/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.
Upcoming Workshops DATE WORKSHOP INSTRUCTOR Oct 12, 2023
High Performance Computing from your Web BrowserPaul Orndorff Oct 19, 2023
High Performance Computing from a Terminal WindowAhmad Sheikhzada, Gladys Andino Oct 23, 2023
Using Containers on RivannaRuoshi Sun Oct 26, 2023
High Performance Computing Best PracticesEd Hall, Ahmad Sheikhzada, Paul Orndorff Oct 30, 2023
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.
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 For example, you have been using Python 3.6 but it is obsolete and will be removed soon, so you need to set up those packages for Python 3.8.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 $('#copybtn541762839').click(function(){ var $temp = $(""); $(“body”).append($temp); $temp.val($('#541762839').text()).select(); document.
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.
Data Analysis
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 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. We can help you wrangle your data into a “tidy” format in order to analyze the features and observations relevant to your question.
