Javascript Visualization for Proteomics Search Results

Search algorithms, post-searching processing, quantitation software, etc. Share and discuss software here.
boscoh
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Javascript Visualization for Proteomics Search Results

Postby boscoh » Sun Feb 09, 2014 4:35 pm

I've been working on a standalone HTML5/Javascript proteomics viewer for the last year, and it's finally in beta-release:

http://boscoh.github.io/peptagram

So far I've got parsers for Morpheus, x!Tandem, TPP, Mascot & Maxquant.

I'd love it if you could have a look and see if it's useful.

If you do try it out, could you send me feedback, and bug reports?

Thanks,

Bosco Ho
Monash Proteomics Facility.
Melbourne, Australia.,

Derek
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Postby Derek » Mon Feb 10, 2014 7:39 am

Bosco, great work so far. I love seeing open web standards for visualization, definitely the way to go.

One comment, the list of proteins on the left was a little confusing at first to look at and comprehend. Maybe a little less detail on the protein description line, leave just the first X characters perhaps displayed?

i.e.

1: P17897 sp|P17897|LYZ1_MOUSE Lys...
2: Q6ZQ06 sp|Q6ZQ06|QN1_MOUSE Pro...

A search bar for the protein descriptions would also be nice as well.

I'll try my hand in writing a parser for OMSSA.

boscoh
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Postby boscoh » Sun Feb 16, 2014 7:08 pm

Thanks Derek,

That'll be great if you could write a parser for OMSSA. I hope my Programming API provides sufficient help. If not, give me a yelp.

As for the protein description in the page, this is deliberate. The app exploits a neat feature of the browser. If you do a browser search, you will be able to search for any bit of text in the protein description in the page, and go directly there. Thus, by packing all that information there, the search becomes more powerful.

Bosco

MSENC
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MS Spectrum viewer derived from dygraphs

Postby MSENC » Tue Apr 08, 2014 7:30 am

Hi, very nice implementation! HTML5 in a modern browser, instead of Java applet or dedicated program, is definitely the future of data visualization.

Are you looking for the contribution to this project? We have good success in extending the dygraphs for MS/MS display as shown below. It's conceivable that we can polish it up and share it with the community if there is sufficient interest. The viewer is zoom-able in both m/z the intensity dimension.

4-8-2014 8-17-52 AM.png
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tsbatth
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Postby tsbatth » Thu Apr 10, 2014 1:32 am

Very cool! Does it also visualize PTM's ?


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