Galaxy Platform For Accessible, Reproducible And Collaborative Biomedical Analyses: 2019 Update

High-throughput data creation technologies, particularly ‘next-generation’ DNA sequencing, have ushered in disruptive and widespread changes to biomedical research. Making sense of the large datasets produced by these technologies requires advanced statistical and computational methods, as well as substantial computational power. This has led to an acute problems in life sciences, as analysts without informatics training try to perform computation-dependent analyses.

Since 2005, the Galaxy project has worked to address this problem by giving a framework that makes advanced computational tools functional by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by giving a Web-based environment where users is capable of doing computational analyses and have every one of the details automatically monitored for later inspection, publication, or reuse.

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In this statement we highlight recently added features enabling biomedical analyses on a sizable range. Multi-step analyses can be carried out by running tools in succession, and Galaxy preserves the complete provenance of every analysis step (2,3). By bridging the space between tool designers and experts, Galaxy helps both constituencies accelerate their research.

The Public Galaxy Server: This is actually the focus of the paper. The site provides substantial CPU and disk space, making it possible to investigate large datasets. The Galaxy software is highly customizable and integrates with a wide variety of compute environments ranging from laptop computers to clusters to compute clouds. A Galaxy example administrator may then install a tool and everything necessary dependencies in an entirely automated way through the Galaxy Web interface or API.

The Galaxy Community: Finally, one of the most important the different parts of the project is the Galaxy community. Galaxy has an easy community of users, tool administrators and developers who maintain Galaxy instances. Developments in the Galaxy community are described below in section Community and Culture. Web-based genome analysis platforms are an evergrowing and long-term part of research. Early platforms for doing genome analyses in a Web browser include Taverna (4,5), GenePattern (6) and Galaxy. Recently, iobio (7), Epiviz (8), the Genome Modeling System (9), and ZENBU (10) have been developed for executing genome analysis and visualization in a Browser.

Galaxy’s large set of available tools, the powerful computing resources offered through the general public Galaxy Server and its own large community set it aside from other analysis systems. Three broad goals drive the development of Galaxy. First, Galaxy seeks to increase access to complex computational analyses for those scientists, including those with limited or no development knowledge. Galaxy’s Web-based graphical user interface (GUI) helps it be easy to do everything needed for relatively large data analyses. Using the Galaxy GUI, users can publish their own data or get data from public databases, choose analysis tools, place tool variables and inputs and run tools.

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