Please include the following text in research proposals to describe the computational and sequencing resources available through the Institute for Systems Genomics (Last Update May 2024):

The Computational Biology Core (CBC) within the Institute for Systems Genomics at the University of Connecticut supports bioinformatics research, teaching, and outreach. High Performance Computing (HPC) resources, including the Xanadu and Mantis clusters, are housed in a secure data center at the Cell and Genome Sciences Building on the UCHC Farmington campus. All servers are freely available to members of the UConn research and their research affiliates.

The Xanadu, Mantis, and NMR high performance compute cluster is comprised of compute nodes with over 12,000 CPU cores, 77 TB of RAM, and capable of processing at 360 TFLOPs. The nodes are a mix of Dell Xeon and Opteron, and Penguin Xeon nodes. Node memory ranges from 128 GB to 2 TB of RAM. Additional resources include 3008 NVIDIA Tesla M2075 and NVIDIA A100 GPU cores. All nodes are equipped with ten-gigabit interfaces and connected to a 10/40/100/400 gigabit network infrastructure.

Isilon, Qumulo, Quantum, and Weka Network Attached Storage systems are provided with a capacity of ~16 petabytes. An additional 3+ petabytes of Scality geo-spread object storage is provided as a long term archival storage solution.

All clusters allow access to over 300 bioinformatic modularized and/or containerized applications. These applications support analysis in phylogenetics, metagenomics, genome assembly, transcriptome assembly, sequence alignment, sequence annotation, variant detection, Chip-Seq, proteomics, and a variety of visualization tools.

The facility is directed by Dr. Jill Wegrzyn and operated by Dr. Vijender Singh and Dr. Noah Reid. Data Center hardware, software and networking support is provided by Stephen King and Michael Wilson. The HPC facility is directed by Dr. Ion Moraru.

The Center for Genome Innovation (CGI) within the Institute for Systems Genomics on the University of Connecticut, Storrs campus, has established next generation library preparation and sequencing capacity, including all necessary ancillary equipment for the following sequencing platforms: Illumina NovaSeq 6000 (x1), MiSeq (x2), Illumina NextSeq 550 (x1), Oxford Nanopore MinION (x5) and PromethION-24 (x1), and PacBio Sequel IIe (x1) and Revio (x1). The Illumina NextSeq 550 sequencer on the Storrs campus has the ability to scan Infinium CytoSNP 850K and Infinium EPIC Methylation arrays for human only. The CGI offers both supervised and unsupervised access to most instrumentation and training for use and implementation, along with an option to process samples through a fee-for-service structure. The CGI is also capable of assisting with protocol development for various applications and technologies.

The sample processing and teaching laboratory is equipped with standard molecular biological equipment, including thermal cyclers for standard and quantitative PCR (CFX96 Real Time, x2), standard and automated gel electrophoresis systems, centrifuges, single and multichannel micropipettors, water baths, incubators, refrigerators and freezers for sample and reagent storage. Specific (major) equipment available for use include the: Beckman Allegra X-12R Refrigerated Centrifuge, Agilent TapeStation 4200 (x2), Agilent Femto Pulse, Qubit 3.0, two PCR hoods, chemical and biosafety hoods, Pippin Prep (including Pippin Prep, Blue Pippin and Pippin HT systems), and a Covaris S2.

Genomics projects are further enhanced by the 10x Chromium Genomics System for single cell applications like mRNA-Seq, ATAC-Seq and immunology profiling. The CGI has a BioRad QX200 Droplet Digital PCR instrument which can be used for absolute copy number, mutation and gene expression detection.

The CGI is directed by Dr. Rachel O'Neill and scientific director, Dr. Bo Reese.