UVA School of Medicine

Research Computing

Enabling scientific breakthroughs at scale with advanced computing

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  • LOLAweb

    The past few years have seen an explosion of interest in understanding the role of regulatory DNA. This interest has driven large-scale production of functional genomics data resources and analytical methods. One popular analysis is to test for enrichment of overlaps between a query set of genomic regions and a database of region sets. In this way, annotations from external data sources can be easily connected to new genomic data.
  • PHACTR1 and Smooth Muscle Cell Behavior

    Coronary artery disease (CAD) is the major cause of morbidity and mortality worldwide. Recent genome wide association studies (GWAS) have revealed more than 50 genomic loci that are associated with increased risk for CAD. However, the pathological mechanisms for majority of the GWAS loci leading to increased susceptibility to this complex disorder are still unclear. SOMRC is working with Redouane Aherrahrou (CPHG) who aims to study the impact of the CAD-associated genetic factors on the cellular and molecular SMC phenotypes.
  • epihet

    SOMRC is working with researchers in the Center for Public Health Genomics to write an R package to calculate Relative Proportion of Sites with Intermediate Methylation (RPIM) scores, which represent the epigenetic heterogeneity in a bisulfite sequencing sample. https://github.com/databio/epihet PI: Nathan Sheffield (Center for Public Health Genomics)
  • simpleCache

    In partnership with researchers in the Center for Public Health Genomics, School of Medicine Research Computing has contributed to the development of a novel package for computationally efficient caching and loading of data in R. simpleCache provides an interface to a series of functions to store and retrieve cached objects, including in the context batch processing or HPC environments. The package further extends base R functionality of saving and loading external representations of objects by enabling caching to pre-defined directories and timed cache operations.
  • 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
  • Courses

    In addition to providing free, in-person workshop training, School of Medicine Research Computing staff teach for-credit courses. Below is a selection of courses that SOMRC has taught, co-taught or provided guest lectures: BIMS 8382: Introduction to Biomedical Data Science Spring 2017, Spring 2018 This course introduces methods, tools, and software for reproducibly managing, manipulating, analyzing, and visualizing large-scale biomedical data. Specifically, the course introduces the R statistical computing environment and packages for manipulating and visualizing high-dimensional data, covers strategies for reproducible research, and culminates with analysis of data from a real RNA-seq experiment using R and Bioconductor packages.
  • Workshops

    School of Medicine Research Computing provides training opportunities covering a variety of data analysis, basic programming and computational topics. All of the classes listed below are taught by SOMRC experts and are freely available to UVa faculty, staff and students.

    Register Register for SOMRC workshops through CADRE Academy, a new portal that presents workshops sequentially in tracks of particular topics. Users can register for upcoming sessions, follow their progress, and find out about related classes on the site.


  • 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.
  • Data Analysis

    School of Medicine Research Computing can help with accessing, preparing, visualizing and analyzing data. We can assist you by implementing your analysis strategy in an appropriate computing language, including R, Python and Matlab. We will work with you to prepare scripts that are are reproducible, efficient and flexible. Manipulation Data analysis generally involves a significant effort to transform, aggregate, subset or otherwise prepare a dataset. That could include dealing with missing values as well as merging or joining multiple datasets.