More tools
From GersteinInfo
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | |||
=Tools portals= | =Tools portals= | ||
| Line 48: | Line 47: | ||
|} | |} | ||
| + | |||
| + | =Tools portals= | ||
| + | =Network Tools= | ||
| + | :{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10" | ||
| + | |- bgcolor="lightsteelblue" | ||
| + | !Tool Name!!Release Date!!class="unsortable"|Description | ||
| + | |-style="height: 100px;" | ||
| + | |style="width:15%; text-align:center;"|[http://networks.gersteinlab.org/genome/interactions/networks/ '''TopNet''']||style="width:7%; text-align:center;"|2004||An automated web tool designed to calculate topological parameters and compare different sub-networks for any given network. | ||
| + | |-style="height: 100px;" | ||
| + | |style="width:15%; text-align:center;"|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style="width:7%; text-align:center;"|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. | ||
| + | |-style="height: 100px;" | ||
| + | |style="width:15%; text-align:center;"|[http://yeasthub.gersteinlab.org '''Yeasthub --BROKEN URL--''']||style="width:7%; text-align:center;"|???||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. | ||
| + | |} | ||
| + | |||
| + | =Network Tools= | ||
| + | :{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10" | ||
| + | |- bgcolor="lightsteelblue" | ||
| + | !Tool Name!!Release Date!!class="unsortable"|Description | ||
| + | |-style="height: 100px;" | ||
| + | |style="width:15%; text-align:center;"|[http://networks.gersteinlab.org/genome/interactions/networks/ '''TopNet''']||style="width:7%; text-align:center;"|2004||An automated web tool designed to calculate topological parameters and compare different sub-networks for any given network. | ||
| + | |-style="height: 100px;" | ||
| + | |style="width:15%; text-align:center;"|[http://tyna.gersteinlab.org/tyna/ '''tYNA''']||style="width:7%; text-align:center;"|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. | ||
| + | |-style="height: 100px;" | ||
| + | |style="width:15%; text-align:center;"|[http://yeasthub.gersteinlab.org '''Yeasthub --BROKEN URL--''']||style="width:7%; text-align:center;"|???||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. | ||
| + | |} | ||
[[even more tools]] | [[even more tools]] | ||
Revision as of 00:35, 19 February 2014
Contents |
Tools portals
below is a list of more tool portals that the lab has developed.
Genecensus
Tool Name Release Date Description 
Genecensus1995-2014 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.
partslist.org
Tool Name Release Date Description 
partslist1995-2014 a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information
genometech
Tool Name Release Date Description 
genometech1995-2014 A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes.
geometry
Tool Name Release Date Description 
geometry1995-2014 calculation of geometrical quantities associated with macromolecular structures and their motions
3vee
Tool Name Release Date Description 
3vee1995-2014 3vee is collection of program for the assessment of volumes in protein files.
Tools portals
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.
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.
