[DAS] Question about das development.
Brian Gilman
gilmanb@genome.wi.mit.edu
Wed, 21 Aug 2002 10:57:41 -0400
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On 8/21/02 10:42 AM, "Bill Gooding" <bgood97@yahoo.com> wrote:
Hello Bill,
Have you looked into Batik to write your viewer??
-B
> Hi,
>
> I was wondering how much trouble it would be, if I wanted to put my donate my
> code to the CVS repository for DAS. I don't really even need access to CVS.
> All I would need is for someone to create a subdirectory for me and checkin
> whatever I give them. I would also want to checkin jar files (precompiled
> files). I wouldn't want those files to be subject to revision control. I
> don't need anyone to announce any software on the DAS site, I want to wait and
> see if anyone thinks it is a good idea. I just want to have a place that
> people can download the software if they want. Also, what about licencing for
> this open source - I was thinking LGPL. It seems to give the most
> flexibility.
>
> Bill Gooding
>
> Bill Gooding wrote:
>> To everyone replying to my message,
>>
>> Thanks for your help, this is the sort of discussion that I wanted to start.
>> On the specific comments:
>>
>> I am perfectly willing to work with Chris on the development of this
>> software. The one thing I would like to insist on is that it be open source.
>> I am sure that this probably goes without saying in this group :-). We
>> really just need a place to put the project and people can download it if
>> they like. As I said, I have developed a system which is based on
>> JSP/Sevlets/Java. I think it is a good starting point. I am sure you would
>> be surprised if I didn't think that :-).
>>
>> As for David Kulp's comments, I recognize that the system load may be a
>> problem. But this problem to me would seem to plague any such system. That
>> is, if you are looking at a whole chomosome down to the base pair level, you
>> will have alot of data. I think that this can be addressed by limiting the
>> size of the queries in the server which shouldn't be too hard. Also, the
>> system I have developed, although it is JSP based, it will be very easy to
>> create a standalone program for it so you don't have to go through a JSP
>> server if you want to download and transform alot of data. The standalone
>> program will use the same codebase as the JSP server (which will also allow
>> easy test scripts to be written for the code) This should somewhat mitigate
>> somewhat the load problem.
>>
>> On your comments about SVG/client integration/Adobe plugins, I really don't
>> want to deal with this issue in the software (if I can avoid it). It seems
>> like it may be problematic to support the plugin and all the browsers that
>> may implement it slightly differently. For now, I think that the user can
>> live with reloading data he needs. I understand this will increase server
>> load. But my vision for this project is not to necessarily create something
>> that would support an extremely high load (at least not at the beginning). I
>> really intend this to be used within a relatively small group of users to
>> simplify the access to data. So in my system, I really want to emphasize
>> customizability. That is, if someone wants to display his data differently
>> he should be able to plugin his XSLT files into the system very easily. I
>> think what I have satisfies that. The advantage of open source would be that
>> people could (hopefull! ! y) donate their own XSLT files to the project.
>> This allows for many different views or processing of the data thus giving
>> the users of the software more flexibility. At this point I would see the
>> issue as a tradeoff between speed and flexibility. Maybe in later
>> development any speed problems could be solved or strongly mitigated.
>>
>> As always, comments on this are welcome.
>>
>> Thanks,
>>
>>
>>
>> Bill Gooding
>>
>>
>>
>> "Kulp, David" wrote:
>>> From the whizbang angle, I've been thinking about a DAS-SVG viewer. The
>>> "problem" is typical for genome browser displays: too many features
>>> significantly slows down display, both in terms of data transmission and SVG
>>> client rendering. I looked a little into how one might deal with dynamic
>>> content and semantic zooming. It turns out that the Adobe viewer provides
>>> two non-standard hooks which allow you to make URL calls and to parse the
>>> returning document into a DOM. Thus, javascript callbacks could be attached
>>> to zoom levels, hidden tracks, or objects, which caused the server to be
>>> queried for additional SVG which was then attached to the existing DOM.
>>> Sounds very cool!
>>>
>>> But another problem is that SVG (at least with Adobe's viewer) has a
>>> hard-limit of 8 levels of zoom, i.e. a 256X zoom, but unless you're fancy,
>>> it's really just 4 levels of zoom in and! ! 4 out. That's not enough to go
>>> from nucleotide to chromosome.
>>>
>>> -d
>>>
>>> -----Original Message-----
>>> From: David Block [mailto:dblock@gnf.org]
>>> Sent: Monday, August 19, 2002 10:33 AM
>>> To: Chris Lewis
>>> Cc: Bill Gooding; das@biodas.org; Lincoln Stein
>>> Subject: Re: [DAS] Question about das development.
>>>
>>>
>>> So close - the author of the first link was at BOSC!
