Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more...
Galaxy = collaboration and reproducibility
Best of all, Galaxy’s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment...
- History is an analysis record | Every step of your analyses is recorded in Galaxy's history system. You can have any number of histories saved. This way you can go back to your analyses anytime.
- Share your analyses | Alice works at Penn State, while Bob suffers from the terrible San Diego climate. Alice wants Bob to see her analyses. Alice clicks the “share” link and enters Bob’s e-mail address. Now Alice’s history is visible to Bob (see “Sharing history” screencast).
- Now your results are reproducible! | When publishing results, replace “the data were analyzed using a collection of in-house scripts” with a URL pointing to Galaxy’s history. Your reviewers will have no further questions. That’s reproducible genomics!
Designed for biologists and developers
Yep, sometimes you can mix water with oil...
- Biologists | Use our public site to access popular sources of data like the UCSC Table Browser. Run analyses right on the spot using a variety of integrated tools. Your results are never deleted and can be easily shared with others.
- Developers | Galaxy is an easy-to-use, open-source, scalable framework for tool and data integration. Stop wasting time writing interfaces and get your tools used by biologists! Galaxy includes everything you need to get started, so download and start integrating!
Why did we do it?
You are an experimental biologist. You keep watching databases fill with more and more data. You keep thinking: even if I knew how to use Excel as a pro, it would probably not load 12,435,654 SNPs. So how do you perform analyses without calling somebody on the Computer Science side of campus? Suppose you want to find human promoters with the highest SNP density. There is no straightforward way of doing it without learning programming first. And this is why...
- Databases are not analyses tools | Databases are where you get the data. Browsers are where you visualize the results. For a bench biologist there is not much in between besides spreadsheets or Perl scripting.
- No tools for new datatypes | Some datatypes generated by high throughput genomics are so new that there are no tools to analyze them. For example, how do you extract sequences of coding exons from the latest 28-way alignments of vertebrate genomes or analyze quality scores from 454/Solexa/SOLiD? With Galaxy.
- Genomics is not really reproducible | The Methods section of too many papers sound like the data were analyzed using a collection of in-house scripts. How do you repeat such a study? Galaxy saves every step of your analysis and allows you to share these workflows with others.
- Too many tools | Bioinformatics publishes hundreds of application notes per year. How does one know which tool to use? Galaxy integrates a multitude of different tools by giving them the same “look and feel” and linking them to data warehouses.