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Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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The old GeneNetwork TWiki was frozen for security issues. You can view it from [http://rhodes.uthsc.edu:81/ here] still.
 
== GeneNetwork ==
== GeneNetwork ==
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GeneNetwork is a database and open source bioinformatics software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence variants to corresponding differences in gene and protein expression and to differences in traits such as health and disease risk. Data sets in GeneNetwork are typically made up of large collections of genotypes (e.g., SNPs) and phenotypes that are obtained from groups of related individuals, including human families, experimental crosses of strains of mice and rats, and organisms as diverse as Drosophila melanogaster, Arabidopsis thaliana, and barley. The inclusion of genotypes for all individuals makes it practical to carry out web-based gene mapping to discover those regions of the genome that contribute to differences in gene expression, cell function, anatomy, physiology, and behavior among individuals.
GeneNetwork is a database and open source bioinformatics software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence variants to corresponding differences in gene and protein expression and to differences in traits such as health and disease risk. Data sets in GeneNetwork are typically made up of large collections of genotypes (e.g., SNPs) and phenotypes that are obtained from groups of related individuals, including human families, experimental crosses of strains of mice and rats, and organisms as diverse as Drosophila melanogaster, Arabidopsis thaliana, and barley. The inclusion of genotypes for all individuals makes it practical to carry out web-based gene mapping to discover those regions of the genome that contribute to differences in gene expression, cell function, anatomy, physiology, and behavior among individuals.
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GeneNetwork 1:
http://www.genenetwork.org/
http://www.genenetwork.org/
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GeneNetwork 2:
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http://gn2.genenetwork.org/
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@wikipedia:
http://en.wikipedia.org/wiki/Genenetwork
http://en.wikipedia.org/wiki/Genenetwork
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== Getting started ==
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Genenetwork 2 uses the Ubuntu 12.04.5 LTS 64-bit operating system and MySQL 5.5.40 as the database. The primary server-side language used is Python 2.7.3. Flask 0.9 and Jinja2 2.6 are used as the framework and templating language respectively. Client-side, we primarily use the Boostrap 3.3.0 javascript/css web framework for look and feel. Some other commonly used JS/CSS libraries are jQuery 1.10.2 (for easier DOM manipulation), DataTables 1.9.4 (for more feature-rich tables), and CKEditor 4.4.5 (for user-added text/html; for example the news page).
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* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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== Data Sources ==
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* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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== Data Sources==
 
* [[Data Sharing Zone]]
* [[Data Sharing Zone]]
* [[Standard Operating Protocols (SOP)]]
* [[Standard Operating Protocols (SOP)]]
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== Servers ==
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* [[Server List]]
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* [[GeneNetwork 1 Production Server]]
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* [[GeneNetwork 2 Production Server]]
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== Cluster systems ==
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* [[Cluster @ Hera]]
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* [[Cluster @ Tanner]]
== System Administration ==
== System Administration ==
* [[Mirror Installation Requirements]]
* [[Mirror Installation Requirements]]
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* [[Password-less_Login]]
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==Cluster systems ==
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== MediaWiki ==
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* [[Cluster @ Hera]]
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* [[How to use Cluster]]
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* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]

Latest revision as of 21:21, 1 February 2016

GeneNetwork MediaWiki has been successfully installed on 29 June 2010 by Lei Yan.

This website contains documentation for the GeneNetwork project at the University of Tennessee Health Science Center.

Consult the User's Guide for information on using the wiki software.

Contents

GeneNetwork

GeneNetwork is a database and open source bioinformatics software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence variants to corresponding differences in gene and protein expression and to differences in traits such as health and disease risk. Data sets in GeneNetwork are typically made up of large collections of genotypes (e.g., SNPs) and phenotypes that are obtained from groups of related individuals, including human families, experimental crosses of strains of mice and rats, and organisms as diverse as Drosophila melanogaster, Arabidopsis thaliana, and barley. The inclusion of genotypes for all individuals makes it practical to carry out web-based gene mapping to discover those regions of the genome that contribute to differences in gene expression, cell function, anatomy, physiology, and behavior among individuals.

GeneNetwork 1: http://www.genenetwork.org/

GeneNetwork 2: http://gn2.genenetwork.org/

@wikipedia: http://en.wikipedia.org/wiki/Genenetwork

Genenetwork 2 uses the Ubuntu 12.04.5 LTS 64-bit operating system and MySQL 5.5.40 as the database. The primary server-side language used is Python 2.7.3. Flask 0.9 and Jinja2 2.6 are used as the framework and templating language respectively. Client-side, we primarily use the Boostrap 3.3.0 javascript/css web framework for look and feel. Some other commonly used JS/CSS libraries are jQuery 1.10.2 (for easier DOM manipulation), DataTables 1.9.4 (for more feature-rich tables), and CKEditor 4.4.5 (for user-added text/html; for example the news page).

Data Sources

Servers

Cluster systems

System Administration

MediaWiki

Personal tools