[DAS] Question about das development.
Bill Gooding
bgood97@yahoo.com
Sun, 18 Aug 2002 21:53:02 -0700 (PDT)
--0-690688350-1029732782=:35991
Content-Type: text/plain; charset=us-ascii
Hi Lincoln,
Thanks for the information. I looked up the links you gave and here is what I found:
1. http://www.svgopen.org/abstracts/lewis_et_al__bioviz_genome_viewer.html - this was a link to an abstact about a system being proposed in Canada. Unfortunately, I couldn't find any associated code for the system. I was really looking for an open source project that I could assist on.
2. http://www.labbook.com/ - This system appears to be another browser, unfortunately I couldn't download it to have a look at it. It appears they may have suspended downloads for the time being since they are releasing new software. Although once again, I was looking for an open source project.
3. http://gb.bioruby.org/ - This appears to be an open source project. I downloaded the code and am currently trying to analyze it. I couldn't find the XSLT files that they were using. However they may be parsing the information directly from a database and turning it into SVG.
What I was really looking to develop was a server that used an XML/XSLT framework to transform the output of a DAS or other XML format into SVG. Ideally the system would be customizable so that a user could easily use his own XSLT files to transform the output to anything he would like. I'll continue to look at the bioRuby information, but I still don't see the kind of system I am talking about available.
Thanks for your help,
Bill Gooding
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 comprehensive 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
---------------------------------
Do You Yahoo!?
HotJobs, a Yahoo! service - Search Thousands of New Jobs
--0-690688350-1029732782=:35991
Content-Type: text/html; charset=us-ascii
<P>Hi Lincoln,
<P>Thanks for the information. I looked up the links you gave and here is what I found:
<P>1. <A href="http://www.svgopen.org/abstracts/lewis_et_al__bioviz_genome_viewer.html">http://www.svgopen.org/abstracts/lewis_et_al__bioviz_genome_viewer.html</A> - this was a link to an abstact about a system being proposed in Canada. Unfortunately, I couldn't find any associated code for the system. I was really looking for an open source project that I could assist on.
<P>2. <A href="http://www.labbook.com/">http://www.labbook.com/</A> - This system appears to be another browser, unfortunately I couldn't download it to have a look at it. It appears they may have suspended downloads for the time being since they are releasing new software. Although once again, I was looking for an open source project.</P>
<P>3. <A href="http://gb.bioruby.org/">http://gb.bioruby.org/</A> - This appears to be an open source project. I downloaded the code and am currently trying to analyze it. I couldn't find the XSLT files that they were using. However they may be parsing the information directly from a database and turning it into SVG.</P>
<P>What I was really looking to develop was a server that used an XML/XSLT framework to transform the output of a DAS or other XML format into SVG. Ideally the system would be customizable so that a user could easily use his own XSLT files to transform the output to anything he would like. I'll continue to look at the bioRuby information, but I still don't see the kind of system I am talking about available. </P>
<P>Thanks for your help,</P>
<P> </P>
<P>Bill Gooding<BR><BR></P>
<P>
<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">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 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 information<BR>> from various servers people use a downloaded java program which implements<BR>> a GUI (Swing/AWT) for displaying information. I was wondering if anyone<BR>> had considered using an XML based server that tranforms the data into SVG<BR>> for display on a browser. That is, something similar to Cocoon. That way,<BR>> differing XML format could be handled in a more comprehensive way. I have<BR>> begun writing code to implement this idea (although it is not Cocoon based<BR>> - I use jave xml api's) and am perfectly willing to donate it to 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 it ? <BR>> I just need a specific link.<BR>><BR>> 2. If such a system does not exist, is anyone interested in the idea 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</BLOCKQUOTE><p><br><hr size=1><b>Do You Yahoo!?</b><br>
<a href="http://rd.yahoo.com/careers/mailsig/new/*http://www.hotjobs.com">HotJobs, a Yahoo! service</a> - Search Thousands of New Jobs
--0-690688350-1029732782=:35991--