Re: [Treebase-devel] [Nexml-discuss] CDAO term inclusion community process

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Hi,

Wayne, thanks for chiming in - I changed the way the properties file
is loaded a little bit (sorry I left the absolute paths in
previously!). Kasia, could you try the following,

- assuming $NEXMLTRUNK is your local equivalent for
https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/
- assuming $MESQUITE_FOLDER is your local equivalent for
http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/Mesquite%20Project/Mesquite_Folder/

* cd $NEXMLTRUNK/java
* export CLASSPATH=$CLASSPATH:"$MESQUITE_FOLDER"
* ant mesquite
* pico "$MESQUITE_FOLDER/classpaths.xml"
* add an entry in classpaths.xml:
<classpath>$NEXMLTRUNK/java/bin/</classpath>, where $NEXMLTRUNK must
be substituted for the real path (either relative or absolute) to the
bin folder in which ant placed the compiled classes. Attached is how I
have it, which works when you check the mesquite trunk and the full
nexml code (trunk and branches) in the same folder (for me that's
~/Documents/workspace but it shouldn't matter)

Now, when Mesquite starts up, could you copy and paste what happens in
the log window when you read the local version of this file:
$NEXMLTRUNK/examples/translations/hyperlink.xml

Hope this helps!

Rutger

On Tue, Jun 9, 2009 at 8:36 PM, Wayne
Maddison<wma...@in...> wrote:
> Sorry, I haven't been following this, but, classpaths.xml should be
> in the Mesquite_Folder that initiates Mesquite starting up.  To see
> if it's being read, include a line like:
>
>  <classpath>../../MySideProject/Mesquite_Folder</classpath>
>
>
> in which case the log should say something like this:
>
> =====
> Modules loading from directory
> /Users/wmaddisn/Mesquite_Workspace/Mesquite
> Project/Mesquite_Folder/Mesquite (500MB).app/../mesquite/
>
>  ancstates basic categ charMatrices charts cont genesis io lists
> minimal parsimony stochchar trees align assoc batchArch coalesce
> consensus correl distance diverse dmanager mb meristic molec
> ornamental pairwise rhetenor search tol treefarm iText jama jsci pal
> trunk
>
> Additional modules loaded from
> /Users/wmaddisn/Mesquite_Workspace/MySideProject/Mesquite_Folder
> =====
>
> However, this puts the paths in Java's classpath.  I suspect this may
> not help with the .properties file; this may use a different sense of
> application's path.  With pPod communication I seem to recall that
> some of the auxiliary files had to live in your initiating
> Mesquite_Folder.
>
> Wayne
>
>
> At 5:53 PM -0400 9.6.2009, Hayden, Katherine M. wrote:
>>Content-type: multipart/alternative;
>>  boundary="Boundary_(ID_3C+aqoD18lMP5R4IySZZ/g)"
>>Content-class: urn:content-classes:message
>>
>>Sorry, I'm a little confused. If my classpaths.xml is in
>>/home/kasia/workspace/Mesquite Project/Mesquite_Folder, then isn't
>>it already in the root of my the Mesquite_Folder?
>>
>>Or are you saying to instead put it in
>>/home/kasia/workspace/Mesquite Project, which is one directory
>>above? (When I do this I no longer have the option to export as
>>NEXML, even when I remember that I have to change the relative paths
>>after bumping up the classpaths.xml file one directory :)
>>
>>
>>Kasia
>>
>>
>>
>>Katherine "Kasia" Hayden
>>Bennington College, Class of 2011
>>312.576.8175
>>kh...@be...
>>
>>
>>
>>-----Original Message-----
>>From: rut...@gm... on behalf of Rutger Vos
>>Sent: Tue 6/9/2009 4:52 PM
>>To: Hayden, Katherine M.
>>Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli;
>>ju...@ig...; nex...@li...;
>>ph...@go...
>>Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>
>>Hi Kasia,
>>
>>I don't think classpaths.xml modifies the system classpath variable,
>>so adding the properties file here won't do anything - as far as I
>>understand the xml file is read by Mesquite's module loading system.
>>Maybe try placing the file in the root of the Mesquite_Folder?
>>
>>Rutger
>>
>>On Sun, Jun 7, 2009 at 9:16 AM, Hayden, Katherine
>>M.<KH...@be...> wrote:
>>>  Rutger,
>>>
>>>  I changed what you suggested and still get the same output.
