Applied Bioinformatics and Data Mining
- The BISR offers a wide variety of different applied bioinformatics analysis services for genetic, genomic and proteomic studies. This includes use of state-of-the-art software such as the Bioconductor package in R to normalize, transform, and analyze your gene expression microarray data using both supervised (e.g., SAM) and unsupervised (cluster analysis) methods.
- The Cancer Center's Microarray and Next-Gen Sequencing core, with which we work closely, is an important generator of array and high-throughput sequencing data for the Bioinformatics core.
- We also offer a number of advanced machine learning and data mining methods for identifying complex patterns of genetic, genomic, and proteomic biomarkers associated with discrete or continuous biomedical endpoints.
- In addition to bioinformatics analysis, the BISR also offers services to assist with the interpretation of 'omics' results. We offer our own Exploratory Visual Analysis (EVA) database and software for exploring analytical results in the context of pathways and Gene Ontology, for example, and we offer access to commercial pathway analysis products to assist you with making connections between your results and specific pathways, or to create your own novel pathways. This includes Pathway Studio; with particular strengths. We also have expertise in the use of publicly-accessible websites for bioinformatics data analysis, including NCBI, Galaxy, UCSC genome browser as well as free access to the commercial genomics software CLC Genomics Workbench and Golden Helix.
Computer Programming and Software Engineering
The BISR offers computer programming support using a wide variety of computer languages and software packages including C, C++, Java, Perl, Python, R, HTML, PHP, Visual Basic, Objective-C, LabView, etc.
Database Development and Administration
Database development, programming and administration services are offered using Oracle and MySQL. Comprehensive Oracle support is made possible through a Dartmouth site license. Thus, there are no chargebacks necessary for the Oracle license. The BISR maintains its own database solution called Metatable Database Development System (MDDS) that was specifically designed and implemented in Oracle for integrating research data and clinical data. This system has already been modified and expanded for several projects, including the NCCC billing and financial database for the shared resources. The BISR currently supports and makes available the GeneTraffic microarray database.
High Performance Computing and Systems Administration
Access to a 2264-processor parallel computer is offered as a BISR service. Faculty members are able to buy access to the system by purchasing one or more nodes at $5000 per 16-cpu node. This price includes hardware and personnel support for four years along with software and maintenance costs. Details of the hardware architecture and other information can be found at at discovery.dartmouth.edu. We also provide computer programming support and/or training to assist you with developing parallel applications.
The BISR employs a talented team of bioinformatics personnel each with a wide range of computational skills. Each of the staff are available to help you with your bioinformatics needs. Please contact Walter Taylor, Joanna Hamilton or Craig Tomlinson if you are considering a sequencing or array-based project.
- Shared Resources Guide
- Bioinformatics (BISR)
- Biostatistics Shared Resource (BSR)
- Clinical Pharmacology (CP)
- Genomics and Molecular Biology Shared Resources (GMBSR)
- Immune Monitoring and Flow Cytometry Resource (IMFC)
- Irradiation, Pre-clinical Imaging and Microscopy Resource (IPIM)
- Mouse Modeling (MM)
- Office of Clinical Research
- Pathology Shared Resource (PSR)
- Trace Element Analysis (TEA)
- RaDar Service Request System
- Office for Cancer Comparative Effectiveness Research
- Regional Cancer Research Shared Resources
- Acknowledgments and Authorship
- Equipment Sale Protocol
- Instrument Request Form