environments. Access to one environment does not automatically grant access to the others: Virtual Machines Domino Data Lab Coming soon - Secure HPC Requesting Access Access to Ivy resources is project-based, limited to PIs and their designees, and requires approval.
  • Secure Computing for Surgical Research

    SOMRC is working with Dr. Eric Schneider to create a secure computing environment for the research of the Healthcare Surgical Outcome team. Data from this project will contain HIPAA identifiers, as well as Medicare information, and requires more security and control of data ingress/egress than projects previously hosted on the Ivy platform. After successful implementation of this project, SOMRC will create a similar computing environment for DoD blast and traumatic brain injury data collected by Dr.
  • Non-Sensitive Data Storage

    /home /home is a free 50GB space provided to users of the Rivanna HPC system and is visible from the Rivanna login and compute nodes. /home is the default working directory when logging on to Rivanna. Users can also access their home directory at /home/$USER, where $USER is an individual’s UVa computing ID. /scratch /scratch is a Lustre high performance parallel filesystem accessible via the Rivanna login and compute nodes.
  • Bioinformatics Packages on Ivy Linux VM

    Available Packages The following bioinformatics packages are available on the Ivy Linux Virtual Machines Bowtie2 Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes. For bowtie2 usage information, please click here HISAT2 HISAT2 is a fast and sensitive tool for aligning short reads against the general human population (as well as single reference genome) * Requires approval before installation For HISAT2 usage information, please click here
  • Bioinformatics Packages on Windows VM

    Available Packages The following bioinformatics packages are available on the Windows Virtual Machines Bowtie2 For more information on bowtie2, please click here HISAT2 Requires approval before installation. For more information on HISAT2, please click here
  • Data Analysis Packages on Ivy Linux VM

    Available Packages The following Data Analysis packages are available on the Ivy Linux Virtual Machines MATLAB MATrix LABoratory (MATLAB for short) is a software designed for quick scientific calculations, such as matrix manipulation, plotting, and others. It has hundreds of built-in functions for a wide variety of computations and several tools designed for specific research disciplines, including statistics and partial differential equations. * Limited licenses available, for more information on MATLAB and licensing, please click here
  • Data Analysis Packages on Ivy Windows VM

    Available Packages The following Data Analysis packages are available on the Ivy Windows Virtual Machines MATLAB MATrix LABoratory (MATLAB for short) is a software designed for quick scientific calculations, such as matrix manipulation, plotting, and others. It has hundreds of built-in functions for a wide variety of computations and several tools designed for specific research disciplines, including statistics and partial differential equations. * Limited licenses available, for more information on MATLAB and licensing, please click here
  • Database Software on Ivy Linux VM

    The following database software are available on the Ivy Linux Virtual Machines MySQL Is the most popular open-source relational database, used in academia and industry worldwide. It has been in use for over 20 years and is backed by a large developer community. It is available in both free and proprietary versions. MariaDB MariaDB is a community developed version of MySQL, and is highly compatible with MySQL and other relational databases.
  • UVa Licensed SPSS on Ivy Windows VM

    SPSS Overview SPSS (or Statistical Package for Social Sciences), was initially developed as a social survey project but later on has grown to encompass statistical applications in almost all disciplines. Different industries use SPSS for their data analysis work. Its features include database management, reporting, graphing, among many others. SPSS Usage SPSS is available only on the Windows VM at the moment. To run SPSS go to: Start Menu > All Programs > IBM SPSS Statistics Licensing We have a limited number of SPSS licenses available, which are provided on a first-come-first-serve basis.
  • UVa Licensed IDL on Ivy Linux VMs

    IDL Overview IDL, short for Interactive Data Language, is an interactive shell based data analysis programming language. Used vastly in medical imaging, it can quickly create visualizations and graphs of large data sets in a few easy steps due to its vector nature. FORTRAN users would be familiar with the IDL syntax. IDL is not to be confused with Java IDL or Microsoft IDL. Basic IDL Usage To start IDL, open a terminal window and type idl.
  • UVa Licensed IDL on Ivy Windows VMs