>>>
>>>  This is what my classpaths.xml file looks like:
>>>
>>>  <?xml version="1.0"?>
>>>  <mesquite>
>>>          <classpath>../../MesquiteGSoC/Mesquite_Folder</classpath>
>>>          <classpath>../../RutgersNexml/java/bin</classpath>
>>>          <!--
>>>
>>><classpath>../../RutgersNexml/java/src/predicateHandlerMapping.properties</classpath>
>>>  -->
>>>          <classpath>../../RutgersNexml/java/src</classpath>
>>>  </mesquite>
>>>
>>>
>>>  I wasn't sure if the .properties file needed to be pointed to directly or if
>>>  its directory needed to be specified, so I tried both. No luck with either.
>>>
>>>  My classpaths.xml file is in ~/workspace/Mesquite Project/Mesquite_Folder.
>>>
>>>
>>>  Can't think of what else might be accounting for the difference.. Do you
>>>  have any other suggestions?
>>>
>>>
>>>  Kasia
>>>
>>>
>>>
>>>  Katherine "Kasia" Hayden
>>>  Bennington College, Class of 2011
>>>  312.576.8175
>>>  kh...@be...
>>>
>>>
>>>
>>>  -----Original Message-----
>>>  From: rut...@gm... on behalf of Rutger Vos
>>>  Sent: Fri 6/5/2009 5:23 PM
>>>  To: Hayden, Katherine M.
>>>  Cc: Arlin Stoltzfus; TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>  > nex...@li...; ph...@go...
>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>
>>>  Hi Katherine,
>>>
>>>  is it possible that the predicateHandlerMapping.properties file isn't
>>>  in your classpath? The output you produced is the default output which
>>>  uses Mesquite's internal name for URLs - "hyperlink" - as a predicate
>>>  instead of the href/rel construct. The properties file defines which
>>>  class is used for which internal name, and it should make Mesquite
>>>  load mesquite.nexml.InterpretNEXML.HyperlinkHandler to write out the
>>>  attachment (but clearly it's not working in your output).
>>>
>>>  Rutger
>>>
>>>  On Fri, Jun 5, 2009 at 8:51 AM, Hayden, Katherine
>>>  M.<KH...@be...> wrote:
>>>>  Hi Rutger,
>>>>
>>>>  I just built this and got different results for my hyperlink.xml output
>>>>  that
>>>>  I thought I'd share. I'm running Ubuntu Jaunty 9.04 and Sun's Java version
>>>>  1.6.0_13.
>>>>
>>>>  Specifically, here's the annotation attached to otu elements:
>>>>
>>>>  <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>
>>>>
>>>>  And here's the whole thing:
>>>>
>>>>  <?xml version="1.0" encoding="UTF-8"?>
>>>>  <nex:nexml
>>>>xmlns:rdf="<http://www.w3.org/1999/02/22-rdf-syntax-ns>http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>>>>
>>>>xmlns:xsd="<http://www.w3.org/2001/XMLSchema>http://www.w3.org/2001/XMLSchema#"
>>>>
>>>>xmlns:xsi="<http://www.w3.org/1999/XMLSchema-instance>http://www.w3.org/1999/XMLSchema-instance"
>>>>  generator="org.nexml.model.impl.DocumentImpl" version="0.8"
>>>>  xmlns:nex="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>    <otus xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>  about="#a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>  id="a30fa7c92-f779-4ec2-9e93-b661ad5d8067" label="Taxa"
>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>      <meta content="0121b10b3afc1" datatype="xsd:string"
>>>>  id="adf36dd59-cc8f-4638-a504-d79e038d2536" property="msq:taxaUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      <otu about="#a813050fb-c62d-4135-a564-9a97bfd2be14"
>>>>  id="a813050fb-c62d-4135-a564-9a97bfd2be14" label="taxon 1">
>>>>        <meta content="http" datatype="xsd:string"
>>>>  id="a49c0ce09-09c4-45c1-bd63-0c110586bffd" property="msq:hyperlink"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="0" datatype="xsd:integer"
>>>>  id="ac65986fc-fcf2-4016-be0a-4e96b318ec1d" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>      <otu about="#ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"
