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[Treebase-guts] SF.net SVN: treebase:[547] trunk/treebase-web/src/main/webapp
|
From: <rv...@us...> - 2010-03-12 00:02:38
|
Revision: 547
http://treebase.svn.sourceforge.net/treebase/?rev=547&view=rev
Author: rvos
Date: 2010-03-12 00:02:30 +0000 (Fri, 12 Mar 2010)
Log Message:
-----------
BIG COMMIT: THIS CHANGES MUCH OF THE STATIC PAGE STYLES
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
trunk/treebase-web/src/main/webapp/common/footer.jsp
trunk/treebase-web/src/main/webapp/common/header.jsp
trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
trunk/treebase-web/src/main/webapp/styles/displaytag.css
trunk/treebase-web/src/main/webapp/styles/styles.css
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
trunk/treebase-web/src/main/webapp/images/TreeBASE.png
trunk/treebase-web/src/main/webapp/images/architecture.jpeg
trunk/treebase-web/src/main/webapp/images/gradient.jpg
trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
trunk/treebase-web/src/main/webapp/images/nescent_logo.png
trunk/treebase-web/src/main/webapp/images/people/
trunk/treebase-web/src/main/webapp/images/people/anon.jpg
trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
trunk/treebase-web/src/main/webapp/images/people/krice.gif
trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml 2010-03-12 00:02:30 UTC (rev 547)
@@ -10,6 +10,7 @@
<pattern>/about.html</pattern>
<pattern>/urlAPI.html</pattern>
<pattern>/people.html</pattern>
+ <pattern>/technology.html</pattern>
</decorator>
<!-- decoration page for search pages -->
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,103 +1,105 @@
-<div class="gutter">
- <h1>Overview</h1>
- <p>
- TreeBASE is a relational database designed to manage and explore information on
- phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996;
- Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data
- matrices, together with information about the relevant publication, taxa,
- morphological and sequence-based characters, and published analyses.
- </p>
- <p>
- The database is designed to allow retrieval of trees and data from different
- studies so that existing phylogenetic results may be reassessed, compared,
- combined and reused. Applications include:
- </p>
- <ul>
- <li>
- to locate information on the phylogeny of particular groups of interest.
- </li>
- <li>
- to obtain datasets for studies of character evolution, including general
- patterns across many groups, such as patterns of homoplasy.
- </li>
- <li>
- in studies of biogeography -- to retrieve trees with representatives in
- particular geographical areas.
- </li>
- <li>
- in studies of coevolution -- to retrieve information on host and parasite
- phylogenies.
- </li>
- <li>
- in studies of congruence and combination of data -- to retrieve all molecular
- and morphological phylogenies for particular groups.
- </li>
- <li>
- in studies of phylogenetic methods -- to retrieve all parsimony or maximum
- likelihood reconstructions, for example, or to download datasets of various
- sorts to test methods.
- </li>
- <li>
- to link together trees of particular groups into more inclusive phylogenies.
- </li>
- <li>
- to discover understudied groups -- a resource for students, funding agencies,
- etc.
- </li>
- <li>
- to retrieve phylogenetic information for use in conservation biology and the
- management of natural resources.
- </li>
- </ul>
- <h2>History, Funding, and Governance</h2>
- <p>
- The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994,
- Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype
- database of phylogenetic studies"). The database underwent a complete
- redevelopment and redesign with funding from the <a href="http://www.phylo.org">
- Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654:
- "Building the Tree of Life -- A National Resource for Phyloinformatics and
- Computational Phylogenetics").
- </p>
- <p>
- TreeBASE was released in March 2010 as one of the main products of The
- Phyloinformatics Research Foundation, Inc., a Connecticut non-profit
- corporation. The Foundation provides direction, governance, and continuity for
- software, data sharing, and communication standards to promote phyloinformatic
- research for the scientific community.
- </p>
- <p>
- The current version of the database is 2.0 (released March 2010), and is hosted
- by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
- NESCent</a>). In previous years the database has been hosted by the
- <a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the
- <a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the
- <a href="http://www.buffalo.edu">University at Buffalo</a>,
- <a href="http://www.harvard.edu">Harvard University</a>,
- <a href="http://www.leiden.edu">Leiden University</a>, and the
- <a href="http://www.ucdavid.edu">University of California, Davis</a>.
- </p>
- <h2>Related resources</h2>
- <ul>
- <li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an
- online reference source and database for every one of the 1.8 million species that
- are named and known on this planet.</li>
- <li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative
- effort of biologists and nature enthusiasts from around the world. On more than
- 10,000 World Wide Web pages, the project provides information about biodiversity,
- the characteristics of different groups of organisms, and their evolutionary history</li>
- <li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular
- software for evolutionary biology, designed to help biologists analyze comparative
- data about organisms in a phylogenetic context.