>>>
>>> Chris - this Bill Gooding wants to collaborate on an SVG viewer starting
>>> from XML and using XSLT - you guys should be collaborating.
>>>
>>> Go for it!
>>> Dave
>>>
>>> On Tuesday, August 13, 2002, at 05:51 AM, Lincoln Stein wrote:
>>>
>>>> > Search for "SVG" and "genome browser" on google. Here's one:
>>>> >
>>>> > http://www.svgopen.org/abstracts/lewis_et_al__bioviz_genome_viewer.html
>>>> >
>>>> > Here's another:
>>>> >
>>>> > http://www.labbook.com/
>>>> >
>>>> > Here's a third (ruby):
>>>> >
>>>> > http://gb.bioruby.org/
>>>> >
>>>> > There's also a commercial java based! ! browser that uses XML as its data
>>>> > transport and SVG for its UI, but for the life of me I can't find the
>>>> > name or
>>>> > URL (it's in development).
>>>> >
>>>> > Lincoln
>>>> >
>>>> > On Monday 12 August 2002 03:12 pm, Bill Gooding wrote:
>>>>> >> Hi,
>>>>> >>
>>>>> >> Although I am new to the mailing list, I have been looking at
>>>>> >> bioinformatics information for a while and had a simple question. From
>>>>> >> what I have seen it appears that in order to access the XML information
>>>>> >> from various servers people use a downloaded java program which
>>>>> >> implements
>>>>> >> a GUI (Swing/AWT) for displaying information. I was wondering if
>>>>> >> anyone
>>>>> >> had considered using an XML based server that tranforms the data into
>>>>> >> SVG
>>>>> >> for display on a browser. That is, something similar to Cocoon. That
>>>>> >> way,
>>>>> >> differing XML format could be handled in a more com! pre! hensive way.
I
>>>>> >> have
>>>>> >> begun writing code to implement this idea (although it is not Cocoon
>>>>> >> based
>>>>> >> - I use jave xml api's) and am perfectly willing to donate it to
>>>>> >> biodas.org
>>>>> >> as open source as a start to developing such a system.
>>>>> >>
>>>>> >> So with that background my question is:
>>>>> >>
>>>>> >> 1. If a system such as I have proposed has been developed, where is
>>>>> >> it ?
>>>>> >> I just need a specific link.
>>>>> >>
>>>>> >> 2. If such a system does not exist, is anyone interested in the idea
>>>>> >> or
>>>>> >> want to discuss it ?
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >> Thanks,
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >> Bill Gooding
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >> ---------------------------------
>>>>> >> Do You Yahoo!?
>>>>> >> HotJobs, a Yahoo! service - Search Thousands of New Jobs
>>>> > _______________________! _____! ___________________
>>>> > DAS mailing list
>>>> > DAS@biodas.org
>>>> > http://biodas.org/mailman/listinfo/das
>>>> >
>>> --
>>> David Block dblock@gnf.org
>>> GNF - San Diego, CA http://www.gnf.org
>>> Genome Informatics / Enterprise Programming
>>> Weblog: http://radio.weblogs.com/0104507/
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS@biodas.org
>>> http://biodas.org/mailman/listinfo/das
>>> _______________________________________________
>>> DAS mailing list
>>> DAS@biodas.org
>>> http://biodas.org/mailman/listinfo/das
>>
>>
>> Do You Yahoo!?
>> HotJobs, a Yahoo! service
>> <http://rd.yahoo.com/careers/mailsig/new/*http://www.hotjobs.com> - Search
>> Thousands of New Jobs
>
>
> Do You Yahoo!?
