Tag Archives: WebGBrowse

Announcement of Updated Tutorial Materials: UniProt, Overview of Genome Browsers, and World Tour of Resources

As many of you know, OpenHelix specializes in helping people access and utilize the gold mine of public bioscience data in order to further research.  One of the ways that we do this is by creating materials to train people – researchers, clinicians, librarians, and anyone interested in science - on where to find data they are interested in, and how to access data at particular public databases and data repositories. We’ve got over 100 such tutorials on everything from PubMed to the Functional Glycomics Gateway (more on that later).

In addition creating these tutorials, we also spend a lot of time to keep them accurate and up-to-date. This can be a challenge, especially when lots of databases or resources all have major releases around the same time. Our team continually assesses and updates our materials and in this post I am happy to announce recently released updates to three of our tutorials: UniProt, World Tour, and Overview of Genome Browsers.

Our Introductory UniProt tutorial shows users how to: perform text searches at UniProt for relevant protein information, search with sequences as a starting point, understand the different types of UniProt records, and create multi-sequence alignments from protein records using Clustal.

Our Overview of Genome Browsers introduces users to introduce Ensembl, Map Viewer, UCSC Genome Browser, the Integrated Microbial Genomes (IMG) browser, and to the GBrowse software system. We also touch on WebGBrowse, JBrowse, the Integrative Genomics Viewer (IGV), the ARGO Genome Browser, the Integrated Genome Browser (IGB)GAGGLE, and the Circular Genome Viewer, or CGView.

Our World Tour of Genomics Resources is free and accessible without registration. It includes a tour of example resources, organized by categories such as Algorithms and Analysis tools, expression resources, genome browsers (both Eukaryotic and Prokaryotic/Microbial) , Literature and text mining resources, and resources focused on nucleotides, proteins, pathways, disease and variation. This main discussion will then lead into a discussion of how to find resources with the free OpenHelix Resource Search Portal, followed by learning to use resources with OpenHelix tutorials, and a discussion of additional methods of learning about resources.

Quick Links:

OpenHelix Introductory UniProt tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=77

OpenHelix Overview to Genome Browsers tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=65

Free OpenHelix World Tour of Genomics Resources tutorial suite: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=119

 


Workshop: World Tour of Genome Browser and Galaxy of Analysis Tools

Would like to just announce that Mary and I will be giving an all-day hands-on workshop on Tuesday, November 2nd, 2010 in Washington DC (my home town), right before the ASHG conference (where we will also be). The title of the workshop is A World Tour of Genome Browsers and a Galaxy of Analysis Tools. We’ll be covering UCSC Genome and Table Browsers, an overview of other genome browsers, BioMart, Galaxy and a tour of genome resources and how to find them. For more information on location, cost, topics you can continue reading here. There are workshops on UCSC and Galaxy at ASHG  for attendess (which we will be at, but Bob, Anton and others will be doing), but those have sold out and filled up. We are offering this workshop for those who would like to learn these topics and more, both DC residents and ASHG attendees.

To purchase a seat and register, go to our upcoming workshops page.

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Official GBrowse 2.0 launch announced

Just got this email from the GBrowse mailing list. Lincoln Stein announces the release of GBrowse 2.0. Here’s the link to the full announcement. Here’s a portion of the text; the full email includes a couple of things not included yet:

With thanks to the many people who have worked long and hard on this project, as well as the people who found and reported bugs during the prerelease stage, I am happy I announce that GBrowse 2.00 is now available for downloading from CPAN, http://search.cpan.org/dist/GBrowse/ and SourceForge, https://sourceforge.net/projects/gmod/files/.

The following are hilights of the many new features that have been added since the 1.70 release:
• A completely rewritten internal rearchitecture loads tracks asynchronously, providing a more responsive user experience.
• Different database backends can be associated with each track, making backend management much simpler.
• A revamped user interface for a less cluttered and more functional end-user experience.
• A UI theming system with three predefined themes, including a cool “transparent” theme.
• A custom track upload and management system gives users much greater control over custom tracks.
• An optional admin interface allows an authorized user to upload and manage public tracks without editing config files.
• An optional user registration and login system allows users to register stable GBrowse accounts and to keep their settings and custom tracks when they move from one computer to another.
• Support for named subtracks (tracks within tracks) and filtering of those subtracks.
• Support for next generation sequencing data.

For those of you who want a quick feel for the new look/features of 2.0 you should check out the Tip of the Week and you can try it out at WebGBrowse.

And yes, we’ll update our GBrowse freely-available tutorial as 2.0 rolls out at more and more sites.  But lots of sites will maintain the previous versions for some time in our experience, so there is still plenty of value in knowing how the previous versions work.

Tip of the Week: WebGBrowse, now v2.0

From the GBrowse mailing list this week comes word of the new version of WebGBrowse.  I talked about WebGBrowse in the past as a very handy tool for creating a GBrowse visualization of data that you may have.  Using WebGBrowse permits you to upload, view, and interact with the data without the overhead of installing a local copy of GBrowse and having to maintain that.  This short Tip of the Week demonstrates how easy it is to interact with this web-based, customizable, implementation of GBrowse.

