UMII is starting to develop informatics services and consulting services to determine solutions for your needs. The goal of UMII is to develop a service layer to interface with high-throughput facilities on one side and the Minnesota Supercomputing Research Informatics Services Support (RISS) on the other side. The data generated in high-throughput facilities (UMGC, CMSP, and Imaging) may require different levels of analysis. UMII provides standardized workflows that serve users without specialized needs. For more advanced services, users should consult with RISS.
Data Wrangling: Embedded in high-throughput facilities, Dr. Fred Dulles streamlines and troubleshoots the migration of data from the high-throughput facilities to their place of analysis, and develops and maintains protocols for data transfer and storage to meet the needs of users of the facilities.
Contact: Fred Dulles, Ph.D., email@example.com
Imaging Informatics: Imaging Informatics services now include image analysis across many different imaging modalities. From fluorescence microscopy, to small animal imaging, neuroimaging and material science. Dr. Thomas Pengo provides analysis support for biological images (any instrument at the University Imaging Centers). Services include 2D image analysis (morphometry, particle analysis, densiometry, etc.) and 3D image analysis (volumetric sample measurement) reconstruction and image editing. Analysis is performed with FIJI, QuPath, MATLAB, Nikon Elements, Imaris, Amira, MATLAB and Python software. Tim Hendrickson provides support for neuroimaging (mostly data acquired at the Center for Magnetic Resonance Research). Analysis tools include FSL, FreeSurfer, the Human Connectome Pipelines and customized analysis pipelines. Guichuan Yu provides support for data taken at the Characterization Facility, including scanning probe microscopy, X-ray diffraction, electron microscopy as well as other material characterization techniques. Analysis tools include open-source software and customized analysis pipelines.
Contact: Thomas Pengo, Ph.d., firstname.lastname@example.org. Office: 1-220 CCRB. Tim Hendrickson, email@example.com. Office: 419A, 717 Delaware. Guichuan Yu, Ph.D., firstname.lastname@example.org. Office: Room 11, CharFac Shepherd Labs
Metagenomics: Trevor Gould provides sequence data analysis for metagenomics data generated through MnDRIVE projects. Services include initial consulting, data processing using a standardized pipeline for 16S data, and standard analysis, such as operational taxonomic unit sequence clusters, alpha and beta diversity, and sample clustering.
Contact: Trevor Gould, 612-625-5439, email@example.com
Mass Spectrometry and Proteomics: Mass Spectrometry and Proteomics: UMII provides consulting services and standard analysis for mass spectrometry data. Currently vacant, please contact Fred Dulles (firstname.lastname@example.org) or the UMII Associate Director (email@example.com).
Next Generation Sequencing Analysis: Dr. Juan Abrahante provides basic analysis for NGS data generated at UMGC (Qmean scores per sample run, number of reads, fastQC reports). An RNA sample pipeline is under development to provide a second, intermediate report, which will include subsampling, QC, fastQC, trimming/filtering, spike-in control alignment, insert-size, abundance estimation with Cufflinks, and abundance estimation with SubRead. In the future, we expect to provide differential gene expression analysis with p-values and FDR using edgeR packages.
Contact: Juan Abrahante, Ph.D., firstname.lastname@example.org