The OpenHelix Blog

The VISTA comparative genome analysis resource updated their interface a few months ago. Additionally, they’ve added VISTA-Point (which replaces and greatly extends VISTA text browser) which, as the site says, allows the user to:

Access complete data and visual presentation of pairwise and multiple alignments of whole genome assemblies.

The homepage has undergone a very nice redesign. Much of the underlying VISTA browser and other tools functionality and use is similar (though updated of course). We understand also that there will be upcoming updates to some tools and the addition of others. Look for that here .

Also, we’ve updated our tutorial to reflect the new site and functions. As before, this tutorial is free to users and sponsored by VISTA. Check it out.

I’m deeply immersed in a new project right now, so my blogging has been light of late.  But in lieu of that–you can check out a new paper on Galaxy that’s just come out!  We were approached by the Current Protocols in Molecular Biology team last year because they saw the need for works that were aimed at the folks who aren’t already in bioinformatics.  So we crafted a couple of papers designed to be useful for people who are doing benchwork and need to accomplish things with bioinformatics tools, but don’t need to be experts or coders.

The Galaxy paper has now been published, and you can check it out here: (subscription required)

Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists

I think it is very effective at step-by-step guidance on some tasks that scientists are likely to need, if I do say so myself as one of the authors .  There are also accompanying screen casts for additional assistance.   You can also see our free tutorial sponsored by the Galaxy team for an overview and orientation of Galaxy as well.

As this Nature editorial says, the as the human genome (and a few hundred others) were completed, the amount of data had become daunting (we know that well here at OpenHelix, we deal with it everyday and daily make that more accessible to scientists through training . But also, importantly, even with all the data, it’s been found that we need more. As the editorial states:

By 2004, large-scale genome projects were already indicating that genome sequences, within and across species, were too similar to be able to explain the diversity of life. It was instead clear that epigenetics — those changes to gene expression caused by chemical modification of DNA and its associated proteins — could explain much about how these similar genetic codes are expressed uniquely in different cells, in different environmental conditions and at different times.

Thus is born the Human Epigenome Consortium (Nature paper, subscription required, here). You can find some of the data from the pilot projec at the Sanger Institute site.

The beginning stages, but I believe it will prove to be quite a treasure trove of data (as if we don’t have a huge unmined dataset now). It was this last comment in the editorial:

.., given that epigenetic coding will be orders of magnitude more complex than genetic coding, its requirement for data crunching may be similar…

Get ready for a lot more resources and tools of greater complexity .

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

NEW FEATURE: We’d also like to invite resource providers to let us know if they have something new to talk about, or something they want to mention to the bioinformatics community. We’ve had some people email us because they weren’t sure if they should post something, and we want to say that’s fine.

So What’s Your Problem? And What’s Your Solution?

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

Got phylogeny? So, you’ve created a phylogeny using some software and would like to draw the tree from the Newick formatted file* you exported. Of course there is no shortage of tree drawing programs out there (or phylogeny generating ones either). We found another one recently; a web-based, API-usable, opensource tree drawing tool that is quite intuitive and functional. It’s called PhyloWidget. The paper describing PhyloWidget is here and you can find some very nicely done step-by-step instructions here. I’ve done a quick 4 minute tutorial here to give you a quick overview. If it looks like something you could use, you might want to delve into it right away, or check out their ‘walk through.’ Happy climbing.

*Here’s the file I use in the tip: ((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154);

A discussion well worth having. Dorothea Salo at “The Book of Trogool’s” recent post on Science Online 2010 (which one of us attended) mentions an interesting exchange she (a librarian) had:

Interlocutor: “So what do you do?
Me: “I’m a librarian.”
Interlocutor: *lengthy pause* So… what are you doing here exactly?

Er, what? A conference about science communication? How on earth can that not be imagined to intrigue a librarian?

This, ladies and gentlemen. THIS. Right here. This disconnect is the number-one threat to science librarianship today—perhaps to all academic librarianship. How can science libraries persist when scientists haven’t the least notion that libraries or librarians are relevant to their work?

I noticed a similar discussion going at STELLA (manifested in topics on embedding, the library of the future and science 2.0). My basic take on this is that researchers are are going to need physical libraries less and less (do they really need them now?) and librarians more and more (but they don’t seem to realize that). I commented as such on the post above.

Deepak Singh has asked a similar question today, and started a discussion.

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.

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.

Just a quick note about a new type of custom track supported on the UCSC Genome Browser.  We get a lot of questions about support for the next-gen sequencing types of data peeople are generating or expect to be generating soon.  This came across the announcement mailing list yesterday.  It also includes some helpful links for more details about this track and about other large data set track types.

We are pleased to announce the availability of another new track type for Custom Tracks: the Binary Alignment/Map (BAM).

BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and index-able representation of nucleotide sequence alignments. Many next-generation sequencing and analysis tools work with SAM/BAM. For custom track display, the main advantage of indexed BAM over PSL and other human-readable alignment formats is that only the portions of the files needed to display a particular region are transferred to UCSC. This makes it possible
to display alignments from files that are so large that the connection to UCSC would time out when attempting to upload the whole file to UCSC. Both the BAM file and its associated index file remain on your web-accessible server (http or ftp), not on the UCSC server. UCSC temporarily caches the accessed portions of the files to speed up interactive display.

Read more about the BAM file type here: http://genome.ucsc.edu/goldenPath/help/bam.html

Read more about the SAM project here: http://samtools.sourceforge.net/

For help with samtools, please contact the SAM tools mailing list:
http://sourceforge.net/mail/?group_id=246254

Read more about other file types available for use in the genome browser for very large data sets:
https://lists.soe.ucsc.edu/pipermail/genome-announce/2009-July/000165.html