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Revision as of 14:38, 24 February 2014

Contents 1 Tools portals 1.1 Genecensus 1.2 partslist.org 1.3 genometech 1.4 geometry 2 Network Tools 3 Microarrays & Proteomics

Tools portals

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

Genecensus

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.

partslist.org

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

genometech

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.

geometry

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

Network Tools

Tool Name	Release Date	Description
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.

Microarrays & Proteomics

Tool Name	Release Date	Description
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.

even more tools