The full announcement can be found here, but briefly here were the highlights for me:

- The users will now have a choice of GBrowse display between versions
1.7 and 2.0.
- The display from one version can be migrated to the other by simple
button clicks. This helps the users to compare their data display between the two versions without much hassle. It also helps the WebGBrowse users in upgrading/migrating their existing GBrowse displays to version 2.0 seamlessly.

This would be great for a smaller project team that can’t maintain their own local copy of GBrowse, or as a way to pilot the project before committing to the whole thing.  I also think this could be a very handy teaching tool for instructors who want to get students up to speed on some of the foundations of genome browser display without too much overhead.

Tip of the week: JBrowse, a game changer?

jbrowse_tipIn most of software and database development the changes that are coming along all the time seem to be tweaks and polishes on the existing strategies. Every so often, though, there’s a big shift in the strategy or mechanism. This week the JBrowse paper I read made me realize that is now firmly underway. Today’s tip of the week will introduce JBrowse, and here I’ll describe some of the reasons this is a game changer.

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Ok, say you get a genome. What next?

There may be a lot of opportunity to get one’s genome of interest sequenced in the near future.  And I don’t only mean your own personal genome–I mean your species of interest.  There should be academic centers and service providers who offer genome sequencing at increasingly reasonable pricing soon.

So let’s say you get your favorite sample done: what next?  We have talked about how cool it is to be able to use the GBrowse or WebGBrowse tools to display your data.  But that is missing a step, actually.  To get appropriate data to display you need to annotate your genome.  You need to curate your genome.  The GMOD suite offers some tools to do this–Apollo can be a part of your strategy. JCVI has an annotation service for prokaryotic genomes that uses Manatee. They frequently offer a prokaryotic annotation course around that process as well.

But the other day I heard about another option that I thought I would mention: the BLAST2GO team is announcing a course on Automated Functional Annotation and Genome Mining.  Here is their announcement via the GOFriends mailing listpersonally I would choose the one in Valencia :)

blast2go_course

•Are you working in sequencing projects?
(EST projects, Next Generation Sequencing, Microarray desing, etc… )
•Do no have thousands of novel sequences that need functional annotation?
•Do you need a user-friendly tool to functionally analyze your data?
The Blast2GO Team is very pleased to announce:

FIRST INTERNATIONAL COURSE IN
AUTOMATED FUNCTIONAL ANNOTATION AND DATA MINING

In this course you will learn tools and tips for functional
annotation, visualization and analysis of novel sequence data making use of Blast2GO.

The course will be offered to 35 participants at 2 locations:
•Valencia, Spain: 28 to 30, September 2009
•Florida, USA: 14 to 16, October, 2009
For more information and registration until the 1 of September please visit:
http://bioinfo.cipf.es/blast2gocourse

But Florida in October wouldn’t be a bad option either!

For more information about just the BLAST2GO part, check out this site: http://blast2go.org/

Got a genome? Need a browser?

helix

From the GBrowse mailing list the other day came notice of a new way to use GBrowse–without programming! A team from Indiana University has lowered the barrier of entry for anyone with a genome they want to display.  They have created an interface and web server for GBrowse that lets you simply upload your data and make some choices for the display…and voilà!  You have a genome browser. It is called WebGBrowse, and I think it is tremendously helpful.  http://webgbrowse.cgb.indiana.edu

As we push forward with more and more sequence data for anyone’s favorite species, and with personal genomes, a rapid and programming-lite option for examining this data needs to exist.  This is a step in that direction.  All you need to do is get your data into GFF3 format (and they give you a sample), you upload it, you pick some display features, and you can be looking at your genome and annotation features in no time at all.

Even if you decide you wanted to build the standard GBrowse version it would be really helpful for the team to mock it up in the WebGBrowse interface to discuss the features.  It might also be an nice way to get students thinking about such displays and then take them over to the regular GBrowse tools.  I could also see creating displays for your gene of interest with various features that are important for your work, or to display for presentations and papers.  I wonder if there is a lower size limit to what you can display…hmm….

I used their sample file to upload and examine and it was very neat and dramatically quick.  I’m going to try to edit that GFF with some sample data that I’ll pull out of NCBI–just to try it out.  One thing that would make my life just that much easier would be to use the GFF file as a web form so I could just load data in that way.  I can see the need for uploading some things (like lists of genes or primers or variations) and I would want a way to save the output for re-upping and sharing, but I would love to be able to handle each of those separately instead of one big GFF.   Another handy feature would be to be able to load a GenBank format file right up.  I wonder if there is a web converter out there for that (I know it exists on the programming side)…I’ll have to look. Or let me know in the comments if you have one. But these are minor enhancement requests–it seems to work great already.  And maybe I’ll learn more as I spend a bit more time with it.

If you are totally new to GBrowse you might want to have a look at our free tutorial on it. Dozens of research groups are using GBrowse to display their data now, and more are coming along all the time.  It will help you to understand the structure and the kinds of things you can expect–and envision what you want to display.

Anyway–congrats to the team that created WebGBrowse.  I think it will be really useful in many ways.  And it is lifting the burden for biologists that don’t have programming resources–that is seriously helpful.

More like this, please :)

ResearchBlogging.orgPodicheti, R., Gollapudi, R., & Dong, Q. (2009). WebGBrowse – a web server for GBrowse Bioinformatics DOI: 10.1093/bioinformatics/btp239