Programming Services

The Bioinformatics Research Center's Programming Core offers assistance with bioinformatics programming issues to members of the university community. This can range from consultation and advice on programming and technology issues to writing web pages and software to solve a bioinformatics-related problem.

From time to time, the BRC also offers short courses in Perl and HTML. Introductions to other programming topics could also be made available (e.g. C++, PHP, XML, JavaScript, relational databases and SQL).

For more information please contact Dr. Dahlia Nielsen at dahlia@statgen.ncsu.edu (919) 515-2586, or Chris Smith at chris@statgen.ncsu.edu (919) 515-8384.

Current and Completed Projects

The list below gives a brief description of some of the projects that the BRC Programming Core has undertaken.

• Data warehouse and web site for the USDA-IFAFS grant "Wood and Fibre Quality of Juvenile Pine".

  This is a large project including a web site with the capability of uploading new data files to the warehouse through a web browser; mechanisms for processing microarray data via SAS; web-based graph plotting tools; data export tools.

  The site is currently password protected, but an example screen-shot can be seen here. (The site will be made publicly available when the data are complete.)

• For the Purugganan Lab: a data pipeline for processing rice sequence chromatogram files and tracking project progress.

  This project is currently in use at the Purugganan lab. The code is now being enhanced so that it is more generally applicable than the rice project for which it was designed. The new version will become the processing pipeline for all sequencing projects in the Purugganan lab and will start being used in late April 2005.

• For Heike Winter: a tool to aid with the investigation of Arabidopsis experimental results. This tool includes a chromosome-based expression level viewer.

  Try it out here.

• SAS code for formatting microarray (quantarray) data for SAS analysis.

  This code combines an experimental design file, the printer output file, the expression level values, and a gene list into a dataset suitable for processing with SAS (or the SAS Microarray Solution). It has proved useful in a number of different projects.

• Simple web page for the collaborative discussion of hookworm papers.

  It can be viewed here