gmod-ajax

Re: [Gmod-ajax] AJAX GBrowse poster feedback from RECOMB

[Ann L. <alo...@gm...>]

Hello,

I just joined the list and saw the interesting discussion on java applets,
javascript, etc.

Did anybody mention Java Web Start as an alternative method of deploying
java applications?

I like it a lot, myself. I've found it to be quite hassle-free - very easy
to set up. You just put your signed, compiled 'jar' files in a web
directory, write a jnlp file, and deploy.

Here are some examples from bioinformatics:

http://www.ccgb.umn.edu/software/java/apps/TableView/
http://www.jalview.org/
http://www.bioviz.org/plant_igb/
http://www.affymetrix.com/support/developer/tools/download_igb.affx

The wikipedia entry has more links:

http://en.wikipedia.org/wiki/Java_Web_Start

My experience with java applets from several years ago was that it was
always very difficult to get the applets to run properly in every user's
browser. The simple applications were not hard, but for more complex
programs with a lot of functionality, it was very difficult to get
everything to work as expected. After having that experience, working with
Java Web Start has been quite fun. It's so much easier!

-Ann

-- 
Ann Loraine
Assistant Professor
University of Alabama at Birmingham
http://www.transvar.org
205-996-4155

Re: [Gmod-ajax] AJAX GBrowse poster feedback from RECOMB

[Mitch S. <mit...@be...>]

Hi Ann!  Congratulations on your professorship.

On Mon, 2007-04-30 at 13:11 -0500, Ann Loraine wrote:
> Did anybody mention Java Web Start as an alternative method of
> deploying java applications?

I've had a nice experience using Web Start applications before, and it
does solve some of the problems with applets.

I think the biggest objection to Java (that I haven't seen anyone
mention in this thread yet) is that it's been tried.  Given your list of
links, it looks like people have already implemented genome browsing
using Java Web Start, and still UCSC seems to be the browser everyone
uses.  

Admittedly, my direct experience with non-computational biologists is
mostly limited to human and mouse researchers, but talking with people
at the RECOMB poster session reinforced my sense that UCSC is the main
one.

So while the language question does deserve consideration, I think the
more important question is, why is UCSC so popular?  It can't be 100%
inertia.  The Java drawbacks that people have mentioned are all good
points, and I'd add that java app(let)s are often not entirely a part of
the web, in that it takes extra effort to make them bookmarkable and
linkable and to follow links from within them.  And the network effects
you get from being part of the web are pretty huge.  Which reminds me
that we need to do a better job of linking out and being bookmarkable
and linkable.

The Java Web Start approach seems even more non-web than applets.  Is it
even possible to have an html link that takes you to a specific region
in a Java Web Start-using genome browser?

The volume of data that UCSC makes available is also a pretty big
strength.

Also, maybe this is a cheap shot, but on the PlantIGB page I see this:
================
Click here if your computer has at least 1 gig of memory.
Click here if your computer has at least 786 meg of memory.
Click here if your computer has at least 512 meg of memory.
================
which is very much not the face I'd like to present to the
non-computer-savvy biologists out there.

Regards,
Mitch

Re: [Gmod-ajax] AJAX GBrowse poster feedback from RECOMB

[Ian H. <ih...@be...>]

My impression was that Java moved from clients to servers around 1996 ;-)

I have started to see some hardcore bioinformatics applications written 
in Java. Ben Paten's PECAN alignment program is written in Java which is 
surely a watershed in the "they-said-it-couldn't-be-done" tradition.

However I agree with most everything people have said against it as a 
language for the web client. The Java virtual machine lacks a close 
interface to the web browser. That is why AJAX is winning out with its 
paradigm of HTML-based UIs, asynchronous operations & increased emphasis 
on client-server messaging.

All ultimately somewhat academic as this particular project is committed 
to Ajax, and while it is useful to have a stock reply to the "why 
javascript" question, the best answer is really our demo site.



Mitch Skinner wrote:
> Hi Ann!  Congratulations on your professorship.
> 
> On Mon, 2007-04-30 at 13:11 -0500, Ann Loraine wrote:
>> Did anybody mention Java Web Start as an alternative method of
>> deploying java applications?
> 
> I've had a nice experience using Web Start applications before, and it
> does solve some of the problems with applets.
> 
> I think the biggest objection to Java (that I haven't seen anyone
> mention in this thread yet) is that it's been tried.  Given your list of
> links, it looks like people have already implemented genome browsing
> using Java Web Start, and still UCSC seems to be the browser everyone
> uses.  
> 
> Admittedly, my direct experience with non-computational biologists is
> mostly limited to human and mouse researchers, but talking with people
> at the RECOMB poster session reinforced my sense that UCSC is the main
> one.
> 
> So while the language question does deserve consideration, I think the
> more important question is, why is UCSC so popular?  It can't be 100%
> inertia.  The Java drawbacks that people have mentioned are all good
> points, and I'd add that java app(let)s are often not entirely a part of
> the web, in that it takes extra effort to make them bookmarkable and
> linkable and to follow links from within them.  And the network effects
> you get from being part of the web are pretty huge.  Which reminds me
> that we need to do a better job of linking out and being bookmarkable
> and linkable.
> 
> The Java Web Start approach seems even more non-web than applets.  Is it
> even possible to have an html link that takes you to a specific region
> in a Java Web Start-using genome browser?
> 
> The volume of data that UCSC makes available is also a pretty big
> strength.
> 
> Also, maybe this is a cheap shot, but on the PlantIGB page I see this:
> ================
> Click here if your computer has at least 1 gig of memory.
> Click here if your computer has at least 786 meg of memory.
> Click here if your computer has at least 512 meg of memory.
> ================
> which is very much not the face I'd like to present to the
> non-computer-savvy biologists out there.
> 
> Regards,
> Mitch
> 
> 
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Re: [Gmod-ajax] AJAX GBrowse poster feedback from RECOMB

