gmod-ajax — JBrowse list

[Gmod-ajax] Feature Mark Up

[Steve T. <st...@mo...>]

Hi,

I thought I'd send this to open up the discussions on the new list!:-)

I haven't checked in this code yet but I have modified generate-tiles.pm and BatchTilesImage.pm to allow marking up of the features in each of the tiles using client side image maps. We may want to 
change this later to do CSS maps but that would be only a small code modification. It basically generates an html file per tile with an inlined image and the appropriate map coordinates. The browser 
XMLHttpRequests the data over when it needs to using Ajax.Updater (from the js library Prototype).

You can see what it looks like on:

http://slave.molbiol.ox.ac.uk/gbrowse/TiledImage/ecoli/prototype_gbrowse.html

Try dragging and clicking on features.

Advantages of current implementation
-----------------------------------
- should work on all browsers and doesn't require any fancy javascript
- will support polygons, ellipses etc
- allows distribution on different servers for tiles

Disadvantages of implementation
-------------------------------
- all html per tile currently generated server side (not sure if this is an advantage or disadvantage at this stage) but may be a pain to do updates

Obviously where javascript:alert('Active image map') you should have the relevant details of the feature and a nicer pop up. The js alerts are pretty annoying at the moment when dragging! I intend to 
put js pop ups similar to the ones we have at http://gbrowse.molbiol.ox.ac.uk/cgi-bin/gbrowse/coli_demo/?name=U00096%3A1..10000.

Let me know what you think. I will check it in if people think it is worthwhile at this stage.

Regards,

Steve
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Weatherall Institute of Molecular Medicine/Sir William Dunn School
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Tel: +44 (0)1865 (2)85732 (Dunn - Thursday to Friday)
Web: http://www.compbio.ox.ac.uk

[Gmod-ajax] welcome and general announcements

[Andrew U. <and...@gm...>]

Greetings!

I would like to welcome everyone to the new AJAX GBrowse mailing list,
and thank you for your interest, participation, support, and so on...
this is very exciting!

Those of you that aren't on the list are being CC'ed and should subscribe here:

https://lists.sourceforge.net/lists/listinfo/gmod-ajax

This list is for announcements, development discussion, and pretty
much anything related to this project... so, let me get the ball
rolling.

0. DEMO

Just so everyone knows, the demo of what we've done so far can be found here:

http://genome.biowiki.org/

1. CVS ACCESS AND SOURCEFORGE STUFF

We are now part of the Generic-Genome-Browser module of the GMOD
SourceForge CVS repository (see the "ajax" subdir).

Developers can check the code out like this:

cvs -z3 -d:ext:YOU...@gm...:/cvsroot/gmod co
-P Generic-Genome-Browser

If you want to be a developer, please get a SF account (at sf.net) and
e-mail your login to Scott Cain (ca...@cs...).

We also have bugtracking through SF (which I haven't taken a look at,
but will in a moment) and a CVS commits mailing list, which you can
subscribe to here:

https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse-ajax-commits

Scott, thanks a million for setting all this up!

2. LIST ADMINISTRIVIA

Currently, if you hit "reply" to a list message, it replies to the
person who originally sent the message.  While this is nice for
announcements and keeps the traffic down, it's not great for
discussion, and discussion is the main reason why we have this list.

I want to change the settings so that hitting "reply" will reply back
to everyone on the list... anyone for or against this?  I'll set this
up if I don't hear otherwise.

3. OTHER RESOURCES

We will be using the GBrowse web of biowiki.org (Ian Holmes' lab wiki)
for posting info about all aspects of the project.  The web is rooted
here:

http://biowiki.org/view/GBrowse/WebHome

In my opinion, the two most important items are our more-or-less
development outline:

http://biowiki.org/view/GBrowse/WishList

and this "documentation dump" I started up the other day (so, it's
woefully incomplete... but evolving):

http://biowiki.org/view/GBrowse/AJAXGBrowseDocs

The documentation dump is a good place to start if you're new to this.

4. JOB ANNOUNCEMENT

We are looking for a full-time Ajax developer for this project.
Spread the word!  More details here:

http://biowiki.org/AjaxProgrammerJob

5. QUESTIONS? REQUESTS? COMMENTS?

Please post to the list or e-mail me.

Cheers,


Andrew Uzilov
Holmes Lab, Dept. of Bioengineering, UC-Berkeley

[Gmod-ajax] testing

[Andrew U. <and...@gm...>]

first post!

seriously though... anyone yet signed up that can vouch that it works?