Nemours Only
Services
The BCF provides several categories of service:
Consultation
The core staff can provide consultation and advice on the design of experiments and the statistical analysis of data.
Data Storage and Manipulation
Massive amounts of raw data may be generated by computational biology experiments (notably, microarray experiments). The core can provide space to store these data securely (crucial data are backed up nightly to avoid loss). Data are stored in a Unix-based relational database format that is custom designed by core staff to simplify data subsetting and porting to multiple file formats for compatibility with multiple software packages.
Data Analysis
Data analyses can be requested of the BCF in a manner analogous to requests for bio-assays from wet laboratories. Types of analyses include standard statistical analyses of data such as ANOVA or t-tests (as well as their non-parametric counterparts), regression analyses (including logistic regression), as well as special purpose analyses such as clustering analyses or eigen analyses of gene microarray data. Analysis results are provided in both written and graphic form suitable for use in manuscript preparation.
Access to computer hardware
For investigators with the time and expertise to perform their own data manipulation and analysis, the BCF can provide access to powerful computer hardware in the form of our 11-node Rocks Linux cluster. This cluster can be used as a batch processing system capable of running ten simultaneous analyses (e.g., examining different parameter values for an analysis), or with specially designed software, can be used as a single parallel processor to perform analyses that are too large to be practical on regular desktop computers.
Access to computer software
The BCF is presently reviewing various software packages of potential interest to biomedical researchers. A number of these are "open source" packages (i.e., available to researchers without cost), but nonetheless require appropriate computational resources and systems expertise to set up and maintain. Examples of open source packages being considered are SAM (Significance Analysis of Microarrays), GenMAPP, the R programming environment, dChip and TIGR MEV. Software may be used by researchers running either directly on their desktop machines, or remotely on the BCF cluster and network accessible.
Special purpose programming
The programming expertise of BCF staff is available on a fee-for-service basis to investigators in the Nemours Biomedical Research department. This service involves the development of special purpose software (broadly defined to include programs written in standard programming languages such as C and Fortran as well as Unix shell scripts, Perl scripts, DOS bat files, complex SQL queries, and dynamic web pages developed in PHP).
Training
BCF staff can provide training on the use of any supported software or hardware to others in the Nemours Biomedical Research department. Several public databases are accessible through the Internet. This core provides support and training for the access of information from web sites maintained by a variety of organizations and institutions including Affymetrix, National Institutes of Health, the Kyoto Encyclopedia of Genes and Genomes project (KEGG project) and the Gene Ontology Consortium.