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 are housed at the Storrs campus (BBC) as well as UCHC (HPC1).  All servers are freely available to members of the UConn research and their affiliates.  The BBC cluster is running Centos (v6.3) and Rocks (v6.1 x64) with 1 Microway Navion Operteron Quadputers (16 x Quad-core 2.5 Ghz AMD 6370P processors with 512 GB RAM), 1 Dell PowerEdge R710, 17 PowerEdge R410 nodes (2 x Quad-core 2.53 GHz Intel Xeon processors with 32 GB RAM), 4 PowerEdge R720 nodes (2 x 8-core 2.00 GHz Intel Xeon processors with 64 GB RAM), and 10 Asus RS161-E4 nodes (2 x Dual-core 2.8 GHz AMD processors with 16 GB RAM).  The cluster is attached to a Dell PowerVault MD1000 disk array containing 18TB of storage (RAID 5).  The cluster is connected via gigabit Ethernet internally.  

The UConn Health High Performance Facility has two production compute clusters.  The first has 18 nodes (Dell C6145 chassis with four 12-core AMD Opteron processors and 128 GB of RAM).  It has a Dell C410x PCI expansion chassis with 16 NVIDIA M2075 GPGPU’s attached to four of the compute nodes.   The server is interconnected with ten-gigabit and has ten-gigabit interfaces to the public network.  

The second compute cluster runs StackIQ (Rocks+) and has 14 nodes (Dell C6145 chassis with four 16-core AMD Opteron processors and either 128 GB RAM or 256 GB RAM).  This cluster has gigabit interconnects and gigabit interfaces to the public network.  Both clusters use a shared Isilon clustered file server of 282TB and 50 gigabit-per-second aggregate throughput. 

An archival storage system is used by all clusters.  It is a scalable Amplidata storage system with an Avere gateway and 1 PB in capacity with 30 gigabit-per-second aggregate throughput.  

All clusters allow access to over 100 bioinformatic 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.  The hardware is supported by two system administrators that work across both campuses (Stephen King and Neranjan Perera).