Galaxy Intro Webinar follow-up post (July 19)

We’ll be having our July 19th Galaxy webinar today, and we find there are questions to follow up afterwards that are often better handled in discussions on the blog.

If there are questions we didn’t have time to get to–or things we want to expand on with more detail–we can discuss them in this thread.

Or if you have other things you’ve been meaning to ask, let us know.

If have registered for the webinar, the same material will be available  in the training movie, slides, and exercises tutorial suite: http://www.openhelix.com/galaxy. You can also sign up to be informed of future webinars coming up on these topics, UCSC, ENCODE and others.

Some questions asked in today’s webinar, with answers:

1) Galaxy seems to downloadable in addition to the PSU portal and the cloud at Amazon. How would you choose?

Each has it’s purposes. From the Galaxy Wiki:
Install your own Galaxy if you want to,

a) Develop it further
b) Add new tools
c) Plug-in new datasources,
d)Run a local production server for your site because you have
Sensitive data (e.g., clinical) or
Large datasets or processing requirements that are too big to be processed on Main

Use the Cloud:

“With sporadic availability of data, individuals and labs may have a need to, over a period of time, process greatly variable amounts of data. Such variability in data volume imposes variable requirements on availability of compute resources used to process given data. Rather than having to purchase and maintain desired compute resources or having to wait a long time for data processing jobs to complete, the Galaxy Team has enabled Galaxy to be instantiated oncloud computing infrastructures”

2) Can I use Galaxy to analyze protein data?

Yes, there are a few tools for analysis on the main instance, but also you can add your own tools to a local instance.

3) What kind of local server? Can you describe the PSU instance as an example? server size, storage. filesystem , etc. ?

Check out this link for needs.

4) Can we use galaxy to align the whole genome sequences of rice to get SNPs?

This link might help.

5) Is there a link to the toolshed from the galaxy interface?

Not that I know, but this is it: http://toolshed.g2.bx.psu.edu/

6) How secure is the data we run on galaxy.psu?

 From the site (emphasis added in answer):

This is a free, public, internet accessible resource. Data transfer and data storage are not encrypted. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to any public site, including this Galaxy server. If you have protected data, large data storage requirements, or short deadlines you are encouraged to setup your own local Galaxy instance or run Galaxy on the cloud.

 

3 thoughts on “Galaxy Intro Webinar follow-up post (July 19)

  1. William Feiereisen

    Does the Galaxy portal at PSU have any special computing hardware (like a parallel supercomputer) to run the compute intensive applications like bowtie for big datasets? Or is the underlying machinery just plain commodity servers?

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