Tag Archives: visualization

SGD variant viewer

Video Tip of the Week: SGD’s Variant Viewer

Variant viewers are very popular. As we get more and more sequence data, the challenge of looking across many samples only gets more and more important. So I always like to see how different groups are doing this. I’m still waiting for the killer app on this–the pan-genome graphs with all the paths along different genomes/regions displayed. But there are many good examples out there now for seeing variations in different species, strains, or different individuals.

This week’s Video Tip of the Week looks at the yeast variation viewer from SGD. It shares some features with other visualization tools (lollipops are hip, lately). But it has a very quick way of switching back and forth from DNA to protein that isn’t always available on variation viewers that I’ve tried before.

So this week’s video tip shows you their quick tour of their recently added variant viewer tool.

I won’t go into any more detail–they have a whole paper in the NAR database issue 2016 that describes the development and the features (below). Go over and try it out, it’s speedy and easy to use.

Quick link:

SGD: http://www.yeastgenome.org/

References:

Cherry, J., Hong, E., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E., Christie, K., Costanzo, M., Dwight, S., Engel, S., Fisk, D., Hirschman, J., Hitz, B., Karra, K., Krieger, C., Miyasato, S., Nash, R., Park, J., Skrzypek, M., Simison, M., Weng, S., & Wong, E. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr1029

Sheppard, T., Hitz, B., Engel, S., Song, G., Balakrishnan, R., Binkley, G., Costanzo, M., Dalusag, K., Demeter, J., Hellerstedt, S., Karra, K., Nash, R., Paskov, K., Skrzypek, M., Weng, S., Wong, E., & Cherry, J. (2016). The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1250

Thanks for joining us

Video Tips of the Week, Annual Review 2015. Part II

As you may know, we’ve been doing these video tips-of-the-week for eight years now. We have completed or collected around 400 little tidbit introductions to various resources through this past year, 2015. At first we had to do all of our own video intros, but as the movie technology became more accessible and more teams made their own, we were able to find a lot more that were done by the resource providers themselves. So we began to collect those as well. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II, 2011 I, 2011 II, 2012 I, 2012 II, 2013 I, 2013 II, 2014 I, 2014 II, 2015 I.

July
July 1: MorphoGraphX, morphogenesis in 4D
July 8: PhenomeCentral
July 15: Introduction to the UCSC Genome Browser
July 22: PathWhiz for graphical appeal and computational readability
July 29: PathWhiz for Pathways, Part II

August
August 5: Araport, Arabidopsis Portal
August 12: World Tour of Genomics Resources, part II
August 19: gene.iobio for genome and variation browsing
August 26: Human Metabolome Database, HMDB

September
September 2: ENCODE Data Coordination Center, phase 3
September 9: UCSC features for ENCODE data utilization
September 16: BANDAGE for visualization of de novo assembly graphs
September 23: UCSC Xena System for functional and cancer genomics
September 30: Global Biotic Interactions database, GloBI

October
October 7: Weave, Web-based Analysis and Visualization Environment
October 14: 100,000 Genomes Project
October 21: PanelApp, from the 100000 Genomes Project
October 28: New Reactome Pathway Portal 3.0

November
November 4: RNACentral, wrangling non-coding RNA for simplifying access
November 11: UCSC Table Browser and Custom Tracks
November 18: Explore Gene Pages at NCBI with Variation and Expression Information
November 25: iDigBio for access to historical specimens and more

December
December 2: KBase, DOE’s Systems Biology Knowledgebase
December 9: Send UCSC Genome Browser sequence to external tools
December 16: Plant Reactome at Gramene
December 23: Video Tips of the Week, Annual Review 2015 (part 1)
December 30: [this post]

Thanks for joining us

Video Tips of the Week, Annual Review 2015. Part 1

As you may know, we’ve been doing these video tips-of-the-week for eight years now. We have completed or collected around 400 little tidbit introductions to various resources through this past year, 2015. At first we had to do all of our own video intros, but as the movie technology became more accessible and more teams made their own, we were able to find a lot more that were done by the resource providers themselves. So we began to collect those as well. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II, 2011 I, 2011 II, 2012 I, 2012 II, 2013 I, 2013 II, 2014 I, 2014 II.

