- Non-alphanumeric characters (from '-') are stripped.
- All search keyword are used in searching links:
e.g. bioinformatics links directory will search for links that contain all three keywords in title, description, or tags. - You can search for an exact phrase by enclosing the query in quotes:
e.g. "bioinformatics links directory" - e.g. Search query "genomic sequences" dna will search for links containing the phrase "genomic sequences" and dna.
- You can include OR uppercase keyword:
e.g. dna OR rna looks for keywords dna or rna. - You can include - prefix or NOT uppercase keyword to define keywords that should not be included:
e.g. dna OR rna NOT protein (alternatively: dna OR rna -protein) will look for links with keywords DNA or RNA, but not protein
Galaxy
http://galaxyproject.org/ [open in a new window]
Galaxy is an open, web-based platform for performing accessible, reproducible, and transparent biomedical research. Complete computational analyses can be built, saved, rerun, modified and shared. Galaxy is available as a free public web server; as open-source software that can be installed and customized to address specific needs; as a virtual machine that can be installed on the cloud; and on many specialized public web servers at user sites.
This content is being maintained by galaxyproject.
links directory index: 475
Documentation
There are many approaches to learning how to use Galaxy. The most popular is probably to just dive in and try it. Galaxy is simple enough to use that you can do many analysis just by exploring the interface. However, you may miss much of the power this way.
Walking through the Galaxy 101 exercise will show you the ins and outs of using Galaxy. This includes loading data (from UCSC in this example), using genome builds, the tool interface, filtering, sorting, and combining datasets, generating statistics, and Galaxy's History, Workflow and sharing support. Galaxy 101 is available in several formats. You can start with either the Galaxy Page or the screencast.
There are a plethora of Screencasts available that demonstrate many aspects of Galaxy from basic features to full-blown complex analysis. See the Screencasts page for more.
Another way to learn Galaxy is by learning from what others have done. Galaxy supports the sharing and publishing of several Galaxy Objects within Galaxy:
- Pages
- Pages are documentation within that Galaxy that explain the steps and reasoning in a particular history or workflow. They provide additional context and can describe why particular choices were made. The list of published pages is a great place to start.
- Histories
- Histories are analyses in Galaxy that show all input, intermediate, and final datasets, as well as every step in the process and the settings used with each. Histories can be imported into your session and rerun as is or modified.
- Workflows
- Workflows specify the steps in a process but not the datasets. Workflows are analyses that are meant to be run, each time with different user-provided datasets.
- Data Libraries
- Datasets that are accessible from within Galaxy or for download.
COGshttp://www.ncbi.nlm.nih.gov/COG/Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.
163 Resources
620 Databases
1376 Tools
