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., firstname.lastname@example.org
Imaging Informatics: Dr. Thomas Pengo is providing imaging informatics analysis for biological images. 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 Nikon Elements, FIJI, Imaris, Matlab and R software. Analysis tools available in the facility include: Nikon Elements for analysis and deconvolution, Imaris for 3D reconstruction and image analysis, ImageJ/FIJI.
Contact: Thomas Pengo, Ph.d., email@example.com. Location: 1-220 CCRB. Hours: 10:00 am to 4:00 pm weekdays and as arranged.
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, firstname.lastname@example.org
Mass Spectrometry and Proteomics: Dr. Yuk Sham provides consulting services and standard analysis for mass spectrometry data.
Contact: Yuk Sham, Ph.D., 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