Tools portals

below is a list of more tool portals that the lab has developed.

Tool Name	Release Date	Description
Genecensus	1995-2014	we proposed a number of novel trees based on the occurrence of specific features, either folds or orthologs, throughout the whole genome. We call thesegenomic trees or whole-genome trees.

Tool Name	Release Date	Description
partslist	1995-2014	a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

Tool Name	Release Date	Description
genometech	1995-2014	A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes.

Tool Name	Release Date	Description
geometry	1995-2014	calculation of geometrical quantities associated with macromolecular structures and their motions

Tool Name	Release Date	Description
3vee	1995-2014	3vee is collection of program for the assessment of volumes in protein files.

Network Tools

Tool Name	Release Date	Description
TopNet	2004	An automated web tool designed to calculate topological parameters and compare different sub-networks for any given network.
tYNA	2006	(TopNet-like Yale Network Analyzer). A Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks etc.
Yeasthub --BROKEN URL--	???	A semantic web-based application which demonstrates how a life sciences data warehouse can be built using a native Resource Description Framework (RDF) data store. This data warehouse allows integration of different types of yeast genome data provided by different resources in different formats including the tabular and RDF formats.

Tool Name	Release Date	Description
ExpressYourself	2003	An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
PARE	2007	(Protein Abundance and mRNA Expression). A tool for comparing protein abundance and mRNA expression data. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which are potentially worth further examination.
ProCAT --BROKEN URL--	2006	A data analysis approach for protein microarrays. ProCAT corrects for background bias and spatial artifacts, identifies significant signals, filters nonspecific spots, and normalizes the resulting signal to protein abundance. ProCAT provides a powerful and flexible new approach for analyzing many types of protein microarrays.
Tilescope --BROKEN URL--	2007	An online analysis pipeline for high-density tiling microarray data. Tilescope normalizes signals between channels and across arrays, combines replicate experiments, score each array element, and identifies genomic features. The program is designed with a modular, three-tiered architecture, facilitating parallelism, and a graphic user-friendly interface, presenting results in an organized web page, downloadable for further analysis.
Tiling	NA	A platform with all our tilling array analysis tools.