Galaxy, a web-based genome analysis tool for experimentalists

Galaxy, a web-based genome analysis tool for experimentalists

2010 January | Daniel Blankenberg¹,⁵, Gregory Von Kuster¹,⁵, Nathaniel Coraor¹,⁵, Guruprasad Ananda¹,⁵, Ross Lazarus²,⁵, Mary Mangan³, Anton Nekrutenko¹,⁵, and James Taylor⁴,⁵
Galaxy is a web-based genome analysis tool that provides experimentalists with simple interfaces to powerful tools, while automatically managing computational details. It allows users without informatics or programming expertise to perform complex large-scale analysis using a web browser. Galaxy is available as a publicly accessible web service or a downloadable package, offering tools for genomic, comparative genomic, and functional genomic data analysis. The tool supports interactive analysis, ensuring transparency and reproducibility of results. It encapsulates high-end computational tools, providing intuitive user interfaces while hiding the details of compute and storage management. This unit describes Galaxy's functionality through a series of examples, focusing on experimentalists. It uses tools available at the public Galaxy service (http://usegalaxy.org) and includes screencasts to demonstrate protocols. The protocols cover basic aspects of Galaxy's functionality, including finding promoters with TAF1 binding sites, identifying exons with the highest number of SNPs, generating workflows, and extracting genomic sequences and alignments. Galaxy also allows sharing of workflows and data, and provides a framework for reproducible and transparent computational analysis. The tool is continuously updated with new features and tools, and users can access screencasts and documentation for further assistance. Galaxy is a valuable resource for both experimental and computational researchers, facilitating collaboration and data sharing across different locations.Galaxy is a web-based genome analysis tool that provides experimentalists with simple interfaces to powerful tools, while automatically managing computational details. It allows users without informatics or programming expertise to perform complex large-scale analysis using a web browser. Galaxy is available as a publicly accessible web service or a downloadable package, offering tools for genomic, comparative genomic, and functional genomic data analysis. The tool supports interactive analysis, ensuring transparency and reproducibility of results. It encapsulates high-end computational tools, providing intuitive user interfaces while hiding the details of compute and storage management. This unit describes Galaxy's functionality through a series of examples, focusing on experimentalists. It uses tools available at the public Galaxy service (http://usegalaxy.org) and includes screencasts to demonstrate protocols. The protocols cover basic aspects of Galaxy's functionality, including finding promoters with TAF1 binding sites, identifying exons with the highest number of SNPs, generating workflows, and extracting genomic sequences and alignments. Galaxy also allows sharing of workflows and data, and provides a framework for reproducible and transparent computational analysis. The tool is continuously updated with new features and tools, and users can access screencasts and documentation for further assistance. Galaxy is a valuable resource for both experimental and computational researchers, facilitating collaboration and data sharing across different locations.
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