- </li>
- </ul>
- <h2>Logo</h2>
- <p>
- The logo displayed on the TreeBASE web-application has been adapted to match the
- color style of the website. Please use the logo shown here for linking to or citing
- TreeBASE.
- <center>
- <img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
- </center>
- </p>
+<div id="contentRight">
+ <div class="gutter">
+ <h1>Overview</h1>
+ <p>
+ TreeBASE is a relational database designed to manage and explore information on
+ phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996;
+ Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data
+ matrices, together with information about the relevant publication, taxa,
+ morphological and sequence-based characters, and published analyses.
+ </p>
+ <p>
+ The database is designed to allow retrieval of trees and data from different
+ studies so that existing phylogenetic results may be reassessed, compared,
+ combined and reused. Applications include:
+ </p>
+ <ul>
+ <li>
+ to locate information on the phylogeny of particular groups of interest.
+ </li>
+ <li>
+ to obtain datasets for studies of character evolution, including general
+ patterns across many groups, such as patterns of homoplasy.
+ </li>
+ <li>
+ in studies of biogeography -- to retrieve trees with representatives in
+ particular geographical areas.
+ </li>
+ <li>
+ in studies of coevolution -- to retrieve information on host and parasite
+ phylogenies.
+ </li>
+ <li>
+ in studies of congruence and combination of data -- to retrieve all molecular
+ and morphological phylogenies for particular groups.
+ </li>
+ <li>
+ in studies of phylogenetic methods -- to retrieve all parsimony or maximum
+ likelihood reconstructions, for example, or to download datasets of various
+ sorts to test methods.
+ </li>
+ <li>
+ to link together trees of particular groups into more inclusive phylogenies.
+ </li>
+ <li>
+ to discover understudied groups -- a resource for students, funding agencies,
+ etc.
+ </li>
+ <li>
+ to retrieve phylogenetic information for use in conservation biology and the
+ management of natural resources.
+ </li>
+ </ul>
+ <h2>History, Funding, and Governance</h2>
+ <p>
+ The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994,
+ Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype
+ database of phylogenetic studies"). The database underwent a complete
+ redevelopment and redesign with funding from the <a href="http://www.phylo.org">
+ Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654:
+ "Building the Tree of Life -- A National Resource for Phyloinformatics and
+ Computational Phylogenetics").
+ </p>
+ <p>
+ TreeBASE was released in March 2010 as one of the main products of The
+ Phyloinformatics Research Foundation, Inc., a Connecticut non-profit
+ corporation. The Foundation provides direction, governance, and continuity for
+ software, data sharing, and communication standards to promote phyloinformatic
+ research for the scientific community.
+ </p>
+ <p>
+ The current version of the database is 2.0 (released March 2010), and is hosted
+ by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
+ NESCent</a>). In previous years the database has been hosted by the
+ <a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the
+ <a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the
+ <a href="http://www.buffalo.edu">University at Buffalo</a>,
+ <a href="http://www.harvard.edu">Harvard University</a>,
+ <a href="http://www.leiden.edu">Leiden University</a>, and the
+ <a href="http://www.ucdavid.edu">University of California, Davis</a>.
+ </p>
+ <h2>Related resources</h2>
+ <ul>
+ <li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an
+ online reference source and database for every one of the 1.8 million species that
+ are named and known on this planet.</li>
+ <li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative
+ effort of biologists and nature enthusiasts from around the world. On more than
+ 10,000 World Wide Web pages, the project provides information about biodiversity,
+ the characteristics of different groups of organisms, and their evolutionary history</li>
+ <li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular
+ software for evolutionary biology, designed to help biologists analyze comparative
+ data about organisms in a phylogenetic context.
+ </li>
+ </ul>
+ <h2>Logo</h2>
+ <p>
+ The logo displayed on the TreeBASE web-application has been adapted to match the
+ color style of the website. Please use the logo shown here for linking to or citing
+ TreeBASE.
+ <center>
+ <img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
+ </center>
+ </p>
+ </div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,33 +1,36 @@
-<div class="gutter">
-<p>
-TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and
-the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species,
-trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the
-public if they are used in a publication that is in press or published in a peer-reviewed scientific
-journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or
-in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using
-a special access code.
