Question

Web 2.0 In Biological Research And Databases

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11.5 years ago

Andrzej Zielezinski 11k

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!

• 5.0k views

ADD COMMENT • link updated 11.5 years ago by Pawel Szczesny 3.2k • written 11.5 years ago by Andrzej Zielezinski 11k

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

ADD REPLY • link 11.5 years ago by Damian Kao 16k

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

ADD REPLY • link 11.5 years ago by Andrzej Zielezinski 11k

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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.

ADD REPLY • link 11.5 years ago by Damian Kao 16k

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Aha, but before Chromozoom there was X:Map.

ADD REPLY • link 11.5 years ago by Neilfws 49k

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Thanks Neilfws! I didn't know that.

ADD REPLY • link 11.5 years ago by Andrzej Zielezinski 11k

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

ADD REPLY • link 11.5 years ago by Giovanni M Dall'Olio 28k

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

ADD REPLY • link 11.5 years ago by Andrzej Zielezinski 11k

score 5 · Answer 1 · 2013-05-30

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11.5 years ago

Martin A Hansen 3.0k

Jbrowse gives the best genome browsing experience IMHO.

ADD COMMENT • link 11.5 years ago by Martin A Hansen 3.0k

score 4 · Answer 2 · 2013-05-31

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11.5 years ago

Pawel Szczesny 3.2k

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:

BioStar (and few other Q&A academic sites, such as http://biology.stackexchange.com/ )
internet fora (such as http://seqanswers.com/ )
crowdsourcing sites (Annotathon is a good example http://annotathon.org/ )
biological games (such as FoldIt or Phylo - gamification is also 2.0)
biological wikis (Wikipedia is hosting a nice list http://en.wikipedia.org/wiki/List_of_biological_wikis )
experiments in scientific publishing (in particular I like KnowledgeBlog http://knowledgeblog.org/ but there are quite a few others relevant to biology)

Good luck!

ADD COMMENT • link 11.5 years ago by Pawel Szczesny 3.2k

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

ADD REPLY • link 11.5 years ago by Andrzej Zielezinski 11k

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

ADD REPLY • link 11.5 years ago by Pawel Szczesny 3.2k

score 3 · Answer 3 · 2013-05-30

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11.5 years ago

Martin A Hansen 3.0k

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

ADD COMMENT • link 11.5 years ago by Martin A Hansen 3.0k

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Wow! This is so cool. Thanks martinahansen.

ADD REPLY • link 11.5 years ago by Andrzej Zielezinski 11k

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

ADD REPLY • link 7.5 years ago by cmdcolin ★ 4.0k

score 2 · Answer 4 · 2013-05-30

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11.5 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/

ADD COMMENT • link 11.5 years ago by Chase Miller ▴ 410

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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.

ADD REPLY • link 11.5 years ago by Andrzej Zielezinski 11k

score 2 · Answer 5 · 2013-05-30

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11.5 years ago

Pierre Lindenbaum 164k

In my bookmarks:

http://bioportal.bioontology.org/

http://www.g-language.org/g3/

http://www.genomicus.biologie.ens.fr/genomicus-71.01/cgi-bin/search.pl

http://galaxyproject.org/

...

ADD COMMENT • link 11.5 years ago by Pierre Lindenbaum 164k

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Thanks Pierre. I'll definitely mention these sites.

ADD REPLY • link 11.5 years ago by Andrzej Zielezinski 11k

score 1 · Answer 6 · 2013-05-30

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11.5 years ago

Alastair Kerr 5.3k

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