Galaxy: a platform for interactive large-scale genome analysis.

By Belinda Giardine, C. Riemer, Ross C. Hardison, Richard Burhans, L. Elnitski, P. Shah, Yi Zhang, Daniel J. Blankenberg, I. Albert, James Taylor and 3 more. Genome Research, 2005

2,176 citations recorded by the source corpus.

Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dda22bbd8e22e50f9c827bf1b1f34b66be17a5eb

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Citations in the corpus

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update (2022, background): “Started in 2005 (7), the Galaxy project is now sustained by a strong, global community of users, educators, developers and administrators.”
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018, neutral): “(1) The main public Galaxy server (https://usegalaxy.”
Ten Simple Rules for Reproducible Computational Research (2013, background): “If you are instead performing your analyses through an integrated framework (such as Gene-Pattern [10], Galaxy [11], LONI pipeline [12], or Taverna [13]), the system may already provide full or partial support for most of the rules.”
obitools: a unix‐inspired software package for DNA metabarcoding (2016, methodology): “The OBITOOLS Galaxy (Giardine et al. 2005) wrapper can be downloaded from the GenOuest core facility”
The UCSC Genome Browser database: update 2011 (2010, methodology): “Output from the Table Browser can also be sent to other tools such as Galaxy (15) or GREAT (see ‘New features’ section) for subsequent analysis.”
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. (2012, background): “Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A: Windshield splatter analysis with the Galaxy metagenomic pipeline.”
Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. (2014, methodology): “Data analysis was performed using the Galaxy web server (Giardine et al., 2005; Blankenberg et al., 2010; Goecks et al., 2010) and INTEGRATIVE GENOM-”
The BioMart community portal: an innovative alternative to large, centralized data repositories (2015, background): “It also supports many third party packages such as Taverna (2), Galaxy (3), Cytoscape (4) and biomaRt (5), which part of the Bioconductor (6) library.”
Network-based machine learning and graph theory algorithms for precision oncology (2017, methodology): “…existing tools can be reimplemented as apps on a platform such as Cytoscape 122 or another software environment similar to GALAXY for data analysis 123 to the development and of the software system precision oncology. scalability is always issue in network-based analysis since it is common to…”
BioMart – biological queries made easy (2009, methodology): “BioMart also has the advantage of being integrated with external software packages such as BioConductor [3], the Distributed Annotation System (DAS) [4], Galaxy [5], Cytoscape [6], Taverna [7].”
The UCSC Genome Browser Database: update 2009 (2008, methodology): “The Table Browser (13) continues to be one of the most widely used features of the GBD toolset and is increasingly used to export data to the Galaxy (14) tools at Penn State for further processing.”
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. (2007, methodology): “2004) or the Galaxy server (Giardine et al. 2005; Blankenberg et al. 2007) to help identify genome-wide trends.”
A Primer on Metagenomics (2010, background): “Galaxy, an online workbench for the analysis of genomic data, can also perform some comparative metagenomic analysis, as well as taxonomic mapping [108].”