> HotJobs, a Yahoo! service
> <http://rd.yahoo.com/careers/mailsig/new/*http://www.hotjobs.com> - Search
> Thousands of New Jobs
--
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617 252 1069 / fax +1 617 252 1902
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<TITLE>Re: [DAS] Question about das development.</TITLE>
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<FONT FACE=3D"Verdana">On 8/21/02 10:42 AM, "Bill Gooding" <bgoo=
d97@yahoo.com> wrote:<BR>
<BR>
Hello Bill,<BR>
<BR>
Have you looked into Batik to write your viewer??<B=
R>
<BR>
&nb=
sp; &=
nbsp; -B<BR>
<BR>
</FONT><BLOCKQUOTE><FONT FACE=3D"Verdana">Hi, <BR>
<BR>
I was wondering how much trouble it would be, if I wanted to put my donate =
my code to the CVS repository for DAS. I don't really even need access=
to CVS. All I would need is for someone to create a subdirectory for =
me and checkin whatever I give them. I would also want to checkin jar =
files (precompiled files). I wouldn't want those files to be subject t=
o revision control. I don't need anyone to announce any software on th=
e DAS site, I want to wait and see if anyone thinks it is a good idea.  =
;I just want to have a place that people can download the software if they w=
ant. Also, what about licencing for this open source - I was thinking =
LGPL. It seems to give the most flexibility. <BR>
<BR>
Bill Gooding <BR>
<BR>
<B><I>Bill Gooding </I></B>wrote: <BR>
</FONT><BLOCKQUOTE><FONT FACE=3D"Verdana">To everyone replying to my message,=
<BR>
<BR>
Thanks for your help, this is the sort of discussion that I wanted to start=
. On the specific comments: <BR>
<BR>
I am perfectly willing to work with Chris on the development of this softwa=
re. The one thing I would like to insist on is that it be open source.=
I am sure that this probably goes without saying in this group :-). &=
nbsp;We really just need a place to put the project and people can download =
it if they like. As I said, I have developed a system which is based o=
n JSP/Sevlets/Java. I think it is a good starting point. I am su=
re you would be surprised if I didn't think that :-). <BR>
<BR>
As for David Kulp's comments, I recognize that the system load may be a pro=
blem. But this problem to me would seem to plague any such system. &nb=
sp;That is, if you are looking at a whole chomosome down to the base pair le=
vel, you will have alot of data. I think that this can be addressed by=
limiting the size of the queries in the server which shouldn't be too hard.=
Also, the system I have developed, although it is JSP based, it will =
be very easy to create a standalone program for it so you don't have to go t=
hrough a JSP server if you want to download and transform alot of data. &nbs=
p;The standalone program will use the same codebase as the JSP server (which=
will also allow easy test scripts to be written for the code) This sh=
ould somewhat mitigate somewhat the load problem. <BR>
<BR>
On your comments about SVG/client integration/Adobe plugins, I really don't=
want to deal with this issue in the software (if I can avoid it). It =
seems like it may be problematic to support the plugin and all the browsers =
that may implement it slightly differently. For now, I think that the =
user can live with reloading data he needs. I understand this will inc=
rease server load. But my vision for this project is not to necessaril=
y create something that would support an extremely high load (at least not a=
t the beginning). I really intend this to be used within a relatively =
small group of users to simplify the access to data. So in my system, =
I really want to emphasize customizability. That is, if someone wants =
to display his data differently he should be able to plugin his XSLT files i=
nto the system very easily. I think what I have satisfies that. =
The advantage of open source would be that people could (hopefull! ! y) dona=
te their own XSLT files to the project. This allows for many different=
views or processing of the data thus giving the users of the software more =
flexibility. At this point I would see the issue as a tradeoff between=
speed and flexibility. Maybe in later development any speed problems =
could be solved or strongly mitigated. <BR>
<BR>
As always, comments on this are welcome. <BR>
<BR>
Thanks, <BR>
<BR>
<BR>
<BR>
Bill Gooding <BR>
<BR>
<BR>
<BR>
<B><I>"Kulp, David" </I></B>wrote: <BR>
</FONT><BLOCKQUOTE><FONT FACE=3D"Verdana">From the whizbang angle, I've been =
thinking about a DAS-SVG viewer. The<BR>
"problem" is typical for genome browser displays: too many featur=
es<BR>
significantly slows down display, both in terms of data transmission and SV=
G<BR>
client rendering. I looked a little into how one might deal with dynamic<BR=
>
content and semantic zooming. It turns out that the Adobe viewer provides<B=