January 2015:
January 7: PhosphoSitePlus, protein post-translational modifications
January 14: Genome assemblers and #Docker
January 21: GWATCH, for flying over chromosomes
January 28: Helium plant pedigree software, because “Plants are weird.”

February 2015:
February 4: COSMIC, Catalogue Of Somatic Mutations In Cancer
February 11: IntOGen, for Integrative OncoGenomics
February 18: RStudio as an interface for using R
February 25: CRISPRdirect for editing tools and off-target information

March 2015:
March 4: Beacon, to locate genome variants of potential clinical significance
March 11: Aquaria, streamlined access to protein structures for biologists
March 18: Designing proteins, using Rosetta
March 25: Protein structure information for public outreach. Really.

April 2015:
April 1: The New OpenHelix Interface
April 8: Jalview for multiple sequence alignment editing and visualization
April 15: Viewing Amino Acid info in the UCSC Genome Browser
April 22: TargetMine, Data Warehouse for Drug Discovery
April 29: Proband for pedigrees with your iPad

May 2015:
May 6: Human Phenotype Ontology, HPO
May 13: PhenogramViz for evaluating phenotypes and CNVs
May 20: NCBI Tree Viewer
May 27: PANDA (Pathway AND Annotation) Explorer for lists of genes

June 2015:
June 3: ClinGen, The Clinical Genome Resource
June 10: GenomeConnect, the ClinGen piece for patients
June 17: ZBrowse for GWAS viewing and exploration
June 24: Handy way to make citations quickly

More next week…. 

SNPpets_2

Friday SNPpets

This week’s SNPpets include quite a range of things. New species genomes projects (pineapple is out, bauhinia being crowdfunded). I dare you to resist a tool called “Time Curves“.  The pre-print on over 60k protein coding human variations. Updates via FlyBase and discussed for QIIME. Best quip of the week: You can buy a DNA test on Amazon and it costs less than the textbook about it. A couple of items on bioinformatics pain. Some new solutions. And more….


SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


 

reddit_icon

What’s the Answer? (publication quality alignment images)

reddit_iconThis week’s highlighted question is from the Bioinformatics subreddit. And I’m using it because it made me laugh. I dare someone to name their alignment tool “Fancy Pants”. That said, it did provide links to a number of different tools that people might find useful, depending on the kind of thing you might want to do do make your stuff look niiiiiiiiice.

reddit question icon

Looking for publication quality alignment (‘fancy pants alignment’ are the words my colleague specifically used)

submitted  by CatsVansBags

Hey all- my colleague and I are looking for an alignment tool (software, website, etc) that makes beautiful looking alignments for publications. ClustalW is what everyone keeps suggesting and its nice but its not niiiiiiiiice. If anyone has any favorites, please fill me in, Thanks!

Some of the tools are things we’ve talked about before. Jalview and AliView, for example. But there are some others too. Have a look at the chatter and check ‘em out yourself if you need some alignments. Or, if you have other tools, suggest them.

{By the way, I am familiar with the tool called FancyGene. But it’s different.}

 

BANDAGE

Video Tip of the Week: BANDAGE for visualization of de novo assembly graphs

Typically we highlight web-based tools for our Tips of the Week. But sometimes there’s a tool that has some novel visualizations that we want to note that might require a user to do a download and installation. This week’s tool is one of those–BANDAGE, a Bioinformatics Application for Navigating De novo Assembly Graphs Easily.

I heard about it on twitter, and I was drawn to the paper right away by the visual representation in that figure:

It happened to come out around the same time I was thinking about the paths used to graphically represent variation data among individuals too. So I had been thinking a lot about ways to show alternate paths of sequence data with graphical representations. And although I don’t do assemblies myself–I focus downstream of that when the data is already refined–it’s useful to think about the challenges of assembling these data sets. And the interest in the tool suggested to me that people who do de novo assemblies might want to hear about this.

The Bandage team has several videos that help to explain the features of their tool. I’ll highlight the overview/introduction here for this weeks Tip of the Week, but if you want to learn more about the details be sure to check out their others.

So have a look at Bandage and see if it helps you to solve de novo assembly issues for your project. Or just think about how others tackle these problems before they get submitted to the databases for everyone’s use. I think people who use data downstream should be aware of the way that the genome assembly folks are faced with the data. I found it really helpful to conceptualize this.

