Biostatistics & Bioinformatics Equipment and Software
The BBSR’s front-line computing capabilities consist of a host of robust Dell desktop-class computers. Depending on the specific needs of the researcher, either a Windows XP system or a Linux-based multi-OS configuration has been implemented to allow execution of a wide variety of scientific analysis software.
All of these client machines connect to various central processing and file storage servers. These servers are all high-performance 64bit AMD Opterons with a large RAM capacity and multi-terabyte disk arrays. Running RedHat Enterprise Linux, they are used for lengthy, CPU-intensive calculations and act as shared facilities for the entire department.
There are also several color and black-and-white laser printers, as well as a fax machine, a scanner and copiers available for departmental use.
Recently, the BBSR purchased a robust quad-core machine dedicated to hosting web applications developed by BBSR members. These applications are either novel or adapted from those in the public domain. Significant computational power is now behind BBSR’s statistical web applications, which enables scientists to analyze data sets with state-of-the-art algorithms.
The BBSR also has a development server (two Quad Core Intel Xeon X5355 CPUs, 16GB 667MHz (8X2G) RAM, and 750GB hard drive) for the purpose of design, development and testing of bioinformatics database systems and/or tools The server is running on the Cent (the open resource version of RedHat) 5.0 Linux operation system. Installed on this machine are: database management systems (Oracle 11g, MySQL 5.0, PostgreSQL), a Web server (Apache), an application server (JBOSS) and development tools (Java Development Toolkit (JDK), Perl, PHP, R/Bioconductor, Oracle JDeveloper, and Oracle Form Developer).
With this development server, we separate our production and development environments, and utilize the most up-to-date information-technology approaches in our system/tool development and at the same time offer our users safe and smooth services over the Web.
The BBSR has access to statistical software packages that provide specialized capabilities. These computer programs facilitate study design and data analysis.
The following is a partial list of the analytical software available on the BBSR’s machines: SAS, STATXACT, S-PLUS, R, Matlab, Mathematica, GAUSS, STATISTICA, STPLAN (performs sample size and related calculations), NQuery (for sample-size computations), PII87 (Simon’s Optimal Two-Stage Designs for Phase II Clinical Trials), Bayesian Plans for Phase II Trials (various programs designed by P. Thall), POWER AND PRECISION, EGRET, EaSt, BART (program designed by D. Spiegelhalter for interim Bayesian analyses of clinical trials), BioConductor (R-based bioinformatics tools), BRB Array Tools (for the analysis of microarray data), dChip (for the analysis of Affymetrix microarray data analysis), CART (for classification and regression trees), IMSL (optimized C program library for numerical analysis), MOSEK (for functional optimization), Mplus, PDQuest (for analysis of two-dimensional gel images) and PAUP (for phylogenetic analysis). All BBSR members also have access to Ingenuity Pathway Analysis for identifying networks from inferred differentially expressed genes.
The BBSR consults with investigators and data managers about utilizing their data for various types of statistical analyses and the preparation of reports. SAS is the system utilized for most statistical analyses. The BBSR also assists investigators in translating their computerized data into the format needed for analyses by various statistical software packages. Efforts in this area do not include the actual setting up of databases or entry of data for investigators.