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The Hartwell Center for Bioinformatics and Biotechnology is a unique department at St. Jude. This department merges research and service to provide state-of-the-art biotechnology and bioinformatics support for St. Jude research programs.
The center is composed of three divisions:
Collectively, these operations include a staff of 70, including 23 who have doctoral degrees.
The Biotechnology division houses six laboratories and staff with expertise crucial to our research efforts.
The High-Throughput DNA Sequencing and Genotyping laboratory has sequenced more than 880,000 DNA templates producing more than 410 million base pairs of DNA sequence data and currently generates 10 million bp/month for St. Jude research programs. Fragment size analysis, microsatellite instability and genotyping expertise is also available; all use high-throughput robotics and automated DNA sequence analysis instrumentation.
The Macromolecular Synthesis laboratory has produced over 170,000 synthetic oligonucleotides and 10,000 synthetic peptides for St. Jude investigators and continues to produce ~27,000 oligonucleotides and ~1000 peptides each year. Oligo synthesis include DNA, DNA analogs, dye-labeled molecules, RT-PCR probes, RNA, LNA etc. Peptide synthesis include standard peptides, modified peptides using amino acid analogs, fluorescently labeled peptides, branched chain peptides, cyclic peptides, peptoids, pna’s and peptide-pna conjugates. The macromolecular synthesis group has recently acquired a microwave peptide synthesizer, which uses microwaves to accelerate peptide coupling reactions.
The Functional Genomics laboratory produces an increasing number of printed DNA microarrays including both cDNA and oligonucleotide arrays. Both standard mouse and human arrays are produced, as well as custom arrays designed and printed in-house at a feature density up to 21,000 genes/chip. The expert staff conducts all aspects of gene expression analysis including RNA quality control, amplification, dye labeling, hybridization, image analysis and preliminary data analysis.
The Proteomics/Mass Spectrometry group provides expertise in high-throughput protein expression analysis, protein identification, and identification and localization of post-translational modifications. To detect changes in expression of specific proteins, this laboratory performs high-resolution separation of proteins by 2-D gel electrophoresis and high performance capillary liquid chromatography. Proteins are identified by tandem mass spectrometry using either a tandem time-of-flight mass spectrometer system (the Model 4700 Proteomics Analyzer from Applied Biosystems) or an ion-trap mass spectrometer (the Finnigan LTQ from Thermo Electron) with on-line ultra high-performance capillary chromatography system (the NanoAcquity from Waters). Proteins are prepared for mass spectrometry with the assistance of Genomic Solutions robotic systems, and mass spectrometric data are subjected to automated database searching with the Mascot, SEQUEST or Protein Prospector search engines. The Proteomics group also performs mass analysis of intact proteins using a Model LCT mass spectrometer from Micromass to assess protein microheterogeneity, identify proteolytic cleavage sites, and identify post-translational modifications. The group also has small-molecule mass spectrometry capability for pharmacokinetic and metabolite analysis using a triple quadrupole mass spectrometer (the Quantum from ThermoElectron), and performs mass spectral imaging of tissues prepared by cryostatic sectioning.
The Molecular Interaction Analysis laboratory investigates the rates at which macromolecules associate and dissociate in the formation of complexes, and the affinities of their binding interactions. Two analytical techniques are utilized to make these measurements. Firstly, surface plasmon resonance provides real-time progress curves for the binding/dissociation of molecules to proteins immobilized on surface. A Biacore 3000 system is used for this work. Secondly, analytical ultracentrifugation provides measurements of the rates at which molecules sediment, giving information about their molecular size and shape, and permits measurements of their equilibrium distribution in centrifugal fields that allows binding affinities to be calculated. A Beckman XL-I ultracentrifuge is used for these analyses. Additionally, tracer sedimentation analysis is performed to investigate interactions that are not easily monitored in either of these instrument systems, including interactions in very complex mixtures of proteins or interactions with molecules present at very low levels. A Beckman Optima TLX bench-top ultracentrifuge is used in conjunction with a Brandel Microfractionator for these experiments. The quantitative information provided by the laboratory provides critical information for understanding the mode of action of proteins, and the efficacy of action of putative pharmaceutical agents.
The Clinical Applications Core Technology laboratory provides expertise in the use, application and analysis of the commercial Affymetrix GeneChip microarray technology. This oligonucleotide-based microarray technology has been used extensively to assess its utility in the diagnosis and classification of disease as well as a host of other applications. The Affymetrix GeneChip platform offers RNA expression microarrays for over 30 different genomes and DNA genotyping microarrays that can interrogate up to 500,000 single nucleotide polymorphisms (SNP’s) The CACT laboratory is equipped with five microarray fluidics stations and two fully automated high-resolution scanners. Since the laboratory began in 2000 the group has generated data from over 12,000 GeneChips for more than 70 research programs at St. Jude.
The Bioinformatics/Research Computing division includes four groups:
An Operations group manages the center’s High Performance Computing Facility (HPCF). This facility
offers an outstanding computational environment in which to conduct research. The HPCF houses a 420-cpu IBM Linux cluster. This super computer as well as other high-end servers support the high-performance bioinformatics, structural analysis and scientific computing needs of the institution. These systems share access to a Storage Area Network consisting of ~60 terabytes of storage space. The HPCF also houses approximately 30 additional servers used as test platforms, staging servers, Web servers, etc. This group also maintains the hospital’s Internet connectivity (I1 and I2) and institutional firewall systems.
The Bioinformatics group includes 10 doctoral-level staff members who provide expert bioinformatics support for St. Jude research programs, teach bioinformatics applications and develop new applications and databases in support of St. Jude research. These staff members support a wide variety of desktop and server-based bioinformatics applications, major public biomolecular databases, and development of knowledge-based database systems required for comprehensive analysis of biomolecular data.
The Software/Database development group includes programmers, database developers, and Web developers to produce, support and maintain any bioinformatics and research applications or databases or Web sites needed to complement our research activities.
The Client Services group provides desktop support to laboratory-based investigators at St. Jude using a distributed support model. Local Support Providers (LSPs) are distributed one per floor in the DTRC (Plaza; 1st -5th floors) and in the IRC (7th – 9th floors). In addition to the LSP positions, 2 Local Support Specialist (LSS) positions focus on advancing the Windows, Macintosh and Linux systems in the research area.
The Molecular Biotechnology division currently includes four faculty members engaged in basic and applied research in the science encompassed by the Hartwell Center.
The level of integration found in the Hartwell Center’s activities is unique and allows the merger of bioinformatics and expression arrays, bioinformatics and proteomics, proteomics and gene expression, synthetic chemistries and mass spectrometry. Everyone works as a team to provide powerful new tools for discovery.