Web 2.0 In Biological Research And Databases
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9.3 years ago

Hi guys,

I'm preparing a lecture about new web technologies in biological online tools and databases. I'm looking for some examples of extremely user-friendly and interactive web apps. Even in my 500 years+ as a vampire I've come up with only one, Chromozoom, a AJAX-driven web-based genome browser that works as smoothly as Google Maps.

If you know similar biological tools of any kind - not only genome browsers, please hit me back.

Thanks!

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It's not a genome browser, but oneZoom is pretty cool: http://www.onezoom.org/

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wow, this project is really awesome! I'll definitely use that. Thanks Damian.

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I started working on a simple annotation viewer tool last week:

http://htmlpreview.github.io/?https://github.com/damiankao/seeker/blob/master/test.html#

It's still very preliminary and probably only works on latest versions of chrome/firefox/safari. The idea is to let people upload annotations on series of sequences and visualize it. It's client-side only, no server required. The demo has a bunch of genes and their protein domain annotations. The export function should work now.

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Aha, but before Chromozoom there was X:Map.

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Thanks Neilfws! I didn't know that.

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can Biostar itself be considered a Web 2.0 application to biological research?

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good idea! I'll mention BioStar for sure. Thanks.

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9.3 years ago

Jbrowse gives the best genome browsing experience IMHO.

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9.3 years ago

Web 2.0 is not only about cool interactive websites, but also (or mainly) about cool vibrant community (such as here ;) ). If Web 2.0 is your focus I would mention:

Good luck!

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Thanks Pawel. These are very good examples. I like the idea of biogaming.

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If you need more examples of games, see this question: Bioinformatics/cheminformatics/biology games

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9.3 years ago

The Ray Cloud Browser is a really cool assembly graph viewer.

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Wow! This is so cool. Thanks martinahansen.

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App seems down but github here https://github.com/sebhtml/Ray-Cloud-Browser

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9.3 years ago
Chase Miller ▴ 410

The washu epigenome browser has some nice interactivity. http://epigenomegateway.wustl.edu/browser/

Not sure if this is outside the scope, but Scribl is a biological genomics graphics library built on HTML5 Canvas that enables developers to add interactive visualizations to websites and web apps. Definitely modern web technology, but focused on developers not users. (Disclaimer: I'm the author) http://chmille4.github.io/Scribl/

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Thanks Chase. These two are really good suggestions. Great job with the Scribl library - looks very impressive. I remember I've read your paper very recently in Bioinformatics.

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Thanks Pierre. I'll definitely mention these sites.

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9.3 years ago

The Distributed Annotation System and related web apps, and clients would be near the top of my list. Nothing more 'web2.0' than a useful data mashup

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Thanks Alastair for reminding me about DAS, I almost forgot it.

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