Facilities and Other Resources

Please include the following text in research proposals to describe the computational and sequencing resources available through the Institute for Systems Genomics (Last Update July 2019):

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 cluster 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 compute cluster is comprised of 51 compute nodes with 2168 CPU cores, 11 TB of RAM, and capable of processing at 50 TFLOPs. 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 1 TB of RAM. Additional resources include 2688 NVIDIA M2075 GPU cores. 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 8+ petabytes. An additional 3.8 petabytes of geo-spread object storage is provided via an Avere gateway with 30 gigabit-per-second aggregate throughput. 

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 two scientists, Dr. Vijender Singh and Dr. Neranjan Perera. 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 MiSeq (x2) and Illumina NextSeq 500 systems (x2), in addition to Oxford Nanopore MinIONs and a PromethION system.  The Illumina NextSeq 500 sequencer on the Storrs campus (main lab) has the ability to scan select Infinium bead arrays as part of the upgrade package to the 550 model. 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 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, 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 Bioanalyzer 2100, Agilent TapeStation 2200 and 4200, Qubit 3.0, two PCR hoods, chemical and biosafety hoods, ABI SeqStudio DNA Analyzer, Affymetrix GeneAtlas and GeneChip hybridization and scanning systems, DigiLab Hydoshear, Pippin Prep (including PippinPrep, Blue Pippin and Pippin HT systems), Fluidigm instruments including the C1, BioMark HD and various Access Arrays, and a Covaris S2. 

Genomics projects are further enhanced by the 10X Chromium Genomics System for long-range whole genome and exome library preparation, as well as single cell applications like mRNA-Seq, ATAC-Seq and immunology profiling.  The BioNano Irys System is also available for use in genome integrity studies looking at structural variation and haplotyping. The CGI also has a BioRad QX200 Droplet Digital PCR instrument which can be used for absolute copy number, mutation and gene expression detection.    

The Chromosome Core division of the CGI (also within the Institute for Systems Genomics on the University of Connecticut, Storrs campus) provides classical chromosome and karyotype analyses via G-banding and FISH as well as CGH/CNV/SNP and transcriptome array testing on multiple platforms.  Molecular karyotyping can also be done using the Infinium CytoSNP 850K array (Illumina).  

The CGI is directed by Dr. Rachel O'Neill and scientific director, Dr. Bo Reese.  The Chromosome Core division is directed by Dr. Rachel O’Neill and Dr. Judy Brown.