-</p>
-<p id="sponsors">
- <img src="images/aem.gif" alt="AEM" width="80" height="26" />
- <img src="images/whs.gif" alt="WHS" width="80" height="26" />
- <img src="images/evo.gif" alt="Evolution" width="80" height="26" />
- <img src="images/fgb.gif" alt="FGB" width="80" height="26" />
- <img src="images/gpprcg.gif" alt="GPPRCG" width="80" height="26" />
- <img src="images/invsys.gif" alt="Invertebrate Systematics" width="80" height="26" />
- <img src="images/psa.gif" alt="PSA" width="80" height="26" />
- <img src="images/tl.gif" alt="Lichenologist" width="80" height="26" />
- <img src="images/mpe.gif" alt="MPE" width="80" height="26" />
- <img src="images/msa.gif" alt="Mycologia" width="80" height="26" />
- <img src="images/mpg.jpg" alt="Mycological Progress" width="80" height="26" />
- <img src="images/myc.gif" alt="Mycological Research" width="80" height="26" />
- <img src="images/mycsci.gif" alt="Myoscience" width="80" height="26" />
- <img src="images/ode.gif" alt="ODE" width="80" height="26" />
- <img src="images/aps.jpg" alt="APS" width="80" height="26" />
- <img src="images/nebs.gif" alt="Rhodora" width="80" height="26" />
- <img src="images/stmyc.gif" alt="Mycology" width="80" height="26" />
- <img src="images/ssb.gif" alt="SSB" width="80" height="26" />
- <img src="images/aspt.gif" alt="Systematic Botany" width="80" height="26" />
- <img src="images/tq.gif" alt="Technical Quarterly" width="80" height="26" />
-</p>
+<div id="contentRight">
+ <div class="gutter">
+ <h1>Welcome to TreeBASE</h1>
+ <p>
+ TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and
+ the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species,
+ trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the
+ public if they are used in a publication that is in press or published in a peer-reviewed scientific
+ journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or
+ in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using
+ a special access code.
+ </p>
+ <p id="sponsors">
+ <img src="images/aem.gif" alt="AEM" width="80" height="26" />
+ <img src="images/whs.gif" alt="WHS" width="80" height="26" />
+ <img src="images/evo.gif" alt="Evolution" width="80" height="26" />
+ <img src="images/fgb.gif" alt="FGB" width="80" height="26" />
+ <img src="images/gpprcg.gif" alt="GPPRCG" width="80" height="26" />
+ <img src="images/invsys.gif" alt="Invertebrate Systematics" width="80" height="26" />
+ <img src="images/psa.gif" alt="PSA" width="80" height="26" />
+ <img src="images/tl.gif" alt="Lichenologist" width="80" height="26" />
+ <img src="images/mpe.gif" alt="MPE" width="80" height="26" />
+ <img src="images/msa.gif" alt="Mycologia" width="80" height="26" />
+ <img src="images/mpg.jpg" alt="Mycological Progress" width="80" height="26" />
+ <img src="images/myc.gif" alt="Mycological Research" width="80" height="26" />
+ <img src="images/mycsci.gif" alt="Myoscience" width="80" height="26" />
+ <img src="images/ode.gif" alt="ODE" width="80" height="26" />
+ <img src="images/aps.jpg" alt="APS" width="80" height="26" />
+ <img src="images/nebs.gif" alt="Rhodora" width="80" height="26" />
+ <img src="images/stmyc.gif" alt="Mycology" width="80" height="26" />
+ <img src="images/ssb.gif" alt="SSB" width="80" height="26" />
+ <img src="images/aspt.gif" alt="Systematic Botany" width="80" height="26" />
+ <img src="images/tq.gif" alt="Technical Quarterly" width="80" height="26" />
+ </p>
+ </div>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,115 +1,118 @@
-<div class="gutter">
- <table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
- <br/><strong>Vladimir Gapeyev</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
- <br/><strong>Youjun Guo</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
- <br/><strong>Hilmar Lapp</strong>
- <br/>Deployment Manager
- </td>
- <td>
- <img src="images/people/bpiel.gif" width="81" height="108" alt="William Piel"/>
- <br/><strong>William Piel</strong>
- <br/>Data Editor
- <br />Prototype Developer
- </td>
- <td>
- <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
- <br/><strong>Val Tannen</strong>
- <br/>Development Leader
- </td>
- <td>
- <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
- <br/><strong>Rutger Vos</strong>
- <br/>Developer
- <br/>API Design
- </td>
- </tr>
- </table>
-
- <table class="peopleTable">
- <thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
- <br/><strong>Lucie Chan</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
- <br/><strong>Shirley Cohen</strong>
- <br/>Student Researcher
- </td>
- <td>
- <img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
- <br/><strong>Mark J. Dominus</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
- <br/><strong>Michael Donoghue</strong>
- <br/>Conceptual Issues
- </td>
- <td>
