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:
- The DNA Technology Core provides high throughput genotyping and fingerprinting. Equipment available includes HiSeq2000, MiSeq, PacBio machines, library preparation services, a Spectrumedix Reveal TDGGE, Luminex Flow System, Affymetrix Microarrays facility, Illumina Golden Gate / bead array genotyping equipment, BeadExpress reader system, and Luminex microsphere sorter (for medium-throughput genotyping).
- The Proteomics Core provides state-of-the-art analytical proteomic services with particular emphasis on label free quantitative proteomic profiling, the analysis of macromolecular complexes, the post-translational modification of their constituents and standard protein identification from complex protein mixtures. The Core has a staff of six including two Ph.D. scientists. For high throughput identification and characterization of proteins and peptides the Core has at its disposal several state of the art LC-MS/MS systems including a new Thermo Scientific Q-Exactive Orbitrap mass spectrometer connected to an EASY nLC II system, a LTQ-FT Ultra hybrid Fourier Transform Ion Cyclotron tandem mass spectrometer connected to a Waters Acuity Ultra High Pressure Nano UPLC, two Thermo Scientific LTQ tandem mass spectrometers connected to a Michrom Paradigm HPLC's, and a Thermo Scientific TSQ Vantage Triple Quadrupole mass spectrometer for quantitative multiple reaction monitoring (MRM) targeted proteomics experiments. Core personnel can also provide amino acid analysis using one of three Hitachi amino acid analyzers and N-terminal sequencing using one of two N-terminal sequencers if needed.
- The Metabolomics Core provides high-quality, cost-effective, state-of-the-art analytical services for metabolomics research and small molecule analysis. The Core offers GC-MS and LC-MS lines for metabolic profiling using high quality standards, Regents, and solvents. It provides assistance with the experimental setup, design, data interpretation, and statistical analysis. The Core has a Pegasus III TOF mass spectrometer (Leco) coupled with Agilent GC and Gerstel autosampler, including the MPS PrepStation and AutomatedLinerEXchange (ALEX); a Thermo Electron LTQ (linear ion trap) mass spectrometer coupled to Surveyor HPLC separation system, and a Thermo-Fisher Scientific LTQ-FT Ultra Fourier transform ion cyclotron tandem mass spectrometer (FTICR) (shared with the Proteomics Core) coupled to NanoMate-ESI robotic device (Advion BioSciences). In addition, we have an Applied Biosystems Qtrap 4000 (shared with the Proteomics Core) coupled to Waters Acquity UPLC separation module equipped with the column manager;
- The Bioinformatics Core provides expertise and infrastructure for the acquisition, curation, analysis, and distribution of large complex datasets as well as develops and performs computations, analyses and simulations addressing a wide variety of biological questions from genomics to network biology. The Core has seven staff members with overlapping expertise in computing infrastructure, Web/database, scientific programming, biological annotation and statistics. The core provides bioinformatics support for the wetlab service cores as well as for individual researchers with individual bioinformatics needs. The computing infrastructure of the Core includes: high performance computing clusters: a 110-node cluster of 4-core AMD Opteron CPUs with 4GB of RAM (32 nodes have 8GB of RAM), a mixed cluster consisting of ~80 nodes of Intel and AMD Opteron CPUs (10 nodes have 32BG RAM), a cluster of 8 GPU nodes each with 448 cores and 6 Gb of memory (to provide a total of 3,584 cores); data storage servers of 300TB spreading across several fileservers including three Sun X4500, Isilon storage cluster and Linux based fileservers; backup servers: a 16TB fileserver in offsite for disk to disk backup, a Sun/StorageTek backup server with a 2TB disk array and a 30-slot LTO3 tape jukebox for tape backup; ultra large memory machines: three servers with 128GB, 144GB and 512GB of RAM respectively; application servers: a Windows server for Windows specific Bioinformatics software tools and work stations for software developers and guests; cloud computing: a preserved instance in Amazon Cloud and tools to access scalable resources provided by the Amazon Cloud Services; network bandwidth: a 10Gbit/s network connection to Corporation for Education Network Initiatives in California (CENIC) and National Lambda Rail.