More tools

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Below is a list of tools that have previously been developed and published by the Gerstein Lab.
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To view tools that have been published and are '''actively being maintained''', please click [http://info.gersteinlab.org/Resources here].
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'''Unpublished resources''' may be viewed by clicking [http://info.gersteinlab.org/Even_more_tools here].
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Literature associated with lab software and servers may be accessed [http://papers.gersteinlab.org/subject/resources/index.html here].
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=Tools portals=
=Tools portals=
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below is a list of more tool portals that the lab has developed.
 
===Genecensus===
===Genecensus===
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
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!Tool Name!!Release Date!!class="unsortable"|Description
!Tool Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [[File:Genecensus-title.jpg‎]] <br> [http://www.genecensus.org/tree/index.cgi?view=1&type=comp-dint-per Genecensus]||style="width:7%; text-align:center;"|1995-2014||
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|style="width:15%; text-align:center;"| [[File:Genecensus-title.jpg‎]] <br> [http://www.genecensus.org/tree/index.cgi?view=1&type=comp-dint-per Genecensus]||style="width:7%; text-align:center;"|1998||
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.  
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.  
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!Tool Name!!Release Date!!class="unsortable"|Description
!Tool Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [[File:Parts-bi-parts-5.jpg‎|center|x85px‎‎]] <br> [http://partslist.org/ partslist]||style="width:7%; text-align:center;"|1995-2014||
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|style="width:15%; text-align:center;"| [[File:Parts-bi-parts-5.jpg‎|center|x85px‎‎]] <br> [http://partslist.org/ partslist]||style="width:7%; text-align:center;"|1995||
a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information
a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information
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!Tool Name!!Release Date!!class="unsortable"|Description
!Tool Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [[File:Headline.gif‎‎‎]] <br> [http://genometech.gersteinlab.org/ genometech]||style="width:7%; text-align:center;"|1995-2014||
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|style="width:15%; text-align:center;"| [[File:Headline.gif‎‎‎]] <br> [http://genometech.gersteinlab.org/ genometech]||style="width:7%; text-align:center;"|1995||
A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes.
A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes.
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|}
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===geometry===
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=Network Tools=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
|- bgcolor="lightsteelblue"
!Tool Name!!Release Date!!class="unsortable"|Description
!Tool Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [[File:Voronoi.png‎‎|center|x85px‎‎]] <br> [http://geometry.molmovdb.org/ geometry]||style="width:7%; text-align:center;"|1995-2014||
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|style="width:15%; text-align:center;"|[http://hub.gersteinlab.org/ir-supp/ '''HUB''']||style="width:7%; text-align:center;"|2001||A tool for leveraging the structure of the semantic web to enhance information retrieval for proteomics. This tool helps Proteomics researchers to be able to quickly retrieve relevant information from the web and the biomedical literature.
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calculation of geometrical quantities associated with macromolecular structures and their motions
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://yeasthub.gersteinlab.org '''Yeasthub''']||style="width:7%; text-align:center;"|1997||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.
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|}
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===3vee===
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=Arrays-Based Tools=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
|- bgcolor="lightsteelblue"
!Tool Name!!Release Date!!class="unsortable"|Description
!Tool Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|-style="height: 100px;"
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|style="width:15%; text-align:center;"| [[File:Topbarbackgrnd.png‎‎‎|center|x85px‎‎]] <br> [http://3vee.molmovdb.org/ 3vee]||style="width:7%; text-align:center;"|1995-2014||
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|style="width:15%; text-align:center;"|[http://purelight.biology.yale.edu:8080/servlets-examples/procat.html '''ProCAT ''']||style="text-align:center;"|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.
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3vee is collection of program for the assessment of volumes in protein files.  
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://tilescope.gersteinlab.org/ '''Tilescope''']||style="text-align:center;"|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.
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|}
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===Clustering===
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=Network Tools=
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:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
|- bgcolor="lightsteelblue"
!Tool Name!!Release Date!!class="unsortable"|Description
!Tool Name!!Release Date!!class="unsortable"|Description
|-style="height: 100px;"
|-style="height: 100px;"
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|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.
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|style="width:15%; text-align:center;"|[http://bioinfo.mbb.yale.edu/expression/cluster '''Local Clustering''']||style="width:7%; text-align:center;"|2001||A new algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data is available as C source code.
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|-style="height: 100px;"
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|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.
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|-style="height: 100px;"
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|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.
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|}
|}
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=Microarrays & Proteomics=
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=Other=
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
:{|class="wikitable sortable" border="1" cellspacing="0" cellpadding="10"
|- bgcolor="lightsteelblue"
|- bgcolor="lightsteelblue"
!Tool Name!!Release Date!!class="unsortable"|Description
!Tool Name!!Release Date!!class="unsortable"|Description
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|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://www.gersteinlab.org/proj/BoCaTFBS/ '''BoCaTFBS''']||style="width:7%; text-align:center;"|2006||A boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. This tool is based on a data mining approach combining noisy data from ChIP-chip experiments with known binding site patterns. BoCaTFBS uses boosted cascades of classifiers for optimum efficiency, in which components are alternating decision trees; it exploits interpositional correlations; and it explicitly integrates massive negative information from ChIP-chip experiments.
|-style="height: 100px;"
|-style="height: 100px;"
|style="width:15%; text-align:center;"|[http://bioinfo.mbb.yale.edu/ExpressYourself '''ExpressYourself''']||style="width:7%; text-align:center;"|2003||An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
|style="width:15%; text-align:center;"|[http://bioinfo.mbb.yale.edu/ExpressYourself '''ExpressYourself''']||style="width:7%; text-align:center;"|2003||An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
|-style="height: 100px;"
|-style="height: 100px;"
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|style="width:15%; text-align:center;"|[http://proteomics.gersteinlab.org '''PARE''']||style="width:7%; text-align:center;"|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.
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|style="width:15%; text-align:center;"|[http://spine.nesg.org '''SPINE''']||style="width:7%; text-align:center;"|2001||A laboratory-information management system (LIMS) for the [http://www.nesg.org NorthEast Structural Genomics Consortium]. The online version is restricted to consortium users, but most of the code is freely available for download.
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|-style="height: 100px;"
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|style="text-align: center;"|[http://purelight.biology.yale.edu:8080/servlets-examples/procat.html '''ProCAT --BROKEN URL--''']||style="text-align:center;"|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.
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|-style="height: 100px;"
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|style="text-align: center;"|[http://tilescope.gersteinlab.org/ '''Tilescope --BROKEN URL--''']||style="text-align:center;"|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.
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|-style="height: 100px;"
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|style="text-align: center;"|[http://tiling.gersteinlab.org '''Tiling''']||style="text-align:center;"|NA||A platform with all our tilling array analysis tools.
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|}
|}
[[even more tools]]
[[even more tools]]

