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Bioinformatics (Galaxy@SLU)

The Department of Pharmacology and Physiology has built a bioinformatics-oriented data analysis server which has been named Galaxy@SLU. It is publicly accessible and is based on Galaxy, one of the most popular open-source data analysis platforms under Python. Galaxy's web interface has made it highly attractive among scientists worldwide. Currently, Galaxy@SLU offers the following analysis tools and workflows, with a focus on ChIP-Seq and RNA-Seq.

  • ChIP-Seq: Peak calling (MACS) and alignment (Bowtie, BWA).
  • RNA-Seq: Alignment and quantification (Tophat, STAR, Cufflinks, HTSeq, Kallisto), differential gene expression (edgeR, DESeq).
  • scRNA-Seq: A set of Single-cell RNA-Seq analysis tools based on Seurat.
  • Other tools: A tool to import TCGA (The Cancer Genome Atlas Data) patient samples.

Registration is required for all users.

View Tutorials

Galaxy@SLU is maintained by Jinsong Zhang (jinsong.zhang@health.slu.edu)

Metabolic Phenotyping Core (MPC)

The Metabolic Phenotyping Core is housed within 6-room suite within the Comparative Medicine Animal Facility and on the 3rd floor of Schwitalla Hall. The MPC core is maintained by Colin Flaveny, Ph.D. (colin.flaveny@health.slu.edu).

The Core has the following equipment:

  • 96-well Seahorse XF Extracellular Flux Bioanalyzer
  • 3 Oroboros-oxygraph devices
  • Vantage DCA A1c blood glucose monitor
  • Animal electroencephalogram (EEG) telemetry system with a locomotor and temperature monitoring
  • BioDAQ food and water intake monitoring system
  • 32-chamber Comprehensive Lab Animal Monitoring System (CLAMS)
  • 6 lane Rodent treadmill
  • Nuclear Magnetic Resonance machine for measuring body composition
  • Blood pressure and Electrocardiogram (ECG) monitor
  • Cobas c11 clinical chemistry bioanalyzer
  • Biotek Synergy Neo 5 Plate reader
  • LiCoR Pearl Trilogy in vivo mouse imaging system

Other MPC/PharmPhys Equipment:

  • Life technologies QuantStudio 7 Flex RT-qPCR
  • a 384 sample semi-automated liquid sample handler
  • a phosphor imager
  • 96-well Luminex 200 bead-based multiplexing system
  • a Corning Epic Label-Free Detection system
  • Ion GeneStudio S5 Next Gen Sequencer
  • Biorad Bioanalyzer
  • Agilent bioanalyzer

Other Facilities and Resources

Animal Care Facility

The 44,000-square-foot Animal Care Facility operated by SLU’s Department of Comparative Medicine has three full-time veterinarians and offers training, colony health surveillance and technical support, as well as consultation and collaborative services.

Animal Imaging Core Facility

The Department of Molecular Microbiology and Immunology’s Animal Imaging Core Facility offers non-invasive, small animal imaging using IVIS Spectrum instrument.

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Flow Cytometry Research Core

SLU’s Flow Cytometry Research Core offers a FACS Callibur flow-cytometer with cell sorter, Biosciences LSR II, capable of 10-color analyses and Biosciences FACSAria, with simultaneous sorting of four populations. It has two full-time staff members and offers discounted rates to SLU researchers.

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Genomics Core Facility

This full-service facility provides investigators with a variety of options for whole genome analysis via microarrays, high-throughput screening, immunoprecipitation and sequencing strategies. The facility is managed by Michelle Pherson, Ph.D., who you can contact at 314-977-9252 or kkunz1@slu.edu.

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High-Performance Computing

The Department of Biochemistry and Molecular Biology maintains a wide variety of computing resources. These range from network and backup services to state-of-the-art high-performance computing. The most recent addition to the department is the Gemini Computing Cluster that leverages modern technologies such as GPU computing capabilities. The cluster consists of 344 CPU cores, 80 GPUs and 1.3 TB of aggregate RAM, providing 135 TFLOPs peak computing power.

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Lipidomics Core Facility

The Lipidomics Core Facility, operated by the department and the Center for Cardiovascular Research at Saint Louis University School of Medicine, is a University resource located in the Doisy Research Center. The facility focuses on small molecule identification and quantification by mass spectrometry.

Instrumentation in this core includes a Thermo Electron Surveyor LC and Quantum Ultra triple quadrupole electrospray ionization mass spectrometer, as well as two HP6890 gas chromatographs with FID detector and HP 5973 MS detector with both electron impact and chemical ionization sources. The facility is managed by Dave Ford, Ph.D. Contact him at 314-977-9264 or david.ford@health.slu.edu.

Protein Core Facility

A shared-use facility that supports expression, purification and analysis of research proteins by providing an array of instrumentation and consultation on strategies for protein production from small to large scale. The facility is managed by Yie-Hwa Chang, Ph.D. Contact him at yiehwa.chang@health.slu.edu.

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NMR Facility

The Saint Louis University Department of Chemistry houses an NMR facility, which is available to all researchers at SLU. The facility has a multinuclear Bruker spectrometer with the field strength of 16.4 Tesla, as well as a newly-installed Bruker Avance HDTM 700MHz NMR spectrometer. These instruments can be used to determine the structures of organic molecules and biomolecules, and can also be used in other dynamic studies.

The facility is located in Shannon Hall and is managed by the Department of Chemistry.

Research Microscopy and Histology Core

Offered by SLU’s Department of Pathology, the Research Microscopy and Histology Core provides a wide range of histological and microscopy services on a fee-for-service basis.

Graduate Scholarships, Fellowships and Assistantships

Saint Louis University’s Office of Graduate Education has multiple scholarship, fellowship and assistantship opportunities for new and returning graduate education students.

View Graduate Scholarships, Fellowships and Assistantships

View Postgraduate Fellowships

Graduate Program Handbook