Applied Bioinformatics and Data Mining ($34.74/hour)
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. For an example, see the recent paper from Mark Israel's lab that includes a bootstrapped hierarchical cluster analysis of microRNA results (Gaur et al. 2007).
The Cancer Center's Genomics core, with whom 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. For an example, see the recent paper from Angeline Andrew and Margaret Karagas that used data mining methods to identify combinations of genetic and environmental risk factors for bladder cancer (Andrew et al. 2006).
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 three different commercial pathway analysis products to assist you with making connections between your results and specific pathways, or to create your own novel pathways. These include Ariadne's Pathway Studio and Ingenuity IPA, each with particular strengths. For an example, see the recent paper by Angeline Andrew that used both of these tools to interpret gene expression microarray results (Andrew et al. 2008).
We also provide access to several open-source and commercial software packages for the analysis of DNA and RNA sequencing data, as well as training in the use of these tools. Our primary analysis tool is the CLC Genomics workbench, a commercial software toolset containing modules for the analysis of most types of sequencing and array data. We also offer access to a local instance of the popular open-source tool Galaxy, which runs on the Dartmouth compute cluster. We also have expertise in the use of various open-source bioinformatics tools such a Bowtie and Tophat, as well as publicly-accessible web sites for bioinformatics data analysis, including NCBI, UCSC genome browser, and many more.
Computer Programming and Software Engineering ($67.25/hour)
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. Most of our programming is carried out on PCs and servers running the Linux operating system. As such, we have access to and make use of the Portland Group compilers, debugger, and profiler (pgcc, pgCC, pgf77, pgf90, pgdbg, pgprof), Intel compilers, debugger, and math library (icc, ifort, idb), GNU compilers and debugger (gcc, g77, gdb), Java compiler and debugger (javac, jdb), and the Data Display debugger (ddd). The senior BISR staff have extensive experience with all these computer languages on the major platforms (Linux, Windows, OSX, and IOS). The BISR also has significant experience designing software and offers this as a service. For an example, see the SCOPE project for identifying regulatory motifs in DNA sequences from the Gross lab.
Database Development and Administration ($73.03/hour)
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 ($60.34/hour)
Access to a 1500-core parallel computer (Discovery) is offered as a BISR service. Faculty members are able to buy access to the system by purchasing one or more nodes at $4,950 per 16-core 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 discovery.dartmouth.edu. We also provide computer programming support and/or training to assist you with developing parallel applications.