Latest revision as of 02:16, 19 May 2016

Below is a list of tools that have previously been developed and published by the Gerstein Lab.

To view tools that have been published and are actively being maintained, please click here.

Unpublished resources may be viewed by clicking here.

Literature associated with lab software and servers may be accessed here.

Contents

Tools portals

Genecensus

Tool NameRelease DateDescription
File:Genecensus-title.jpg‎
Genecensus		1998

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 NameRelease DateDescription
x85px‎‎

partslist		1995

a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

genometech

Tool NameRelease DateDescription
File:Headline.gif‎‎‎
genometech		1995

A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes.

Network Tools

Tool NameRelease DateDescription
HUB2001A tool for leveraging the structure of the semantic web to enhance information retrieval for proteomics. This tool helps Proteomics researchers to be able to quickly retrieve relevant information from the web and the biomedical literature.
Yeasthub1997A 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.


Arrays-Based Tools

Tool NameRelease DateDescription
ProCAT 2006A 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.
Tilescope2007An 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.

Clustering

Tool NameRelease DateDescription
Local Clustering2001A new algorithm for local clustering to find timeshifted and/or inverted relationships in gene expression data is available as C source code.

Other

Tool NameRelease DateDescription
BoCaTFBS2006A boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. This tool is based on a data mining approach combining noisy data from ChIP-chip experiments with known binding site patterns. BoCaTFBS uses boosted cascades of classifiers for optimum efficiency, in which components are alternating decision trees; it exploits interpositional correlations; and it explicitly integrates massive negative information from ChIP-chip experiments.
ExpressYourself2003An interactive platform for background correction, normalization, scoring, and quality assessment of raw microarray data.
SPINE2001A laboratory-information management system (LIMS) for the NorthEast Structural Genomics Consortium. The online version is restricted to consortium users, but most of the code is freely available for download.

even more tools

Retrieved from "https://info.gersteinlab.org/More_tools"
Personal tools