[DAS] Question about das development.
Kulp, David
david_kulp@affymetrix.com
Wed, 21 Aug 2002 08:51:40 -0700
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Regarding open source licenses, I suggest taking a look at
http://www.opensource.org/ <http://www.opensource.org/> . It maintains a
set of "approved" licenses. Differences among some licenses are explained
on the site.
-d
-----Original Message-----
From: Bill Gooding [mailto:bgood97@yahoo.com]
Sent: Wednesday, August 21, 2002 8:36 AM
To: lstein@cshl.org; das@biodas.org
Subject: Re: [DAS] Question about das development.
Hi,
Thanks, Lincoln. That's exactly what I needed to know. And even if my jar
files become a problem in the das repository, you can always destroy the
history on them.
As to these open source licences, to tell you the truth, I don't really have
a detailed understanding of any of them. I am not sure any lawyer has a
detailed understanding either :-). I am intending to allow free access to
the code, so all I really want to is protect myself from trouble. What I do
understand about LGPL, is that anyone can take the source code and use
it,extend it,sell it, even relicense it however they like (including me).
If they do any of these things, they have to ackowledge that they got the
code from my package (that is LGPL) and give a link to where others can get
the code. If this is true (and I think it is, please correct me if not),
then this should be fine. The only problem might be if they decide to
randomly patent some extension (which I don't think they could do, given
that it would be an extension).
Thanks,
Bill
Lincoln Stein wrote:
Hi Bill,
Not much trouble at all. You can send me the files and just tell me where in
the CVS tree you'd like them to appear.
If you already have a CVS on the code, you can simply tar up that portion of
the repository itself and send me that. This way we can keep the history on
your jar files.
My favorite open source license is the new Open Academic License, which is
derived from the Berkeley one. But LGPL is fine.
Lincoln
On Wednesday 21 August 2002 10:42 am, Bill Gooding wrote:
> 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
&! gt; 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
> s! omewhat 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 advan! tage of open source would be that people could
> (hopefull! y) donate their own XSLT files to the project. This all! ows
> 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 wro! te:
> >> 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 compre! 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
--
========================================================================
Lincoln D. Stein Cold Spring Harbor Laboratory
lstein@cshl.org Cold Spring Harbor, NY
========================================================================
_____
Do You Yahoo!?
HotJobs, <http://rd.yahoo.com/careers/mailsig/new/*http://www.hotjobs.com>
a Yahoo! service - Search Thousands of New Jobs
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<DIV><SPAN class=588025315-21082002><FONT face=Arial color=#800000
size=2>Regarding open source licenses, I suggest taking a look at <A
href="http://www.opensource.org/">http://www.opensource.org/</A>. It
maintains a set of "approved" licenses. Differences among some licenses
are explained on the site.</FONT></SPAN></DIV>
<DIV><SPAN class=588025315-21082002><FONT face=Arial color=#800000
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=588025315-21082002><FONT face=Arial color=#800000
size=2>-d</FONT></SPAN></DIV>
<BLOCKQUOTE>
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> Bill Gooding
[mailto:bgood97@yahoo.com]<BR><B>Sent:</B> Wednesday, August 21, 2002 8:36
AM<BR><B>To:</B> lstein@cshl.org; das@biodas.org<BR><B>Subject:</B> Re: [DAS]
Question about das development.<BR><BR></FONT></DIV>
<P>Hi,
<P>Thanks, Lincoln. That's exactly what I needed to know. And even
if my jar files become a problem in the das repository, you can always destroy
the history on them.
<P>As to these open source licences, to tell you the truth, I don't really
have a detailed understanding of any of them. I am not sure any lawyer
has a detailed understanding either :-). I am intending to allow free
access to the code, so all I really want to is protect myself from
trouble. What I do understand about LGPL, is that anyone can take the
source code and use it,extend it,sell it, even relicense it however they
like (including me). If they do any of these things, they have to
ackowledge that they got the code from my package (that is LGPL) and give a
link to where others can get the code. If this is true (and I think it
is, please correct me if not), then this should be fine. The only
problem might be if they decide to randomly patent some extension (which I
don't think they could do, given that it would be an extension).