Quick link:

BANDAGE: http://rrwick.github.io/Bandage/

Reference:

Wick, R., Schultz, M., Zobel, J., & Holt, K. (2015). Bandage: interactive visualization of genome assemblies Bioinformatics DOI: 10.1093/bioinformatics/btv383

What’s the answer? (circular browsers)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question gets at the problem of visualization that is going to be increasingly challenging. Some genomes need to be represented differently. I’m still waiting for a genome browser that can show both linear chromosomes and a mitochondrial genome at the same time :)

Question: What are some good interactive circular genome browsers?

Hi all,

I am looking for a interactive genome browser for circular (viral) genomes. Something that lets users view genome features in the context of the genome while allowing for backend and user customization. I need something that is interactive not simply a program to draw a static genome representation. I am familiar with a few:

Are there others that I should be considering?

R. Burke Squires

I added my thoughts about one clever way I saw it done, using bacteriophage genomes. My Tip of the Week on phiGenome shows you more. But check out the others, and if you have other suggestions please add them.

Video Tip of the Week: Visualizing the Galaxy


An antennae galaxy

Well, not that kind of galaxy (though visualizing those are quite nice), this kind of Galaxy. Galaxy is an excellent tool to analyze, reproduce and share genomics data and the Galaxy folks are always updating, improving and adding features to the tool. We have a tutorial for Galaxy to help you get started using this tool. As you might have guessed from the previous sentence, Galaxy is a moving target. The basics (and that’s what the tutorial is for) are the same, but the tutorial is in the process of being updated to reflect some of those changes. That update should be out sooner rather than later, but that said, we just can’t fit everything into the tutorial. The relatively new visualization tool is something that will not be in the tutorial. As there are no tutorials on visualization at the Galaxy site that I can find (if you know of any, link them here!), I’ve included a quick intro to visualizations using Galaxy in this tip of the week.

There are other ways to visualize the data analyzed at Galaxy. Galaxy datasets can often be viewed directly at UCSC Genome Browser, Ensembl, RViewer or in GeneTrack within Galaxy. Those are all excellent tools and powerful ways to view and explore your analysis in depth. In addition, the Galaxy visualization tool is a way to quickly visualize your data to help  discovery,  direct further analysis and share what you’ve found. It is obviously not a full fledged browser, but is very useful in doing a simple visualization of your data from within Galaxy. Today’s tip gives a quick introduction to Galaxy visualization.

Quick Links:
Galaxy (OH tutorial-subscr.)
UCSC Genome Browser (OH tutorials-free)
Ensembl (OH tutorials-subscr.)
RViewer
GeneTrack

P.S. You might here some bird song in the background. I am in, and working from, Hawaii for the next month (yeah, it’s tough work but someone has got to do it). No way to get those birds (or the frogs at night) to be silent for a bit.

BioVis 2012–a conference on visualization of biological data

This announcement came across the Cytoscape mailing list today. Ah, if I were young again I’d do a project on this–I love to think about how to display and interact with the bonanza of data we’ve got rolling in. Announcement below, with links to the conference embedded. You can see the original on the Cytoscape mailing list here.

++++++++++

Dear colleagues,

Are you already planing your trip to BioVis (http://www.biovis.net) in Seattle this October? If not, then this a good time to get started. BioVis will take place on October 14th and 15th as part of the IEEE VisWeek conference.

DEADLINES
Poster and contest entries are due on June 27th. For details about the contest see below.

KEYNOTE
Our program is quickly taking shape and we are happy to announce that Christof Koch, CTO of the Allen Institute of Brain Science and Professor of Biology and Engineering at Caltech will be the BioVis 2012 keynote speaker. He will speak about the computational and informatics challenges of “MindScope”, a large-scale effort to synthesize genomic, anatomical, physiological and theoretical knowledge into a description of the wiring scheme of the cortex, at both the structural and the functional levels.