    IDL Overview IDL, short for Interactive Data Language, is an interactive shell based data analysis programming language. Used vastly in medical imaging, it can quickly create visualizations and graphs of large data sets in a few easy steps due to its vector nature. FORTRAN users would be familiar with the IDL syntax. IDL is not to be confused with Java IDL or Microsoft IDL. Licensing We have a limited number of IDL Licenses available, which are provided on a first-come-first-serve basis.
  • UVa Licensed MATLAB on Ivy Linux Virtual Machines

    MATLAB Overview MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming environment. MATLAB stands for MATrix LABoratory. MATLAB was made to provide easy access to matrix software developed by the LINPACK (linear system package) and EISPACK (Eigen system package) projects. MATLAB includes a programming language environment with built-in editing and debugging tools, and supports object-oriented programming. Programming in MATLAB MATLAB has many advantages compared to conventional computer languages (e.
  • UVa Licensed MATLAB on Ivy Windows Virtual Machines

    MATLAB Overview MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming environment. MATLAB stands for MATrix LABoratory. MATLAB was made to provide easy access to matrix software developed by the LINPACK (linear system package) and EISPACK (Eigen system package) projects. MATLAB includes a programming language environment with built-in editing and debugging tools, and supports object-oriented programming. Programming in MATLAB MATLAB has many advantages compared to conventional computer languages (e.
  • UVa Licensed SAS on the Ivy Linux VM

    SAS Overview SAS is a command-driven software package used for statistical analysis and data visualization. It is available in . It is one of the most widely used statistical software packages in both industry and academia. You may use it if you have a large number of statistical algorithms. It is not limited to an industry, and could be used in both scientific and non-scientific contexts. We only offer the Teaching & Research version at the moment.
  • UVa Licensed SAS on the Ivy Windows VM

    SAS Overview SAS is a command-driven software package used for statistical analysis and data visualization. It is available in . It is one of the most widely used statistical software packages in both industry and academia. You may use it if you have a large number of statistical algorithms. It is not limited to an industry, and could be used in both scientific and non-scientific contexts. We only offer the Teaching & Research version at the moment.
  • User Licensed Stata on Ivy Linux VMs

    Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statiscs and Data. It is used in various disciplines, including biomedicine, economics, epidemiology, among others. It is capable of performing statistical analysis, simulations, regression, and data management. Besides the standard version Stata also ships with the MP version (multi=processing), and SE for large databases. NB Users requesting an installation of Stata would be required to bring their own license.
  • User Licensed Stata on Ivy Windows VMs

    Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statiscs and Data. It is used in various disciplines, including biomedicine, economics, epidemiology, among others. It is capable of performing statistical analysis, simulations, regression, and data management. Besides the standard version Stata also ships with the MP version (multi=processing), and SE for large databases. NB Users requesting an installation of Stata would be required to bring their own license.
  • cTAKES on Ivy Linux VMs

    cTAKES Overview cTAKES or The clinical Text Analysis and Knowledge Extraction System, is a Mayo Clinic developed Natural Language Processing (NLP) tool used to extract information out of clinical records. It is open-source, and built on the Apache Unstructured Information Management Architecture. cTAKES is modular, expandable, for a number of generic use cases, and contains excellent best practice notes. cTAKES Usage cTAKES components Some of cTAKES components are listed below:
  • cTAKES on Ivy Windows VMs

    cTAKES Overview cTAKES or The clinical Text Analysis and Knowledge Extraction System, is a Mayo Clinic developed Natural Language Processing (NLP) tool used to extract information out of clinical records. It is open-source, and built on the Apache Unstructured Information Management Architecture. cTAKES is modular, expandable, for a number of generic use cases, and contains excellent best practice notes. cTAKES Usage cTAKES components Some of cTAKES components are listed below:
  • Image Processing Software on Ivy Linux VM

    Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Linux VM KNIME KNIME is open source analytics platform for data mining and pipelining. KNIME’s Image Processing Plugin allows users to perform common image processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ. ImageJ ImageJ is a Java-based image processing program developed at the NIH.
  • Image Processing Software on Ivy Windows VM

    Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Windows VM Axiovision Axiovision is software for microscopy image processing and analysis. Axiovision is highly configurableto meet the needs of your individual workflows. KNIME KNIME is open source analytics platform for data mining and pipelining. KNIME’s Image Processing Plugin allows users to perform common image processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ.
  • Preinstalled Java SDK on Ivy Windows VM

    Java SDK Overview Ivy Windows VMs are installed with Java SDK 1.8. Java is a popular Object Oriented programming language and is used in a multitude of scenarios. It is available under the GNU General Public License for all users. The SDK consists of a large number of tools such as javac that help in application development. Running Java commands from the Command Prompt Open a Windows Command Prompt and enter java followed by the desired command.
  • Preinstalled Rodeo On Ivy Windows VM

    Rodeo Overview Our Windows VMs are installed with Rodeo version 1.3, as of the last update. Rodeo is a lightweight, Python based, IDE for data science. It has a very streamlined code-to-plot workflow, with easily extensible packages that make it simple to analyze difficult patterns in data. It includes many data analysis features under one roof, and adopts features from iPython Notebook (it actually runs atop the iPython kernel). Like most Python projects, it is open source and available for free.
  • Preinstalled Rodeo on Ivy Linux VM

    Rodeo Overview Our Linux VMs are installed with Rodeo version 2.5, as of the last update. Rodeo is a lightweight, Python based, IDE for data science. It has a very streamlined code-to-plot workflow, with easily extensible packages that make it simple to analyze difficult patterns in data. It includes many data analysis features under one roof, and adopts features from iPython Notebook (it actually runs atop the iPython kernel). Like most Python projects, it is open source and available for free.
  • Preinstalled Strawberry Perl on Ivy Windows VM

    Perl Our VMs have Strawberry Perl 5.24 available as part of the Windows VM, as of the last writing. Licensed as open source under the GPL, it is most often used to develop mission critical software, and has excellent integration with markup languages such as HTML, XML, amongst others. Since it is both Object Oriented as well as procedural, it could be used within a multitude of programming projects. It includes built in database integration via its DBI module.
  • Sumatra PDF on Ivy Windows VM

    Sumatra PDF Overview Sumatra PDF is an open source software to view PDF files in Windows. It could be used to view PDF documents stored within the Ivy VM. As of the latest version, Sumatra supports multiple formats including PDF, EPUB, MOBI, and XPS. Running Sumatra PDF From the Start menu, go to All Programs and search for Sumatra PDF. Click on the icon to run it. More Information For more information, visit the Sumatra PDF official website.
  • Preinstalled R on Ivy Linux VM

    R Overview R is an open source programming language, used by Data Miners, Scientists, Data Analysts, and Statisticians. It is available under the GNU GPL V2 license from the Comprehensive R Archive Network R can be used for many statistical, modeling, and graphical solutions. It is very Object Oriented in nature and is easily extensible. Running the command line R console Type R at the terminal to launch the R console.
  • Preinstalled R on Ivy Windows VM

    R Overview R is an open source programming language, used by Data Miners, Scientists, Data Analysts, and Statisticians. It is available under the GNU GPL V2 license from the Comprehensive R Archive Network R can be used for many statistical, modeling, and graphical solutions. It is very Object Oriented in nature and is easily extensible. Running Rstudio from the desktop You can start R in a Graphical interface using the RStudio application from the desktop
  • Preinstalled Python 2 and Python 3 with Anaconda on Ivy Linux VM

    Anaconda Our VMs have python 2 and 3 available as part of the Anaconda distribution. Anaconda comes installed with many packages best suited for scientific computing, data processing, and data analysis, while making deployment very simple. Its package manager conda installs and updates python packages and dependencies, keeping different package versions isolated on a project-by-project basis. Anaconda is available as open source under the New BSD license. It also ships with pip, the common python package manager.
  • Preinstalled Python 2 and Python 3 with Anaconda on Ivy Windows VM

