The Bumgarner lab is located in the recently re-modeled state-of-the-art Rosen building. This facility was designed with high-availability computing and high-throughput genomics in mind and is unique amongst UW facilities.
Infrastructure:
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Networking: 100bT and fiber networking throughout the building provide high speed connectivity within. The building is also on a major trunk of the Gigabit internet network for Seattle.
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Power backup: Many of the outlets in the building (including all the one in the labs and the computer room) are on a building wide uninterruptible power supply (UPS). The UPS system is backed up by two diesel generators that each have 24 hours of fuel and which are regularly tested. Power for lab freezers and refrigerators are also backed up with the generator system.
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Computing facility: Computer servers within the building are stored in a secure (key-card access) room designed specifically for computing. A dry fire suppression system protects the equipment from fire related disasters and a redundant cooling system protects the equipment from air conditioning failure. Overhead racks provide easy access for power and network cabling.
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Earthquake safety: The Rosen building was fully rebuilt in 1999/2000 and was retrofitted to the highest earthquake standards of almost any building in the city.
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Tissue culture: Several BSL2 and one large BSL3 tissue culture labs are available within the building. FACS analysis is available within the BSL3 space.
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Location and aesthetics: The Rosen building is located about 3 miles from the main campus in the beautiful and rapidly developing South Lake Union area. Shuttle service (every 20 mins) to campus is provided on weekdays and the building is a 15 min walk from downtown shopping. The interior and exterior of the building provide a bright and cheery environment in which to work.
Equipment:
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Microarray: A full range of microarray equipment capable of processing both Affymetrix and glass slide arrays exists within the lab. {pictures}
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Differential Gel Electrophoresis (DiGE): Proteomics capability within the lab consists of a 2-D gel electrophoresis system and imaging equipment from Amersham (now GE Life Sciences) {link to DIGE info on their site} . In brief, this system allows us to to 2-D gel electrophoresis on 1,2 or 3 samples (each labeled with a different fluorophore) simultaneously.
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Three 96-well PCR machines (two with 384 well heads) provide the lab with capabilities for high throughput genotyping using the Affymetrix SNP chip system.
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BioAnalyzer: The lab contains an Agilent bioanalyzer (capillary electrophoresis) system that we use daily for RNA analysis and quality control.
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A wide range of other standard molecular biology equipment (centrifuges, large and small format gel boxes, ovens, incubators etc.) are available within the lab.
Computing equipment:
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Several high speed (>1.5Ghz) Pentium IV computers with 1GB RAM, large hard drives and 19" or larger monitors are available for data analysis. Four are housed in racks in the Rosen facility and are provided for remote terminal login and three are housed on desks in the Rosen bldg. All are equipped with ImageQuantV from Molecular Dynamics, SpotFire client software, Affymetrix GCOS software and our custom software for image and data analysis.
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Data storage and database services are provided by two 8 processor Sun V880's with 32GB RAM, and one 16 processor Sun E6500 located at Rosen. The V880’s provide high speed, "number crunching" ability for jobs that require large amounts of RAM and provide file service to a 2 terabyte RAID array for used data storage.
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Nightly backups are obtained using a 4-drive 50-tapeLTO-2 robotic tape backup system as well as a 8-tape LTO-2 failover robotic tape backup system. An dual 2.8 GHz Pentium IV Xeon processor computer with 8GB RAM and 600GB of local RAID drives is used to house a GeneTraffic database and analysis server. This system provides permanent data storage and analysis for both single color and two-color microarray data. Also available for general file storage are two RAID arrays attached to redundant file servers providing over 3.2 terabytes of disk space.
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Additional statistical analysis resources include a dual 2.5GHz Athlon MP processor computer with 8GB RAM as well as an 7-processor Sun E4500 with 8GB RAM. In addition, we have purchased and integrated Spotfire analysis software with the GeneTraffic server. Spotfire provides high end visualization and analysis tools for array (and other types of) data.
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Finally, we have also integrated SpotFire with an R statistical analysis server. This provides the ability to perform more customized analyses that may not be hard coded within the other tools. One HP4600 color printer and several other laser printers are available on the local network.