<P>Thanks,
<P>Bill
<P>
<P> <B><I>Lincoln Stein <LSTEIN@CSHL.ORG></I></B>wrote:
<BLOCKQUOTE
style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi
Bill,<BR><BR>Not much trouble at all. You can send me the files and just
tell me where in <BR>the CVS tree you'd like them to appear.<BR><BR>If you
already have a CVS on the code, you can simply tar up that portion of
<BR>the repository itself and send me that. This way we can keep the history
on <BR>your jar files.<BR><BR>My favorite open source license is the new
Open Academic License, which is <BR>derived from the Berkeley one. But LGPL
is fine.<BR><BR>Lincoln<BR><BR><BR>On Wednesday 21 August 2002 10:42 am,
Bill Gooding wrote:<BR>> Hi,<BR>> I was wondering how much trouble it
would be, if I wanted to put my donate<BR>> my code to the CVS repository
for DAS. I don't really even need access to<BR>> CVS. All I would need is
for someone to create a subdirectory for me and<BR>> checkin whatever I
give them. I would also want to checkin jar files<BR>> (precompiled
files! ). I wouldn't want those files to be subject to revision<BR>>
control. I don't need anyone to announce any software on the DAS site,
I<BR>> want to wait and see if anyone thinks it is a good idea. I just
want to<BR>> have a place that people can download the software if they
want. Also,<BR>> what about licencing for this open source - I was
thinking LGPL. It seems<BR>> to give the most flexibility. Bill
Gooding<BR>> Bill Gooding wrote:<BR>> To everyone replying to my
message,<BR>> Thanks for your help, this is the sort of discussion that I
wanted to<BR>> start. On the specific comments: I am perfectly willing to
work with Chris<BR>> on the development of this software. The one thing I
would like to insist<BR>> on is that it be open source. I am sure that
this probably goes without<BR>> saying in this group :-). We really just
need a place to put the project<BR>> and people can download it if they
like. As I said, I have developed a<BR>&! gt; system which is based on
JSP/Sevlets/Java. I think it is a good starting<BR>> point. I am sure you
would be surprised if I didn't think that :-). As for<BR>> David Kulp's
comments, I recognize that the system load may be a problem. <BR>> But
this problem to me would seem to plague any such system. That is, if<BR>>
you are looking at a whole chomosome down to the base pair level, you
will<BR>> have alot of data. I think that this can be addressed by
limiting the size<BR>> of the queries in the server which shouldn't be
too hard. Also, the system<BR>> I have developed, although it is JSP
based, it will be very easy to create<BR>> a standalone program for it so
you don't have to go through a JSP server if<BR>> you want to download
and transform alot of data. The standalone program<BR>> will use the same
codebase as the JSP server (which will also allow easy<BR>> test scripts
to be written for the code) This should somewhat mitigate<BR>> s! omewhat
the load problem. On your comments about SVG/client<BR>>
integration/Adobe plugins, I really don't want to deal with this issue
in<BR>> the software (if I can avoid it). It seems like it may be
problematic to<BR>> support the plugin and all the browsers that may
implement it slightly<BR>> differently. For now, I think that the user
can live with reloading data<BR>> he needs. I understand this will
increase server load. But my vision for<BR>> this project is not to
necessarily create something that would support an<BR>> extremely high
load (at least not at the beginning). I really intend this<BR>> to be
used within a relatively small group of users to simplify the access<BR>>
to data. So in my system, I really want to emphasize customizability.
<BR>> That is, if someone wants to display his data differently he should
be able<BR>> to plugin his XSLT files into the system very easily. I
think what I have<BR>> satisfies that. The advan! tage of open source
would be that people could<BR>> (hopefull! y) donate their own XSLT files
to the project. This all! ows<BR>> for many different views or processing
of the data thus giving the users of<BR>> the software more flexibility.
At this point I would see the issue as a<BR>> tradeoff between speed and
flexibility. Maybe in later development any<BR>> speed problems could be
solved or strongly mitigated. As always, comments<BR>> on this are
welcome.<BR>> Thanks,<BR>><BR>> Bill Gooding<BR>><BR>> "Kulp,
David" wrote: From the whizbang angle, I've been thinking about a<BR>>
DAS-SVG viewer. The "problem" is typical for genome browser displays:
too<BR>> many features significantly slows down display, both in terms of
data<BR>> transmission and SVG client rendering. I looked a little into
how one might<BR>> deal with dynamic content and semantic zooming. It
turns out that the Adobe<BR>> viewer provides two non-standard hooks!
which allow you to make URL calls<BR>> and to parse the returning
document into a DOM. Thus, javascript callbacks<BR>> could be attached to
zoom levels, hidden tracks, or objects, which caused<BR>> the server to
be queried for additional SVG which was then attached to the<BR>>
existing DOM. 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<BR>> 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>> > Search for "SVG" and "genome browser" on google. Here's
one:<BR>> ><BR>> >
http://www.svgopen.org/abstracts/lewis_et_al__bioviz_genome_viewer.html<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 data<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 wro! te:<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 information<BR>> >> from
various servers people use a downloaded java program which<BR>> >>
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 into<BR>> >>
SVG<BR>> >> for display on a browser. That is, something similar to
Cocoon. That<BR>> >> way,<BR>> >> differing XML format
could be handled in a more compre! hensive way. I<BR>> >>
have<BR>> >> begun writing code to implement this idea (although it
is not Cocoon<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 is<BR>> >> it ?<BR>> >>
I just need a specific link.<BR>> >><BR>> >> 2. If such a
system does not exist, is anyone interested in the idea<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>> > ____________________________! ___________________<BR!>>
> DAS mailing list<BR>> > DAS@biodas.org<BR>> >
http://biodas.org/mailman/listinfo/das<BR><BR>--
<BR>========================================================================<BR>Lincoln
D. Stein Cold Spring Harbor Laboratory<BR>lstein@cshl.org Cold Spring
Harbor,
NY<BR>========================================================================</BLOCKQUOTE>
<P><BR>
<HR SIZE=1>
<B>Do You Yahoo!?</B><BR><A
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