[Suzanna L. <su...@be...>]

On Apr 30, 2007, at 1:10 PM, Mitch Skinner wrote:

> Hi Ann!  Congratulations on your professorship.
>
> On Mon, 2007-04-30 at 13:11 -0500, Ann Loraine wrote:
>> Did anybody mention Java Web Start as an alternative method of
>> deploying java applications?
>
> I've had a nice experience using Web Start applications before, and it
> does solve some of the problems with applets.
>
> I think the biggest objection to Java (that I haven't seen anyone
> mention in this thread yet) is that it's been tried.  Given your  
> list of
> links, it looks like people have already implemented genome browsing
> using Java Web Start, and still UCSC seems to be the browser everyone
> uses.

Yes, but I think that we also have to consider that it might just be  
the data. If you're looking for actual genomic data they've made it  
really easy for people to add their own. The data is the most  
comprehensive and up-to-date set available, with one-stop shopping.  
The browser is not the primary consideration here.

>
> Admittedly, my direct experience with non-computational biologists is
> mostly limited to human and mouse researchers, but talking with people
> at the RECOMB poster session reinforced my sense that UCSC is the main
> one.
>
> So while the language question does deserve consideration, I think the
> more important question is, why is UCSC so popular?  It can't be 100%
> inertia.  The Java drawbacks that people have mentioned are all good
> points, and I'd add that java app(let)s are often not entirely a  
> part of
> the web, in that it takes extra effort to make them bookmarkable and
> linkable and to follow links from within them.  And the network  
> effects
> you get from being part of the web are pretty huge.  Which reminds me
> that we need to do a better job of linking out and being bookmarkable
> and linkable.
>
> The Java Web Start approach seems even more non-web than applets.   
> Is it
> even possible to have an html link that takes you to a specific region
> in a Java Web Start-using genome browser?
>
> The volume of data that UCSC makes available is also a pretty big
> strength.
>
> Also, maybe this is a cheap shot, but on the PlantIGB page I see this:
> ================
> Click here if your computer has at least 1 gig of memory.
> Click here if your computer has at least 786 meg of memory.
> Click here if your computer has at least 512 meg of memory.
> ================
> which is very much not the face I'd like to present to the
> non-computer-savvy biologists out there.
>
> Regards,
> Mitch
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] AJAX GBrowse poster feedback from RECOMB

[Hilmar L. <hl...@gm...>]

On May 2, 2007, at 9:47 AM, Suzanna Lewis wrote:

>> I think the biggest objection to Java (that I haven't seen anyone
>> mention in this thread yet) is that it's been tried.  Given your
>> list of
>> links, it looks like people have already implemented genome browsing
>> using Java Web Start, and still UCSC seems to be the browser everyone
>> uses.
>
> Yes, but I think that we also have to consider that it might just be
> the data. If you're looking for actual genomic data they've made it
> really easy for people to add their own. The data is the most
> comprehensive and up-to-date set available, with one-stop shopping.
> The browser is not the primary consideration here.

I'd second that, and would add ease of use (incl. speed and minimal  
system requirements on the client's end), and ease of adding one's  
own data, and downloading data.

Less obvious possibly but what's also great about the UCSC browser is  
that it's actually very easy to save the image and stick it into a  
PPT presentation. You may laugh about this, but the researchers I was  
working with were doing this all the time (and I was too when I  
worked on particular loci).

I'd also argue that in the future (and possibly already) most use of  
a genome browser will be made through aggregated content or mash-ups.  
That's one of the cool things about Google maps - it's easy to stick  
it into your own page while it remains interactive yet doesn't  
disturb or control the rest of the page.

Just my one cent ...

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================

Re: [Gmod-ajax] AJAX GBrowse poster feedback from RECOMB

[Ian H. <ih...@be...>]

I'd add speed: UCSC's rendering engine is all in C and very fast.

However I think Suzi's point about the data is the winner, by a long 
chalk. I hope one day we can offer that much data at a genome wiki site.

Hilmar, I'd say you're absolutely right about mashups. I don't know if 
there's actually anything stopping our browser from being used as a 
component of a larger page right now. In any case this doesn't seem hard 
to do, given our general approach, and we hope to demo this before too long.


Hilmar Lapp wrote:
> On May 2, 2007, at 9:47 AM, Suzanna Lewis wrote:
> 
>>> I think the biggest objection to Java (that I haven't seen anyone
>>> mention in this thread yet) is that it's been tried.  Given your
>>> list of
>>> links, it looks like people have already implemented genome browsing
>>> using Java Web Start, and still UCSC seems to be the browser everyone
>>> uses.
>> Yes, but I think that we also have to consider that it might just be
>> the data. If you're looking for actual genomic data they've made it
>> really easy for people to add their own. The data is the most
>> comprehensive and up-to-date set available, with one-stop shopping.
>> The browser is not the primary consideration here.
> 
> I'd second that, and would add ease of use (incl. speed and minimal  
> system requirements on the client's end), and ease of adding one's  
> own data, and downloading data.
> 
> Less obvious possibly but what's also great about the UCSC browser is  
> that it's actually very easy to save the image and stick it into a  
> PPT presentation. You may laugh about this, but the researchers I was  
> working with were doing this all the time (and I was too when I  
> worked on particular loci).
> 
> I'd also argue that in the future (and possibly already) most use of  
> a genome browser will be made through aggregated content or mash-ups.  
> That's one of the cool things about Google maps - it's easy to stick  
> it into your own page while it remains interactive yet doesn't  
> disturb or control the rest of the page.
> 
> Just my one cent ...
> 
> 	-hilmar