    Anaconda Our VMs have python 2 and 3 available as part of the Anaconda distribution. Anaconda comes installed with many packages best suited for scientific computing, data processing, and data analysis, while making deployment very simple. Its package manager conda installs and updates python packages and dependencies, keeping different package versions isolated on a project-by-project basis. Anaconda is available as open source under the New BSD license. It also ships with pip, the common python package manager.
  • Quick Start

    User Support School of Medicine Research Computing (SOMRC) is committed to providing individualized support for researchers who are engaged in computationally intensive projects. We offer support in a variety of contexts: Support tickets in ZenDesk Documentation & FAQs Weekly Office Hours Hands-On Workshops In-person Consultations Learn more
    Services SOMRC has expertise in the following service areas. Click on an area for more information: Bioinformatics & Genomics Cloud Solutions Data Analysis Image Processing Scientific Computing Request a Consultation

  • Ivy Domino Data Lab (DDL) Quick Start

    Domino Data Lab (DDL) provides a central environment and features for data science projects including project management, collaboration with team members, and setting up hardware configuration for a project. Account Request Access to DDL to Ivy is managed through the Ivy account request process. Accounts are issued on a per project basis, with PIs (and any project members) being granted individual accounts to log into the DDL platform. Once the request has been approved and all associated members have completed the necessary documentation, each individual project member can sign into DDL with his / her UVa Eservices user name and password.
  • Computing Systems

    UVA Research Computing can help you find the right system for your computational workloads. From supercomputers to HIPAA secure systems to cloud-based deployments with advanced infrastructure, various systems are available to researchers. Rivanna HPC A traditional high performance cluster with job scheduler, large file system, modules, and MPI processing. Please see the ARCS page for how to begin working in Rivanna. Get Started on Rivanna
    Ivy Secure Platform A multi-platform, HIPAA-compliant system for secure data that includes dedicated virtual machines (Linux and Windows), Domino Data Lab, and Hadoop/Spark.

  • Preinstalled Office 2016 on Ivy Windows VM

    Microsoft Office Overview The Ivy Windows VMs are installed with Microsoft Office 2016. Features such as OneDrive are not available since Ivy is not connected to the public internet. Therefore in order to load documents in and out of the VM, you would have to use the Globus DTN. Softwares available The following software are available for use on the Ivy Windows VM: Word 2016 Excel 2016 PowerPoint 2016 Access 2016 OneNote 2016 Outlook 2016 Publisher 2016 Running Office All Office software could be accessed from the Start menu using Start > All Programs
  • User Guides

    High Performance Computing Standard and high security HPC to run your code, generally written in R, Python or shell scripts. Get Started › Learn More › – Storage Need large, or extremely large storage offsite or on grounds? Can you count in GB, TB, or PB? Learn more about storage options and pricing. Get Started › Cloud Have an idea you’d like to test?
  • High Performance Computing

    This page is for HPC information.
  • Scientific Computing

    School of Medicine Research Computing supports SOM and UVa Medical Center researchers who are interested in writing code to address their scientific inquiries. Whether these programming tasks are implemented interactively, in a series of scripts or as an open-source software package, services are available to provide guidance and enable collaborative development. SOMRC has specific expertise in object oriented programming in Matlab, R, and Python. Examples of service areas include: Collaborating on package development Reviewing and debugging code Preparing scripts to automate or expedite tasks Developing web interfaces for interactive data exploration Advising on integration of existing software tools UVA has two local HPC facilities available to researchers: Rivanna and Ivy.
  • Perl

    Perl Our VMs have Perl 5.16.3 available as part of the base linux VM. Licensed as open source under the GPL, it is most often used to develop mission critical software, and has excellent integration with markup languages such as HTML, XML, amongst others. Since it is both Object Oriented as well as procedural, it could be used within a multitude of programming projects. It includes built in database integration via its DBI module.