Facilities and Resources

Laboratory equipment

We are an interdisciplinary lab that is part of the department of Computer Science and the Genome Center at UC Davis. Our experimental lab has 1000 square feet of laboratory space located on the fifth floor of the Genome and Biomedical Sciences Facility (GBSF). Our laboratory is equipped or have access to all aspects of recombinant DNA manipulation, genetic analysis and expression profiling. This include electrophoresis equipment, incubators, PCR/qRT-PCR machines, freezers, containment hood, balances, ultra/super-speed centrifuges, a sonicator and a NBS BioFlo 115 bioreactor, among others.

Computational resources

The lab has access to the Genome Center computing facilities and bioinformatics support which includes a 110-node, 440 core cluster of dual-core/dual-processor AMD Opteron machines with at least 4GB RAM (32 nodes have 8GB); an 8 node, 28 screen data visualization wall; a 14 graphics processing unit (GPU) Nvidia cluster; a mixed cluster consisting of 57 nodes of Intel and AMD Opteron machines; a Windows server set up for remote desktop access; a 32-core Opteron large-memory machine with 512GB RAM; a 16-core Opteron machine with 128GB RAM; and 8 dual-processor Itanium2 machines. There is over 50TB of storage spread across several fileservers (including a Sun X4500), a 5.5TB backup fileserver, and a Sun/StorageTek backup server with a 2TB disk array and a 30-slot LTO3 tape jukebox. Additionally, the lab has access to the computing resources of the CS department that houses a 40-node High Performance Computing (HPC) cluster. The Computer Science cluster contains 80 CPU's, 160GB of RAM and a 4TB shared storage system. Nodes of the cluster interact through gigabit Ethernet and are available to Computer Science faculty, researchers, students and other campus departments with HPC needs. The cluster is managed by ROCKS 4.2 and cluster job management is performed by Sun Grid Engine. Through NSF grant #0941360 the lab is one of the PRAC teams with an allocation to the Blue Waters Supercomputer for the next 5 years. The Blue Waters project is a $207 million, NSF-funded, state-of-the-art Petascale supercomputer that will be hosted in NSCA (Illinois), and will it is scheduled to become operational in late 2011. The lab has also a 1,200,000 SU Teragrid allocation through grant TG-ASC110007 in various supercomputing systems. Office space for the Tagkopoulos Lab is provided in the 5th of the Genomic and Biomedical Sciences Facility, where the UC Davis Genome Center is located. Additionally, office space has been provided for the PI, and any graduate students or postdoctoral researchers of the lab by the department of Computer Science, which is located in Kemper Hall at the UC Davis Campus.

Genome Center Cores

The Genome Center operates professional cores that are staffed with professionals (5-10 people per core). These services are available on recharge basis and are the following: