The OpenHelix Blog » UCSC Table Browser

Video Tip of the Week: GenomeSpace, an integrator of integrators

Trey — Wed, 30 May 2012 13:00:18 +0000

Recently, the Broad Institute announced a new tool: GenomeSpace. When I first looked at it, admittedly a very cursory look, I wasn’t sure how it would be much different than an integrator of tools like Galaxy or GenePattern. Obviously that cursory look was wrong at first glance since both Galaxy and GenePattern are in their list of tools that are supported. So what is GenomeSpace? Well, you can read the answer here at their “What is GenomeSpace” page . Basically, GenomeSpace has several functions. As described here, “GenomeSpace supports several bioinformatics tools, all integrated to allow easy accessibility, easy conversion, and frictionless sharing.” It is a space (in that every expanding Amazon cloud) that allows you to store your data files and, importantly, GenomeSpace allows you to seamlessly move those files between the tools to complete complex, or simple, analyses. It achieves this by automatically converting file formats and by allowing the user to attach their accounts at the tools to their account at GenomeSpace, thus alleviating the need to log in several times when using more than one tool.

To get a good idea of what GenomeSpace might be able to do for a researcher, check out the recipes on the site. As Anton states:

GenomeSpace is an integration of integrators,” Nekrutenko said. “The benefit to the user is that this brings together distinctive collections of functionalities offered by individual tools.”

The site is new, and only in beta. They only recently opened up registration from their invite-only stage. As such, there are some bugs and some features that aren’t quite at full capacity. For example, the Galaxy and UCSC Table Browser integration is with the test versions of those tools during beta. Thus, for example, your account at Galaxy will not be recognized when trying to link that account with GenomeSpace. I had to create a new one on the test site. And, if you go to the public version of the Table Browser, it will look different (no link to GenomeSpace as there is on the test site). Currently there are seven tools, more to come.

All that aside, it’s definitely a tool to get acquainted with. And with that in mind, take a quick introductory spin with me in this week’s video tip to get an idea of what you might be able to do.

Quick Links:

GenomeSpace
UCSC Table Browser (OH tutorial)
Galaxy (OH Tutorial)
Cytoscape (OH Tutorial)
Genomica
GenePattern
IGV
InSilicoDB

Broad Institute
NHGRI

UCSC Table Browser webinar follow-up post (May 24)

Trey — Thu, 24 May 2012 16:19:11 +0000

We’ll be having our May 24th 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 you can’t make the webinar, the same material is covered in the training movie, slides, and exercises that are freely available, sponsored by the UCSC team: http://www.openhelix.com/ucscadv. You can also sign up to be informed of future webinars coming up on these topics, Galaxy, ENCODE and others.

Webinars on how to use UCSC Genome and Table browsers

Trey — Mon, 07 May 2012 20:11:12 +0000

As we have in the past, we are offering free webinars in the coming weeks on the UCSC Genome Browser and Advanced discovery using the Table Browser and custom tracks. These have been quite popular in the past, so sign up soon!

The Intro to the Genome Browser webinar will be Thursday, May 17th at 10am Pacific time (1pm ET). Check here for your time zone.

The Table Browser and custom tracks webinar will be Thursday, May 24th at 10am Pacific time (1pm ET). Check here for your time zone.

You can register here for the UCSC Genome Browser Intro and register separately here for the Table Browser and custom tracks webinar. You’ll need to register at OpenHelix if you haven’t already. It’s free and you’ll get no emails from us unless you opt in to our most excellent newsletter or ask to be notified of future webinars :D. Registration and attendance are free.

We have several months of free webinars planned including on ENCODE, Galaxy, PDB and others. Keep tabs with us here or on the webinars page (or though email notification) to be notified when those free webinars are coming.