Software

Coming Soon !
	MADGE Microarray Database of Gene Expression	MADGE The Microarray Database of Gene Expression (MADGE)system was designed to track and store the various pieces of data generated by the NIDDK Center. This includes the clone collection storage data, annotation data, workflow queues, microarray data, data repositories, sample submission information, and project/investigator information. This application was designed using a 3-tier client server model. The data access layer (1st tier) contains the relational database system (SQL Server v7.0) tuned to support a large number of transactions. The data services layer (2nd tier) is an object oriented interface with methods and properties to access the underlying database tables. This layer is a distributed COM server with full database transaction support. The application layer (3rd tier) is an internet based user interface that contains both client and server side code for dynamic interactions with the user. The advantage of an N-tier design is the scalability and deployment flexibility. The system was developed in a multiphase process to insure a robust user-friendly system. Here is a brief description of each phase.

	UF Flagging and Normalization Program	We developed and validated a new model for microarray signal intensity that has one multiplicative variation and one additive background variation. Using replicative experiments and simulated data, we found that the signal intensity is the most critical parameter that influences the performance of normalization, accuracy of ratio estimates, reproducibility, specificity and sensitivity of microarray experiments. Therefore, we developed a statistical procedure to flag spots with weak signal intensity based on the standard deviation of background differences between a spot and the neighboring spots. One of the results of these experiments was the development of a computer program that will flag the spots based on these statistical criteria and calculate the normalized data based on the high quality spots. The stand alone version of the software can be found in two forms, the zip file and the self extracting file. Click on the link for the file you want to download. Extract the files and run setup.exe to install the program. Read the readme.1st file for instructions on the use and installation

	MCG StatAR	StatAR is a simple program used to calculate basic statistics on replicate or grouped microarray data. The program will calculate the mean, geometric mean, median, standard deviation or CV for your data set. The program uses a modified Cluster file to determine which experiments belong together. One can Log transform the data before analysis as well as combine multiple files into one file. The program is a windows based program that uses the Microsoft Installer to install the program. You can download the program here. You can either open from the download and it will install on your machine or you can save it locally for multiple installs. Due to name conflicts we have temporarily disabled downloads until we can re-compile the program with the new name (StatAR)