[Bioperl-l] Firefox extension project

Stefan Kirov stefan.kirov at bms.com
Thu Jun 17 10:53:32 EDT 2010

There isn't much about perl in this post, so I apologize for spamming 
the list, but I assumed there would be people interested in this.

Please do not reply to the list, again this is not bioperl related.

I have opened sourced a Firefox extension I have been developing and 
using for a while. The whole idea is to have a sequence analysis swiss 
army knife built in right in the browser.
I started with incorporating some cool Javascript libraries, written by 
Paul Stothard (http://www.bioinformatics.org/sms2/). I have not 
incorporated all of those, but will if I find the time.
In addition, you can decide to install emboss and clustalw (the 
extension comes with the source for clustal and emboss) and run them 
locally, which can be handy.
I have started working also on SVG biograph libraries but these are 
quite incomplete, but I have been able to implement one graphical 
viewer- ORF finder, which I find quite handy.
There are basic sequence parsing and fetching (NCBI) as well. Other 
things that work: very simple logical operations on sets, protein 
digest/ion generation tool.
Sequence lists and projects should be functional in next release.

There are 2 way to access the tools: right click and by opening the sidebar.

The code behind this project is mainly Javascript, XUL, CSS and shell 
wrapper scripts. There is also some sqlite involved.
I would be interested to hear any feedback, but would be even more 
excited if there are people who know these technologies (or willing to 
learn) and want to join in.
Testers are also more than welcome. Since this is prealpha you need to 
be careful- I would advise anyone to have this extension installed in a 
non-production environment.
I will upload a VirtualBox image to the SVN project in the next few days 
as well.

Here is the project page:
Best way to contact me is kirovs at gmail

Finally, developing extensions in firefox is just as much fun as 
programming perl (maybe more ;-) ).

Stefan Kirov

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