>>>>  id="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3" label="taxon 2">
>>>>        <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a8c2301c6-55b8-463e-af78-da3c5a8eb436"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="1" datatype="xsd:integer"
>>>>  id="a0a697790-2018-4a5a-84e8-a805ce23dc95" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>      <otu about="#aae2e01e9-7c71-4293-9d4e-0f2d2002485d"
>>>>  id="aae2e01e9-7c71-4293-9d4e-0f2d2002485d" label="taxon 3">
>>>>        <meta
>>>>content="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>  datatype="xsd:string" id="a4713c006-3815-414e-a64c-c62c770ae6d9"
>>>>  property="msq:hyperlink" xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="2" datatype="xsd:integer"
>>>>  id="ac881653e-1ed1-40af-8227-e2005a4cee4d" property="msq:taxonUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>      </otu>
>>>>    </otus>
>>>>    <trees id="afdb44f28-fcf6-4904-84d7-78a9d6afecce" label="Simulated
>>>>  Trees"
>>>>  otus="a30fa7c92-f779-4ec2-9e93-b661ad5d8067"
>>>>  xmlns="<http://www.nexml.org/1.0>http://www.nexml.org/1.0">
>>>>      <tree
>>>>xmlns:msq="<http://mesquiteproject.org>http://mesquiteproject.org#"
>>>>  about="#a72f25756-9b46-465a-9865-24960220a821"
>>>>  id="a72f25756-9b46-465a-9865-24960220a821" label="Tree # 1 simulated by
>>>>  Uniform speciation (Yule)"
>>>>
>>>>xmlns:xsi="<http://www.w3.org/2001/XMLSchema-instance>http://www.w3.org/2001/XMLSchema-instance"
>>  >> xsi:type="nex:FloatTree">
>>>>        <meta content="1" datatype="xsd:long"
>>>>  id="a5ab09661-ee5c-48cc-8017-ec8b91c51398" property="msq:treeUID"
>>>>  xsi:type="nex:LiteralMeta"/>
>>>>        <meta content="2" datatype="xsd:integer"
>>>>  id="a93297efc-f077-43fd-88b1-e5a0866c0303"
>>>>  property="msq:treePolytomyAssumption" xsi:type="nex:LiteralMeta"/>
>>>>        <node id="a5ae62a35-5617-46d0-a873-8e37533603e1" label=""/>
>>>>        <node id="a7ede845d-5b13-4fcc-ac25-73f472963e42" label="taxon 3"
>>>>  otu="aae2e01e9-7c71-4293-9d4e-0f2d2002485d"/>
>>>>        <node id="ae9e03f83-0241-489c-9006-70f606344b48" label=""/>
>>>>        <node id="afca8e713-a823-4cf5-b3f4-eb6a825c5518" label="taxon 2"
>>>>  otu="ae0cf73e3-063a-4e52-bebe-e546e7fbe5e3"/>
>>>>        <node id="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346" label="taxon 1"
>>>>  otu="a813050fb-c62d-4135-a564-9a97bfd2be14"/>
>>>>        <edge id="ac31fb749-d444-480c-8ec2-47f34ef11149" length="10.0"
>>>>  source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>  target="a7ede845d-5b13-4fcc-ac25-73f472963e42"/>
>>>>        <edge id="a6ec736dc-4db1-4b96-94ef-fdda1ce12bbd"
>>>>  length="3.1643765725844055" source="a5ae62a35-5617-46d0-a873-8e37533603e1"
>>>>  target="ae9e03f83-0241-489c-9006-70f606344b48"/>
>>>>        <edge id="afe019984-8683-4f05-9b2d-954ddfce7f38"
>>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>  target="afca8e713-a823-4cf5-b3f4-eb6a825c5518"/>
>>>>        <edge id="a116f17be-c512-4680-a850-c4d467451f68"
>>>>  length="6.835623427415595" source="ae9e03f83-0241-489c-9006-70f606344b48"
>>>>  target="a2d5aa115-782e-4ecd-8fc7-ce9097cc5346"/>
>>>>      </tree>
>>>>    </trees>
>>>>  </nex:nexml>
>>>>
>>>>
>>>>  Kasia
>>>>
>>>>
>>>>
>>>>  Katherine "Kasia" Hayden
>>>>  Bennington College, Class of 2011
>>>>  312.576.8175
>>>>  kh...@be...
>>>>
>>>>
>>>>
>>>>  -----Original Message-----
>>>>  From: Rutger Vos
>>>>[<mailto:rv...@in...>mailto:rv...@in...]
>>>>  Sent: Fri 6/5/2009 3:53 AM
>>>>  To: Arlin Stoltzfus
>>>>  Cc: TreeBASE Developers; Enrico Pontelli; ju...@ig...;
>>>>  nex...@li...; ph...@go...
