Web 2.0 In Biological Research And Databases

Question

[Andrzej Zielezinski]

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!

[Damian Kao]

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

[Andrzej Zielezinski]

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

[Damian Kao]

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.

[Neilfws]

Aha, but before Chromozoom there was X:Map.

[Andrzej Zielezinski]

Thanks Neilfws! I didn't know that.

[Giovanni M Dall'Olio]

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

[Andrzej Zielezinski]

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

Answer 1

[Martin A Hansen]

Jbrowse gives the best genome browsing experience IMHO.

Answer 2

[Pawel Szczesny]

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!

[Andrzej Zielezinski]

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

[Pawel Szczesny]

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

Answer 3

[Martin A Hansen]

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

[Andrzej Zielezinski]

Wow! This is so cool. Thanks martinahansen.

[cmdcolin]

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

Answer 4

[Chase Miller]

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/

[Andrzej Zielezinski]

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.

Answer 5

[Pierre Lindenbaum]

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/

...

[Andrzej Zielezinski]

Thanks Pierre. I'll definitely mention these sites.

Answer 6

[Alastair Kerr]

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

[Andrzej Zielezinski]

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