Facilities and Other Resources

Please include the following text in research proposals to describe the computational resources available (As of June 2017):

Center for Genome Innovation

Laboratory: 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: Applied Biosystems 5500xl with EZ Bead Enrichment System, two Illumina MiSeq and two Illumina NextSeq 500 systems, in addition to several Oxford Nanopore MinIONs. The laboratory is equipped with standard molecular biological equipment and resources, including thermal cyclers, standard and automated gel electrophoresis systems, centrifuges, micropipettors, water baths, incubators, refrigerators and freezers for sample and reagent storage.  Ancillary equipment available for use include the: Beckman Allegra X-12R Refrigerated Centrifuge, Agilent Bioanalyzer 2100, Agilent TapeStation 2200, two PCR hoods, chemical and biosafety hoods, ABI 3500 DNA Analyzer, Affymetrix GeneAtlas and GeneChip hybridization and scanning systems, a Hydoshear, Pippin Prep, Fluidigm instruments including the C1, BioMark HD and various Access Arrays, and a Covaris S2.  Genomics projects are further enhanced by the recent addition of the 10X Chromium Genomics System for long-range whole genome and exome library preparation, as well as single cell mRNA-Seq.  The BioNano Irys System is also available for use in genome integrity studies looking at structural variation and haplotyping.  The CGI offers both supervised and unsupervised access to 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

The CGI is directed by Dr. Rachel O'Neill and operated by scientist, Dr. Bo Reese.

Computational Biology Core

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

The UConn Health High Performance Facilities Xanadu compute cluster is comprised of 44 nodes. The nodes are a mix of Dell C6145 chassis with four 12-core AMD Opteron processors and Dell R730 chassis with two, 18-core Intel Xeon E5-2697v4 processors. Node memory ranges from 128 GB to 512 GB of RAM. Additional resources include NVIDIA M2075 448 core GPU’s. All nodes are equipped with ten-gigabit interfaces and connected to a 10/40/100 gigabit network infrastructure.

Isilon and Qumulo Network Attached Storage systems are provided with a capacity of 6+ petabytes. An additional 3+ petabytes of geo-spread cloud storage is provided via an Avere gateway with 30 gigabit-per-second aggregate throughput. 

All clusters allow access to over 100 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 two scientists, Dr. Vijender Singh and Dr. Neranjan Perera. Data Center hardware, software and networking support is provided by Stephen King and Michael Wilson.