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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[[File:GeneNet Banner2009c.png|link=http://www.genenetwork.org/]]

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.

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).

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 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).