Cancer Institute

  • Bioinformatics Core Services and Policy

    The Cancer Bioinformatics Core provides high quality; custom bioinformatics and statistical genetic analysis support services and solutions to basic science, clinical and translational researchers. We develop and apply statistically rigorous solutions for the design of studies, analysis and mining a wide variety of "omics" and other biological data, and integration of these data with clinical information to facilitate translation of genomic discoveries to the bedside and to accelerate the realization of genomic and personalized medicine in cancer. We integrate the research, service and education missions of UMMC. The core is equipped with laptops, work stations, LINUX cluster, mass storage for database and data mining application, graphics workstations for visualization and popular bioinformatics and genomics software packages. The services provided are on a cost-recovery basis.

    Services

    • Bioinformatics support

      • Provision of advice on bioinformatics analysis, use of appropriate software and databases, and management of large-scale research data
      • Provision of educational and training seminars on bioinformatics to students, medical professionals and biomedical investigators
      • Perform bioinformatics analysis and mining of various "omics" and other biological data, and integration of these data with clinical information
      • Develop novel methods and software to provide bioinformatics solutions to emerging biological questions
      • Providing translational bioinformatics services to the Cancer Institute
      • Assist investigators with planning and design of grant applications
    • Statistical genetics support

      • Provision of advice on statistical genomic/genetic data analysis and use of appropriate software and databases
      • Perform genomics/genetic analyses using existing software
      • Management of large-scale genotype and phenotypic data and design of large-scale population genomic studies
    • Sequence analysis support

      • Give advice and instruction on the selection and use of sequence analysis software and databases
      • Perform sequence analyses
      • Implement and maintain analysis pipelines to process next generation sequence data
      • Manage very large volumes of raw data, including deletion policy
      • Analyse different types of NGS data appropriately (e.g. genomic sequence, digital transcriptomics, methylation etc)
      • Develop databases to store NGS data
    • Scientific computing support

      • Management of the Cancer Bioinformatics computer servers and LINUX cluster
      • Maintenance of large-scale genomics and other biological databases
      • Evaluation and maintenance of bioinformatics tools and Statistical Genetics software packages
    • Database development and curation and general programming

      • Management of the bioinformatics core's genotyping and microarray database servers
      • Maintenance and curation of the database content, including regular off-site backup
      • General database maintenance tasks
      • Provide training to users in the use of database interfaces
      • Reformatting data into a form suitable for upload
      • Construct and perform complex database queries to extract data
      • Development of databases and interfaces to integrate "omics" with clinical and other biological databases, and with external data sources
      • Development of new database functionality (e.g. data analyses, small-scale databases for particular experiments) on request
    • Microarrays and functional genomics

      • Maintenance of microarray analysis software packages
      • Provide guidance and help with design and analysis of microarray experiments
      • Perform microarray analyses for the Cancer Institute
      • Collaborate with the Genomics Core over the development of new functional assays
      • Devise and develop new methodologies for the analysis of microarray and functional data, particularly in regard to their integration with genetic data
      • Integrative analysis of "omics", GWAS and clinical data

    Policy

    • Cost of services provided by the Cancer Bioinformatics Core

      All the services are provided on a fee-for-service and collaborative research funding mechanisms. All fee-for-service must be agreed upon at the start of the project and must be paid for upon completion. Should the investigator chose to withdraw or terminate the project, hourly fees will apply. Collaborative grant funding will be agreed upon during grant application or negotiated if the grant is funded and on-going, and will be assessed on a continuous basis as agreed by the parties. Both payment mechanisms will include labor and computing costs. A 30-minute free service will be provided to each investigator for each project at first visit to assess the investigator's needs and the project. All costs will be assessed on a case by case.

    • Human subjects research and IRB approval

      The Cancer Bioinformatics Core is committed to protecting the rights and welfare of individuals participating as subjects in research. In order to efficiently and effectively assist with projects where data has been or is being collected, we require information regarding IRB approval or exemption from one of the Universities IRB committees. We are requesting IRB information on all research involving human subjects in which actual data sets are reviewed or analyzed. Requests from clients not affiliated with UMMC will be reviewed by the Institute staff on a case-by-case basis to determine research aspects and whether IRB approval is required. IRB information may be requested before the project can proceed. The information requested can consist of a copy of the official approval letter from the IRB committee, an email, fax, or departmental letter from the PI stating the approval date and committee name. For more information about the Universities IRB policies, click here.