Galaxy = interactive and reproducible genomics ( USE NOW! | DOWNLOAD | WATCH | BLOG)

It is designed to help two communities that often have difficulty communicating:

1. Experimental biologists: "I really have no time to program but I want to do whole-genome analyses to find targets for experimental validation".
2. Computational biologists: "I develop algorithms but have no time to develop interfaces".

So, decide which category you belong to and read on...

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Experimental (watch a sample analysis)

Suppose you want to find top hundred protein-coding exons in human genome with the highest density of single nucleotide polymorphisms (SNPs). Answering this question is not trivial. To do so one needs to compare all human exons to all human SNPs. To put this into perspective the current version of human genome (hg18) includes 357,517 known exons and 12,351,941 SNPs. Watch how Galaxy makes such an analysis quick and easy.

Learn more:

• Getting data from UCSC Table Browser
• Handling genomic coordinates in Galaxy
• Screencasts highlighting various aspects of Galaxy's functionality
• Information on user accounts and data security
• Genomic sequences and alignments available through Galaxy
• Statistical genetics tool kit for Galaxy

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Computational (watch how to download or add a tool)

Suppose you wrote a fantastic tool for statistical analyses of DNA sequences, which can help experimental biologists to narrow down potential list of target sites for experimental validation. The only problem is that it is a command line tool like this:

myProgram inputAlignment parameter1 parameter2 parameter3 outputFile

and you really have no time or inspiration to develop a nice user interface. Fortunately, it is very easy to add tools like yours to Galaxy. In return Galaxy will provide good looking unified interface and will allow your experimental colleagues to manage input data, change parameters, and make sense of the results.

Galaxy aims to be a zero configuration entirely self-contained system that provides a lightweight webserver, an embedded database and a multi-threaded job manager. All tools (and their parameters) can be specified via simple XML based configuration files.

Learn more:

• Installing local mirrors of Galaxy
• Adding new tools
• Writing custom code that can be run at various times of the execution process
• Plugging external data sources into Galaxy
• Adding additional ENCODE datasets to the import tool
• Adding multiple alignments into Galaxy

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What if?

Report any problems, bugs, and suggestions to the galaxy-bugs email. You can also subscribe to our mailing list Galaxy-User to receive updates.