>>>>  Subject: Re: [Nexml-discuss] CDAO term inclusion community process
>>>>
>>>>  Hi,
>>>>
>>>>  Can we work along a use case? I've just committed some code to import
>>>>  and export nexml (with annotations) into mesquite using the
>>>>  hackathon's nexml/java API. To run it, here's what you do (ok, just
>>>>  play along - you don't *have* to build this):
>>>>
>>>>  * svn co
>>>><https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java>https://nexml.svn.sourceforge.net/svnroot/nexml/trunk/nexml/java
>>>>  * cd java
>>>>  * export CLASSPATH=$CLASSPATH:/path/to/Mesquite_Folder
>>>>  * ant mesquite
>>>>
>>>>  Then, inside your Mesquite_Folder, either create or edit your
>>>>  classpaths.xml file, which should contain an entry that points to the
>>>>  bin folder that the ant task created:
>>>>
>>>>  <?xml version="1.0"?>
>>>>  <mesquite>
>>>>              <!-- perhaps other classpath entries here -->
>>>>          <classpath>/path/to/java/bin</classpath>
>>>>  </mesquite>
>>>>
>>>>  Now, start mesquite and open this url from within mesquite (File >
>>>>  Open other... > URL...):
>>>>
>>>>
>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.nex
>>>>
>>>>  You'll see a tree with some dummy URLs on the terminal nodes. If you
>>>>  look in the nexus "source" you can see these URLs are written in the
>>>>  notes block. If you now choose file > export, NeXML should be one of
>>>>  the options so you can write hyperlink.xml out to a file. The produced
>>>>  output should look like this:
>>>>
>>>>
>>>><http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml>http://nexml-dev.nescent.org/nexml/examples/translations/hyperlink.xml
>>>>
>>>>  The salient point of the output is the annotation attached to otu
>>>>  elements:
>>>>
>>>>  <meta
>>>>href="<http://8ball.sdsc.edu:6666/treebase-web>http://8ball.sdsc.edu:6666/treebase-web"
>>>>     rel="cdao:has_External_Reference" [...other attributes are
>>>>  irrelevant for now...] />
>>>>
>>>>  According to the RDFa rules, we can just use the "href" attribute to
>>>>  store a url, and the "rel" attribute will describe the relationship
>>  >> between the subject (the earliest enclosing element that has an
>>>>  "about" attribute) and the resource on the other end. I *think* we
>>>>  agreed that such a simple relationship could be described as
>>>>  has_External_Reference, we use it on the wiki and I've found it in the
>>>>  CDAO owl file.
>>>>
>>>>  So what about other annotations? You can see in the produced nexml
>>>>  that mesquite is also storing internal object IDs to various
>>>>  predicates under the msq: namespace prefix (i.e. msq:taxaUID,
>>>>  msq:taxonUID and msq:treeUID). Can we have something like these as
>>>>  properties in CDAO? The TreeBASE2 team has been sketching out some
>>>>  service queries which we would like to implement, and we want the
>>>>  search fields we expose be mediated by CDAO. One of the obvious search
>>>>  fields would be something like cdao.treeUID, where perhaps the value
>>>>  would be a namespaced id string (TreeBASE:Tr3242, for example).
>>>>
>>>>  Can we have something like that? I like Hilmar's suggestion of being
>>>>  able to put it in a queue somewhere, but I would be very interested to
>>>>  see what Brandon comes up with for term suggestion interface -
>>>>  obviously it will be better for all involved if the term suggestion
>>>>  was as specific as possible, perhaps already fitted into CDAO's class
>>>>  hierarchy (as opposed to a rambling email like this one).
>>>>
>>>>  Rutger
>>>>
>>>>  On Thu, Jun 4, 2009 at 8:20 AM, Arlin Stoltzfus<sto...@um...>
>>>>  wrote:
>>>>>  We're listening.  Brandon has developed a term-request server to process
>>>>>  requests for concepts and relations, but its still in an early stage.  In
>>>>>  a
>>>>>  few weeks we will be in a better position to have this discussion.
>>>>>
>>>>>  Arlin
>>>>>
>>>>>  On May 29, 2009, at 10:31 AM, Rutger Vos wrote:
>>>>>
>>>>>>  Hi,
>>>>>>
>>>>>>  I've done enough experimentation to establish the correct syntax for
>>>>>>  attaching valid RDFa attachments to nexml so that standard RDFa
>>>>>>  extractors can turn <meta/> elements - the new dictionaries - into RDF
>>>>>>  triples. I've implemented this in the java and perl APIs (Jeet: I hope
>>>>>>  that the examples I've mailed out give you enough of a template to do
>>>>>>  this in python too, but please let me know of I can help - I know that
>>>>>>  the wiki needs updating, for starters).
