UVA Research Computing

Research Computing

Creating innovative solutions for researchers

/tag/tools

  • BART Web

    BART (Binding Analysis for Regulation of Transcription) Web Working with researchers in the Zang Lab in the Center for Public Health Genomics (CPHG), RC helped launch BARTweb, an interactive web-based tool for users to analyze their Genelist or ChIP-seq datasets. BARTweb is a containerized Flask front-end (written in Python) that ingests files and submits them to a more robust Python-based genomics pipeline running on Rivanna, UVA’s high performance computing cluster (HPC). This architecture – of a public web application that uses a supercomputer to process data – is a new model for UVA, and one that eases the learning curve for researchers who may not have access to an HPC system or the expertise to run a BART pipeline in the command-line.
  • Bioinformatics Resources on Rivanna

    UVA research community has access to numerous bioinformatics software installed and ready-to-use on Rivanna. They are all available via the LMod module system. In addition, Click here for a comprehensive list. Popular Bioinformatics Software Below are some popular tools and useful links for their documentation and usage: .tg {border-collapse:collapse;border-spacing:0;border-color:#ccc;} .tg td{font-family:Arial, sans-serif;font-size:14px;padding:10px 5px;border-style:solid;border-width:0px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#fff;} .tg th{font-family:Arial, sans-serif;font-size:14px;font-weight:normal;padding:10px 5px;border-style:solid;border-width:0px;overflow:hidden;word-break:normal;border-color:#ccc;color:#333;background-color:#f0f0f0;} .tg .tg-hy9w{background-color:#eceeef;border-color:inherit;vertical-align:middle;} .tg .tg-dc35{background-color:#f9f9f9;border-color:inherit;vertical-align:middle;} .tg .tg-hy9w-nw{background-color:#eceeef;border-color:inherit;vertical-align:middle;white-space:nowrap;} .tg .tg-dc35-nw{background-color:#f9f9f9;border-color:inherit;vertical-align:middle;white-space:nowrap;} .tg .tg-0qmj{font-weight:bold;background-color:#eceeef;border-color:inherit;vertical-align:middle;} .scroll thead, .scroll tbody {display: block} .scroll tbody {overflow-y: auto; height: 500px;} .scroll thead tr:after {content: “;overflow-y: scroll; visibility: hidden; height: 0;} Tool Version Description Useful Links BEDTools 2.
  • Bioinformatics User Guides

    Bioinformatics on Rivanna UVA’s High-performance Computing Cluster All faculty, research staff and graduate students of UVA have access to Rivanna, university’s high-performance computing system with 290+ compute nodes (6500+ cores) for high-throughput multithreaded jobs, parallel jobs as well as memmory intensive large-scale data analyses. The architecture is specifically suited for large scale distributed genomic data analysis, with 100+ bioinformatics software packages installed and ready to use. Learn more Bioinformatics using FireCloud FireCloud Home