CONTEST
We are excited to introduce our second annual data visualization challenge. Like last year’s contest, this contest draws its inspiration from biological expression Quantitative Trait Locus (eQTL) data analysis. In 2011 we looked at how this data, which essentially catalogs how (potentially millions of) genotypic differences in an individual, cooperate to produce (potentially tens of thousands of) gene expression differences. While obviously a grand challenge, and pressing need for the biological and medical fields, the real payoff for this data comes from being able to use easily accessible sources of this data for an individual, for example blood, or saliva, to make predictions about difficult to access organs, such as brain or heart, where the immense regulatory network contains both similarities and differences.

To address this need, our 2102 challenge builds on the successes of 2011 and addresses differential eQTL – analysis of the differences between eQTL regulatory networks in different tissues, and the corresponding challenge of conveying the biological meaning contained in immense volumes of metadata, regarding these differences.

We invite contest contributions, big and small, to either the needs of visualizing and presenting the eQTL difference data, or the metadata, or any sub-aspect of these challenging problems. These are significant unsolved needs in the biological and life-sciences communities, and every contribution, will make a positive impact in this exciting and emerging field. There are two phases of competition and one has a choice of participating in either phase.

For more information, please see http://www.biovis.net/contest. The contest entries are due June 27, 2012.

We are looking forward to seeing you this October,

Jessie Kennedy, Raghu Machiraju and Nils Gehlenborg
BioVis 2012 General Chairs

PS: I love to test this sort of software if anyone wants to hire me to do some of that!

Video Tip of the Week: A 3D Worm!

In this era of big data and computational tools, it’s easy to generate huge amounts of texty and statistical data that offers great insights into biology, and delivers leads to design experiments in actual organisms and cells. But the cell and developmental biologist in me still yearns for great visualization tools to explore the results, beyond rows and columns and p-values. I think that better visualizations of the “-omics” data is still one of the unmet needs in this arena, and I’ve talked about that more than once but most recently here.

I’ve been keeping an eye on the progress at WormBase because I knew that they were going to be changing over to their new interface soon (it’s there now and you should see the slick new look, and that means I have to update our tutorial once it’s all stable). So I was watching their blog for updates. One of the posts they had was for a different project, though, and I was really intrigued. They were touting the OpenWorm browser, which offers a 3D representation of a worm that you can interact with. I was hooked. Heh. (Hookworm–get it? Eh, nevermind….)

So I looked into the tool a bit more. There’s no publication on the current iteration (but it is referenced in the WormBase paper below), but I was reading up on some components and I watched the several videos on the OpenWorm site that talk in more detail about the goals and the project. The very enthusiastic talk by Stephen Larson comparing the worm to Lt. Data from StarTrek was quite engaging and accessible, and a nice demonstration of public outreach for complex science.

So, it’s not Lt. WormData yet exactly. But it’s a nice effort and I can see how it could be useful for visualizing complex data as it gets layered on to the physical structures. Transcription factor binding signals. Levels of expression of RNA-seq data. Opening chromatin. Protein modifications. All kinds of important biological stuff which I usually think of as “tracks” on genome browser could definitely be represented here. I hope it expands and that we can do these sorts of things for other organisms and cells and tissues.

And quite frankly it was just fun to drive it around. Check it out. Take this worm for a spin. And really–you can spin it… It looks like the future to me.

Quick links:

OpenWorm project information: http://www.openworm.org/

OpenWorm code project page: http://code.google.com/p/openworm/

OpenWorm 3D browser: http://browser.openworm.org

WormBase Virtual worm: http://caltech.wormbase.org/virtualworm/

WormBase (new site: http://www.wormbase.org ) and (legacy site: http://legacy.wormbase.org/)

Reference for WormBase:

Yook, K., Harris, T., Bieri, T., Cabunoc, A., Chan, J., Chen, W., Davis, P., de la Cruz, N., Duong, A., Fang, R., Ganesan, U., Grove, C., Howe, K., Kadam, S., Kishore, R., Lee, R., Li, Y., Muller, H., Nakamura, C., Nash, B., Ozersky, P., Paulini, M., Raciti, D., Rangarajan, A., Schindelman, G., Shi, X., Schwarz, E., Ann Tuli, M., Van Auken, K., Wang, D., Wang, X., Williams, G., Hodgkin, J., Berriman, M., Durbin, R., Kersey, P., Spieth, J., Stein, L., & Sternberg, P. (2011). WormBase 2012: more genomes, more data, new website Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr954