Question: Web 2.0 In Biological Research And Databases
5
gravatar for a.zielezinski
6.2 years ago by
a.zielezinski8.8k
a.zielezinski8.8k wrote:

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!

• 2.9k views
ADD COMMENTlink modified 6.2 years ago by Pawel Szczesny3.2k • written 6.2 years ago by a.zielezinski8.8k
3

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

ADD REPLYlink written 6.2 years ago by Damian Kao15k

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

ADD REPLYlink written 6.2 years ago by a.zielezinski8.8k

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 REPLYlink modified 6.2 years ago • written 6.2 years ago by Damian Kao15k
2

Aha, but before Chromozoom there was X:Map.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Neilfws48k

Thanks Neilfws! I didn't know that.

ADD REPLYlink written 6.2 years ago by a.zielezinski8.8k
2

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

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Giovanni M Dall'Olio26k

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

ADD REPLYlink written 6.2 years ago by a.zielezinski8.8k
5
gravatar for Martin A Hansen
6.2 years ago by
Martin A Hansen3.0k
Denmark
Martin A Hansen3.0k wrote:

Jbrowse gives the best genome browsing experience IMHO.

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Martin A Hansen3.0k
4
gravatar for Pawel Szczesny
6.2 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

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!

ADD COMMENTlink written 6.2 years ago by Pawel Szczesny3.2k

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

ADD REPLYlink written 6.2 years ago by a.zielezinski8.8k

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

ADD REPLYlink written 6.2 years ago by Pawel Szczesny3.2k
3
gravatar for Martin A Hansen
6.2 years ago by
Martin A Hansen3.0k
Denmark
Martin A Hansen3.0k wrote:

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

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Martin A Hansen3.0k
1

Wow! This is so cool. Thanks martinahansen.

ADD REPLYlink written 6.2 years ago by a.zielezinski8.8k

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

ADD REPLYlink written 2.2 years ago by cmdcolin1.2k
2
gravatar for Chase Miller
6.2 years ago by
Chase Miller400
University of Utah
Chase Miller400 wrote:

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 COMMENTlink modified 6.2 years ago • written 6.2 years ago by Chase Miller400

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 REPLYlink written 6.2 years ago by a.zielezinski8.8k
2
gravatar for Pierre Lindenbaum
6.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

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 COMMENTlink written 6.2 years ago by Pierre Lindenbaum122k

Thanks Pierre. I'll definitely mention these sites.

ADD REPLYlink written 6.2 years ago by a.zielezinski8.8k
1
gravatar for Alastair Kerr
6.2 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

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

ADD COMMENTlink written 6.2 years ago by Alastair Kerr5.2k

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

ADD REPLYlink written 6.2 years ago by a.zielezinski8.8k
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