>>>>>>
>>>>>>  The key issue now is the definition of predicates, i.e. the value of
>>>>>>  the @property and @rel attributes. Over the course of many EvoInfo
>>>>>>  discussions it's been decided that CDAO will be the principal artifact
>>>>>>  for their mediation - so what's the community process for inclusion of
>>>>>>  new predicates?
>>>>>>
>>>>>>  Val and I have sketched out a couple of TreeBASE services whose search
>>>>>>  keys should be part of a controlled vocabulary (things like tree.id,
>>>>>>  tree.label, etc.), and this is just one use case of a project having a
>>>>>>  potentially large number of predicates (other example: Mesquite).
>>>>>>
>>>>>>  It would be great if team CDAO could tell us where to send our list of
>>>>>>  proposed terms and where we can download an amended version of CDAO
>>>>>>  that includes them :-)
>>>>>>
>>>>>>  I note that there is a wiki page about this
>>>>>>
>>>>>>(<https://www.nescent.org/wg_evoinfo/CDAO_term_request>https://www.nescent.org/wg_evoinfo/CDAO_term_request),
>>>>>>but ideally
>>>>>>  there would be some sort of issue tracker with structured input fields
>>>>>>  (e.g. subject/predicate/object name="XXX", suggested superclass="YYY",
>>>>>>  suggested datatype(s)="ZZZ", description="..."). Behind this tracker
>>>>>>  would be a team of curators that will promptly pick up a posted issue
>>>>>>  and work towards a solution.
>>>>>>
>>>>>>  I realize that this involves a support commitment from team CDAO, but
>>>>>>  I think that's what we agreed to over free-form key/value pairs,
>>>>>>  homegrown vocabularies or a BioMoby-like free-for-all.
>>>>>>
>>>>>>  Any comments?
>>>>>>
>>>>>>  Rutger
>>>>>>
>>>>>>  --
>>>>>>  Dr. Rutger A. Vos
>>>>>>  Department of zoology
>>>>>>  University of British Columbia
>>>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>  --
>>>>  Dr. Rutger A. Vos
>>>>  Department of zoology
>>  >> University of British Columbia
>>>>  <http://www.nexml.org>http://www.nexml.org
>>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>>
>>>>
>>>>
>>>>------------------------------------------------------------------------------
>>>>  OpenSolaris 2009.06 is a cutting edge operating system for enterprises
>>>>  looking to deploy the next generation of Solaris that includes the latest
>>>>  innovations from Sun and the OpenSource community. Download a copy and
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>>>>  Go to:
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>>>>  _______________________________________________
>>>>  Nexml-discuss mailing list
>>>>  Nex...@li...
>>>>
>>>><https://lists.sourceforge.net/lists/listinfo/nexml-discuss>https://lists.sourceforge.net/lists/listinfo/nexml-discuss
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>  --
>>>  Dr. Rutger A. Vos
>>>  Department of zoology
>>>  University of British Columbia
>>>  <http://www.nexml.org>http://www.nexml.org
>>>  <http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>>
>>>
>>
>>
>>
>>--
>>Dr. Rutger A. Vos
>>Department of zoology
>>University of British Columbia
>><http://www.nexml.org>http://www.nexml.org
>><http://rutgervos.blogspot.com>http://rutgervos.blogspot.com
>>
>>
>>
>>------------------------------------------------------------------------------
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>
>
> --
> --------------------------------------------------------
> Wayne Maddison
>  Professor and Canada Research Chair
>          Depts. of Zoology and Botany and
>          Biodiversity Research Centre
>  & Director
>          Beaty Biodiversity Museum
>  6270 University Boulevard
>  University of British Columbia
>  Vancouver, BC  V6T 1Z4   Canada
>
> email: wma...@in...   FAX: +1 604 822-2416
>
> Mesquite: http://mesquiteproject.org
> MacClade: http://macclade.org
> Salticidae:  http://salticidae.org
> Tree of Life: http://tolweb.org
> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
> Home page: http://salticidae.org/wpm/home.html
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
> Check out the new simplified licensing option that enables unlimited
> royalty-free distribution of the report engine for externally facing
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-- 
Dr. Rutger A. Vos
Department of zoology
University of British Columbia
http://www.nexml.org
http://rutgervos.blogspot.com