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Resources for grant proposals


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RESOURCES FOR GRANT PROPOSALS Last updated December 11, 2014
Grant proposals often require or benefit from a description of CGRB’s capabilities and services. Budget justifications usually require a detailed description of the biocomputing services sufficient to show the fees for them are allowable as direct costs. The following text contains passages that can be copied and included into your grant proposals.
If you need a more specific support letter, please email Brett Tyler (brett.tyler@oregonstate.edu) at least 5 days before your deadline, including the name of the funding agency and the specific program you are applying to, the title and abstract of the proposal, and any other specific information you need included. Fully written draft letters are always welcome.
If you wish to budget salaries for one or more of the CGRB staff into your proposal for the purpose of funding a long-term collaboration with the CGRB, please contact Brett Tyler (brett.tyler@oregonstate.edu) to discuss your plans, at least 3 weeks before your deadline.
Justification for CGRB Biocomputing fees
Research Computing Services

Funds are requested for research computing services provided by the Center for Genome Research and Biocomputing.  These services include software setup, optimization, maintenance and backup of the project research computers, use of the CGRB computing grid including the research software tools installed on the grid, and consultation on software usage and development. These functions are specific to the proposed research and do NOT include general computing services such as desktop support or internet access.


Description of CGRB Laboratory Capabilities (Equipment and Facilities)
The CGRB provides the following laboratory services:
• High Throughput DNA sequencing (Illumina HiSeq2000; Illumina MiSeq; Roche 454 Jr), including library preparation

• Sanger DNA sequencing (ABI 3730 DNA Analyzer)

• Genotyping (ABI3730 DNA Analyzer)

• Confocal microscopy (Zeiss LSM 510 META), conducted by CGRB staff, or by trained users

• Laser Capture Microdissection (Zeiss PALM MicroBeam IV) conducted by CGRB staff, or by trained users

• Affymetrix Microarray analysis (through Oregon Health Sciences University)

• Bioanalyzer (Agilent Bioanalyzer 2100)

• Real time PCR (ABI PRISM® 7500 FAST Sequence Detection System) conducted by CGRB staff, or by trained users


The CGRB also hosts shared minor equipment including: Kodak X-OMAT Processor; Invitrogen Qubit Fluorometer; Promega QuantiFluor Fluorometer; NanoDrop ND-1000 UV-Vis Spectrophotometer; Molecular Devices Spectra MAX 190 Microplate Spectrophotometer; Qiagen Rapidplate (liquid handler); GE Storm 820 PhosphorImager; Genetix Qpix2 Colony Picker.
CGRB lab staff (Mark Dasenko, Anne-Marie Girard, Dacey Mercer and Aaron Trippe) are also available to provide collaborative custom laboratory services.

Description of CGRB Bioinformatics and Biocomputing Capabilities
The CGRB employs six full-time staff and one part-time statistician dedicated to biocomputing and bioinformatics (Professor Yuan Jiang, statistician; Dr. Brent Kronmiller, bioinformatics analyst; three bioinformatics trainer/analysts, Dr. Shawn O’Neil, Dr. Adelaide Rhodes and Dr. Kelly Vining; and two computational scientists, Mr. Matthew Peterson and Mr. Chris Sullivan). This staff has extensive expertise in DNA sequence analysis, including genome sequencing, RNAseq and genotyping-by-sequencing; biological databases; bioinformatics applications; and software development. The CGRB encourages researchers to invest in computational hardware that will be integrated into the overall fabric of the infrastructure. The CGRB computational staff work together with the individual researchers to find and build computational hardware that is optimized to answer the questions posed by the research work it supports.
The overarching goal of the CGRB Bioinformatics and Biocomputing group is to facilitate biological research through the use of computational tools. Services provided by the Bioinformatics and Biocomputing group include: processing of high throughput DNA sequence (HTS) data; provision of data management software including tools and procedures for analysis and distribution of HTS and biological imaging data; setup, optimization, maintenance and backup of the research computers owned by investigators and housed in the CGRB server room; access to grid computing resources on the CGRB cluster or on external clusters; maintenance of an in-house graphical user interface (Easy Terminal Alternative; ETA) that facilitates access to and pipelining of command line software; access to virtual servers with web and database services; training of investigators in programming and use of bioinformatics software; hosting a large variety of in-house and commercial bioinformatics tools; statistical consultation, experimental design and analysis; and collaborative research.
The CGRB’s biocomputing infrastructure includes a distributed service architecture, a large compute cluster, a secure network and climate controlled server space. The current architecture contains:
• >1 petabyte redundant storage

• 1728 processor cluster

• 3 Dell PowerEdge 910 servers with 1 Tb memory each

• 10 Gbps network backbone

• 10 Gbps network for HTS and Backup file servers

• 10 Gbps access to campus-wide science DMZ and internet2

• 1 Gbps network for all nodes

• 80 kVA Uninterruptible Power Supply (UPS)



• 120 kW building generator

• 17 ton of air handling


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