Data Sciences Cluster

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Biostatistics Shared Resource

Mission

The mission of the Biostatistics Shared Resource (BSR) is to promote excellence in cancer research at UW Carbone Cancer Center (UWCCC) by providing outstanding and crucial biostatistical support and collaboration to UWCCC members in research ranging from laboratory, to clinical, to population science.

Services

CONSULTING ON THE PLANNING AND EXPERIMENTAL DESIGN OF STUDIES

  • Advice on appropriate experimental design
  • Problem definition and statistical methodology
  • Identification of suitable study endpoints
  • Sample size estimation or power analysis
  • Definition of data items required
  • Determination of randomization and stratification
  • Development and review of protocols
  • Statistical support for grant applications development

IF NECESSARY AND FOR CLINICAL AND POPULATION-BASED STUDIES:

  • Selection of study subjects and appropriate control groups
  • Recruitment strategies
  • Availability of data from related studies
  • Design of case report form

ASSISTING IN THE CONDUCT OF STUDIES

  • Monitoring of studies
  • Data management or electronic transfer of data from other related studies
  • Development of systems for quality control, progress reports, and presentation of interim analyses

ANALYZING COMPLETED STUDIES

  • Determination of appropriate statistical methodology
  • Production of final study reports including graphs and tables or other summaries suitable for scientific presentation and publication
  • Interpretation of statistical results, appropriate documentation and relevant literature

Equipment

BSR consists of a pool of PhD-level and MS-level biostatisticians dedicated to cancer research and with a broad range of expertise, who provide collaborative support to all UWCCC members.

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Cancer Informatics Shared Resource

Mission

The mission of the Cancer Informatics Shared Resource (CISR) is to promote high quality, innovative cancer research by providing members of UW Carbone Cancer Center (UWCCC) with modern and efficient informatics, including advancements in bioinformatics, clinical informatics, image analysis and computational science.

Services

  • Genetics/Genomics (bulk and single-cell)
  • Gene expression (RNA-seq bulk and single-cell
  • Chromatin Immunoprecipitation (ChIP-seq)
  • Proteomics
  • DNA methylation
  • Flow cytometry
  • Microbiome data
  • Data integration of single-cell omics data including single cell gene expression, single-cell feature barcoding, single-cell TCR repertoire, single-cell ATAC-seq, Visium (spatial transcriptomics)
  • Data integration of omics, clinical data, imaging data, etc.
  • Image analysis
  • Clinical data
  • Laboratory and computational biology software tools
  • EMR data mining (including NLP)
  • Data visualization
  • Machine learning predictions
  • Software and new algorithm development

Equipment

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Cancer Prevention and Outcomes Data Shared Resource

Mission

The mission of Cancer Prevention and Outcomes Data (C-POD) Shared Resource is to reduce the burden of cancer by facilitating high-impact population health science and translational research among researchers from the UW Carbone Cancer Center and across the UW campus.

Services

  • Project development
  • Data collection
  • Data dissemination

Equipment

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Science Computing Cooperative (SSCC)

Mission

The mission of the SMPH Research Computing Infrastructure initiative is to advance SMPH researchers’ capabilities in computational research. As a first step SMPH has partnered with the Social Science Computing Cooperative (SSCC) to give SMPH researchers access to Silo, SSCC’s secure computing environment, which provides a seamless data storage and computing system for research. SMPH has also funded an expansion of Silo to give it the capacity for data intensive -omics and other computationally intensive research. The Clinical Health Informatics Institute (CHI2) liaise with SMPH researchers and SSCC.

Services:

  • Project consultation with the CHI2.
  • Powerful Linux and Windows based servers with a variety of research software installed.
  • Secure data storage.
  • Support for use of Silo by CHI2 in partnership with SSCC staff.
  • SMPH researchers also have priority access to SSCC’s training. While it is primarily intended for the social sciences, the data science and statistical analysis skills it teaches are useful to many researchers.

Equipment:

  • Phase one of the Silo expansion includes 3 interactive Linux servers, 2 high performance Linux servers, 9 HTCondor servers, and 4 Windows servers, for a total of 816 cores
  • Software installed includes Python, R/RStudio Server, SAS, Stata, and many specialized programs for biomedical research.
  • Data storage is provided by DoIT, with an initial capacity of 400TB.
  • Phase two has a similar budget to be spent in the current fiscal year, with the equipment to be purchased based on identified needs.

Contact

Website: https://ictr.wisc.edu/chi2/ and https://ssc.wisc.edu/
Email:  chi2info@hslc.wisc.edu
Phone: (608) 262-9917

WiSOR Qualitative Core

Mission

Qualitative Core’s mission is to support faculty and staff who is involved in health services research by offering consultation, support, and expertise on qualitative study design, methodology, data collection and analysis, and publication.

Services

  • Assistance with grant writing (including budgetary planning)
  • Qualitative study design and preparation (methodological decisions)
  • Qualitative study measure/protocol development
  • Assistance with data collection and analysis
  • Training on the coding and analysis of qualitative data (including NVivo software)
  • Training for focus group moderators and interviewers (including mock interviews)
  • Manuscript writing, editing, and publishing
  • Transcribing the audio recordings and editing them for analysis

Equipment

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WiSOR Transcription Core

Mission

The Transcription Core’s mission is to provide high-quality transcriptions of recordings of interviews, focus groups, and doctor-patient consultations.

Services

  • Transcribe audio recordings

 Equipment

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