/tag/python
Workshops
UVA 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 experts and are freely available to UVa faculty, staff and students.
New to High-Performance Computing? We offer orientation sessions to introduce you to the Afton & Rivanna HPC systems on Wednesdays (appointment required).
Wednesdays 3:00-4:00pm Sign up for an “Intro to HPC” session Upcoming Workshops DATE WORKSHOP INSTRUCTOR There are currently no training events scheduled. Please check back soon! Research Computing is partnering with the Research Library and the Health Sciences Library to deliver workshops covering a variety of research computing topics.
education,
workshops
bioinformatics,
containers,
HPC,
image processing,
Ivy,
Matlab,
programming,
Python,
R,
Rivanna,
Shiny
ACCORD
Welcome to ACCORD (Assuring Controls Compliance of Research Data), a web-based platform which allows researchers from public universities across the state of Virginia to analyze and store their sensitive data in a central location.
ACCORD is appropriate for de-identified PII, FERPA, de-identified HIPAA, business confidential, and other types of de-identified sensitive data
Thanks to funding provided by the National Science Foundation (Award #: 1919667), ACCORD is available at no cost to researchers in the state of Virginia.
Partners Listed below are our partner universities for ACCORD:
Get Started About Learn about ACCORD.
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ACCORD Environments
Back to Overview
After creating a project and logging into the ACCORD platform, you will next choose an environment. The environments currently available on ACCORD are listed below. We welcome your suggestions for additional environments to be included in the future.
RStudio RStudio is the standard IDE for research using the R programming language. JupyterLab Jupyter Lab allows for interactive, notebook-based analysis of data. A good choice for pulling quick results or refining your code in numerous languages including Python, R, Julia, bash, and others. Theia Python Theia Python is a rich IDE that allows researchers to manage their files and data, write code with an intelligent editor, and execute code within a terminal session.
Migrating Python packages
Scenario You have installed Python packages locally in one version and now wish to use them in a different version. For example, you have been using Python 3.6 but it is obsolete and will be removed soon, so you need to set up those packages for Python 3.8. There are several ways to accomplish this, depending on the package manager. In this how-to we will discuss pip and conda.
You will need to load the module for the newer Python version. For this example,
module load anaconda/2020.11-py3.8 Pip The Python packages are installed in a hidden location under your home directory:
Refgenie: A Reference Genome Resource Manager
Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; e.g., many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this.
Refgenie is a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.
