Tag Archives: vizualization

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Friday SNPpets

This week’s SNPpets illustrate that everyone’s back in the saddle after the holidays with plenty of chatter. New and updated databases, tools, and other news abound. The financial threat to well known databases like FlyBase, MGI, OMIM, Reactome, UniProt, etc–took my breath away though. Loved the RStudio cheat sheet. And the ProteinPaint lollipop plots of mutations looks great.


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…


https://twitter.com/sciencemagazine/status/682955226698100737

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Friday SNPpets

A pretty unusual week. Cutting-edge science and as well as access to medical literature that’s hundreds of years old. Predictions about the future. New ways to use one of my favorite visualization tools (UpSet) and influential visualizations from the past. Veterans genomes and minion genomes. And more….


Welcome 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…


https://twitter.com/CAGC_ACCG/status/622428563153686528

Friday SNPpets

This week’s SNPpets include an interactive timeline of cancer research, NIH’s statement on cloud-stored genomics data, Facebook and genomics data, hilarious typos in some published equations, and more….


Welcome 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…

Video Tip of the Week: MizBee Synteny Browser

In my last tip of the week I was really pleased about the opportunity to see the data from a paper set up in a custom GBrowse, but it also reminded me of the limitations of some current strategies for visualization that we are facing. In that case one of the things that I wanted was to be able to visualize both nuclear genes + expression with mitochondrial genes + expression. Right now there’s no way to do that easily in a graphical browser (as far as I know).

Improved visualization strategies that offer increased flexibility about the features being viewed, and that scale up to the current data deluge, are both going to be necessary. So when I spotted this tweet about a group doing visualization I was intrigued:

RT @mcmahanl: RT @chlalanne: Check out Miriah Meyer’s work in #dataviz for #bioinformatics, http://t.co/xo5Ei7K (via @FILWD)

The video tip this week is produced by the Meyer team, and you can click on that image to go to the page where you can see it.

Miriah Meyer’s group has as number of interesting visualization projects underway. Check out the list here: http://www.cs.utah.edu/~miriah/projects/ .  The MizBee tool that explores syntenic relationships graphically is the specific focus of the movie, but you’ll see there’s other tools as well.

Proximity, size, orientation and similarity can be visualized with the MizBee Synteny Browser tools, and the video shows how to interact with the browser and to examine features and regions of interest.

I’m also intrigued by the MulteeSum project. And I was wondering if putting that spatial data from the mitochondrial project (nuclear vs mitochondrial) and various tissues could be done with this. It might get at the features I wanted to compare visually from that very cool work. The example in their papers shows expression in a fly embryo that is very compelling. The Pathline tool may offer another way to do that too.

It’s great to see these efforts to manage and visualize the tremendous volume of data. I think if I was able to do another post-doc at this point that would be a great place to get immersed in something that’s really crucial for the future.

Quick links:

Meyer’s group projects: http://www.cs.utah.edu/~miriah/projects/

MizBee specifically: http://www.cs.utah.edu/~miriah/mizbee/Overview.html

References:

Meyer, M., Munzner, T., & Pfister, H. (2009). MizBee: A Multiscale Synteny Browser IEEE Transactions on Visualization and Computer Graphics, 15 (6), 897-904 DOI: 10.1109/TVCG.2009.167

Meyer, M., Munzner, T., DePace, A., & Pfister, H. (2010). MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data IEEE Transactions on Visualization and Computer Graphics, 16 (6), 908-917 DOI: 10.1109/TVCG.2010.137

Meyer, M., Wong, B., Styczynski, M., Munzner, T., & Pfister, H. (2010). Pathline: A Tool For Comparative Functional Genomics Computer Graphics Forum, 29 (3), 1043-1052 DOI: 10.1111/j.1467-8659.2009.01710.x