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
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.