R>
two non-standard hooks which allow you to make URL calls and to parse the<B=
R>
returning document into a DOM. Thus, javascript callbacks could be attached=
<BR>
to zoom levels, hidden tracks, or objects, which caused the server to be<BR=
>
queried for additional SVG which was then attached to the existing DOM.<BR>
Sounds very cool!<BR>
<BR>
But another problem is that SVG (at least with Adobe's viewer) has a<BR>
hard-limit of 8 levels of zoom, i.e. a 256X zoom, but unless you're fancy,<=
BR>
it's really just 4 levels of zoom in and! ! 4 out. That's not enough to go<=
BR>
from nucleotide to chromosome.<BR>
<BR>
-d<BR>
<BR>
-----Original Message-----<BR>
From: David Block [mailto:dblock@gnf.org]<BR>
Sent: Monday, August 19, 2002 10:33 AM<BR>
To: Chris Lewis<BR>
Cc: Bill Gooding; das@biodas.org; Lincoln Stein<BR>
Subject: Re: [DAS] Question about das development.<BR>
<BR>
<BR>
So close - the author of the first link was at BOSC!<BR>
<BR>
Chris - this Bill Gooding wants to collaborate on an SVG viewer starting <B=
R>
from XML and using XSLT - you guys should be collaborating.<BR>
<BR>
Go for it!<BR>
Dave<BR>
<BR>
On Tuesday, August 13, 2002, at 05:51 AM, Lincoln Stein wrote:<BR>
<BR>
> Search for "SVG" and "genome browser" on google. H=
ere's one:<BR>
><BR>
> http://www.svgopen.org/abstracts/lewis_et_al__bioviz_genome_viewer.htm=
l<BR>
><BR>
> Here's another:<BR>
><BR>
> http://www.labbook.com/<BR>
><BR>
> Here's a third (ruby):<BR>
><BR>
> http://gb.bioruby.org/<BR>
><BR>
> There's also a commercial java based! ! browser that uses XML as its d=
ata<BR>
> transport and SVG for its UI, but for the life of me I can't find the =
<BR>
> name or<BR>
> URL (it's in development).<BR>
><BR>
> Lincoln<BR>
><BR>
> On Monday 12 August 2002 03:12 pm, Bill Gooding wrote:<BR>
>> Hi,<BR>
>><BR>
>> Although I am new to the mailing list, I have been looking at<BR>
>> bioinformatics information for a while and had a simple question. =
From<BR>
>> what I have seen it appears that in order to access the XML inform=
ation<BR>
>> from various servers people use a downloaded java program which <B=
R>
>> implements<BR>
>> a GUI (Swing/AWT) for displaying information. I was wondering if <=
BR>
>> anyone<BR>
>> had considered using an XML based server that tranforms the data i=
nto <BR>
>> SVG<BR>
>> for display on a browser. That is, something similar to Cocoon. Th=
at <BR>
>> way,<BR>
>> differing XML format could be handled in a more com! pre! hensive =
way. I <BR>
>> have<BR>
>> begun writing code to implement this idea (although it is not Coco=
on <BR>
>> based<BR>
>> - I use jave xml api's) and am perfectly willing to donate it to <=
BR>
>> biodas.org<BR>
>> as open source as a start to developing such a system.<BR>
>><BR>
>> So with that background my question is:<BR>
>><BR>
>> 1. If a system such as I have proposed has been developed, where i=
s <BR>
>> it ?<BR>
>> I just need a specific link.<BR>
>><BR>
>> 2. If such a system does not exist, is anyone interested in the id=
ea <BR>
>> or<BR>
>> want to discuss it ?<BR>
>><BR>
>><BR>
>><BR>
>> Thanks,<BR>
>><BR>
>><BR>
>><BR>
>> Bill Gooding<BR>
>><BR>
>><BR>
>><BR>
>> ---------------------------------<BR>
>> Do You Yahoo!?<BR>
>> HotJobs, a Yahoo! service - Search Thousands of New Jobs<BR>
> _______________________! _____! ___________________<BR>
> DAS mailing list<BR>
> DAS@biodas.org<BR>
> http://biodas.org/mailman/listinfo/das<BR>
><BR>
--<BR>
David Block dblock@gnf.org<BR>
GNF - San Diego, CA http://www.gnf.org<BR>
Genome Informatics / Enterprise Programming<BR>
Weblog: http://radio.weblogs.com/0104507/<BR>
<BR>
_______________________________________________<BR>
DAS mailing list<BR>
DAS@biodas.org<BR>
http://biodas.org/mailman/listinfo/das<BR>
_______________________________________________<BR>
DAS mailing list<BR>
DAS@biodas.org<BR>
http://biodas.org/mailman/listinfo/das<BR>
</FONT></BLOCKQUOTE><FONT FACE=3D"Verdana"><BR>
<HR ALIGN=3DCENTER SIZE=3D"1" WIDTH=3D"100%"><B>Do You Yahoo!?<BR>
</B>HotJobs, a Yahoo! service <http://rd.yahoo.com/careers/mailsig/new/*=
http://www.hotjobs.com> - Search Thousands of New Jobs<BR>
</FONT></BLOCKQUOTE><FONT FACE=3D"Verdana"><BR>
<HR ALIGN=3DCENTER SIZE=3D"1" WIDTH=3D"100%"><B>Do You Yahoo!?<BR>
</B>HotJobs, a Yahoo! service <http://rd.yahoo.com/careers/mailsig/new/*=
http://www.hotjobs.com> - Search Thousands of New Jobs<BR>
</FONT></BLOCKQUOTE><FONT FACE=3D"Verdana"><BR>
<BR>
-- <BR>
Brian Gilman <gilmanb@genome.wi.mit.edu><BR>
Group Leader Medical & Population Genetics Dept.<BR>
MIT/Whitehead Inst. Center for Genome Research<BR>
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA<BR>
phone +1 617 252 1069 / fax +1 617 252 1902<BR>
</FONT>
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