- <img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
- <br/><strong>Torsten Eriksson</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
- <br/><strong>Madhusudan Gujral</strong>
- <br/>Developer
- </td>
- </tr>
- <tr>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
- <br/><strong>Chris Henze</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
- <br/><strong>Ken Rice</strong>
- <br/>Prototype Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
- <br/><strong>Jin Ruan</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
- <br/><strong>Mike Sanderson</strong>
- <br/>Conceptual Issues
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
- <br/><strong>Can van Tran</strong>
- <br/>Developer
- </td>
- <td>
- <img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
- <br/><strong>Tracy Zhao</strong>
- <br/>Developer
- </td>
- </tr>
- </table>
-
- <h2>Phyloinformatics Research Foundation Inc, Board</h2>
- <ul>
- <li>Michael Donoghue</li>
- <li>David Maddison</li>
- <li>William Piel</li>
- <li>Val Tannen</li>
- </ul>
+<div id="contentRight">
+ <div class="gutter">
+ <h1>People</h1>
+ <table class="peopleTable">
+ <thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
+ <br/><strong>Vladimir Gapeyev</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
+ <br/><strong>Youjun Guo</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
+ <br/><strong>Hilmar Lapp</strong>
+ <br/>Deployment Manager
+ </td>
+ <td>
+ <img src="images/people/bpiel.gif" width="81" height="108" alt="William Piel"/>
+ <br/><strong>William Piel</strong>
+ <br/>Data Editor
+ <br />Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
+ <br/><strong>Val Tannen</strong>
+ <br/>Development Leader
+ </td>
+ <td>
+ <img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
+ <br/><strong>Rutger Vos</strong>
+ <br/>Developer
+ <br/>API Design
+ </td>
+ </tr>
+ </table>
+
+ <table class="peopleTable">
+ <thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
+ <br/><strong>Lucie Chan</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
+ <br/><strong>Shirley Cohen</strong>
+ <br/>Student Researcher
+ </td>
+ <td>
+ <img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
+ <br/><strong>Mark J. Dominus</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
+ <br/><strong>Michael Donoghue</strong>
+ <br/>Conceptual Issues
+ </td>
+ <td>
+ <img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
+ <br/><strong>Torsten Eriksson</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
+ <br/><strong>Madhusudan Gujral</strong>
+ <br/>Developer
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
+ <br/><strong>Chris Henze</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
+ <br/><strong>Ken Rice</strong>
+ <br/>Prototype Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
+ <br/><strong>Jin Ruan</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
+ <br/><strong>Mike Sanderson</strong>
+ <br/>Conceptual Issues
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
+ <br/><strong>Can van Tran</strong>
+ <br/>Developer
+ </td>
+ <td>
+ <img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
+ <br/><strong>Tracy Zhao</strong>
+ <br/>Developer
+ </td>
+ </tr>
+ </table>
+
+ <h2>Phyloinformatics Research Foundation Inc, Board</h2>
+ <ul>
+ <li>Michael Donoghue</li>
+ <li>David Maddison</li>
+ <li>William Piel</li>
+ <li>Val Tannen</li>
+ </ul>
+ </div>
</div>
\ No newline at end of file
Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -0,0 +1,152 @@
+<div id="contentRight">
+ <div class="gutter">
+ <h1>Technology</h1>
+ <h2>Data Content</h2>
+ <p>
+ The primary data objects in TreeBASE are bibliographic references to published
+ phylogenetic studies, taxon by character data matrices, and phylogenetic trees
+ resulting from the analysis of such data matrices. Information is also
+ available that links data matrices and trees, including types of analyses
+ performed, software used, etc. Wherever possible, taxon labels are mapped to
+ uBio's name services and NCBI's taxonomy.
+ </p>
+ <h2>Implementation Technologies</h2>
+ <ul>
+ <li>Database: <a href="http://www.postgresql.org/">PostgreSQL 8.3</a></li>
+ <li>Programming language: Java (web-application), Perl (data migration and
+ maintenance)</li>
+ <li>Database ORM: <a href="http://www.hibernate.org/">Hibernate</a></li>
+ <li>Web-application framework: <a href="http://www.springsource.org/">
+ Spring</a></li>
+ <li>Submission file parsing: <a href="http://mesquiteproject.org/">
+ Mesquite</a></li>
+ <li>Tree Visualization: <a href="http://www.phylowidget.org/">
+ PhyloWidget</a></li>
+ </ul>
+ <h2>Source Code</h2>
+ <p>
+ Development of <a href="https://sourceforge.net/projects/treebase/">TreeBASE
+ is hosted at SourceForge</a>. All source code can be downloaded from the
+ <a href="https://sourceforge.net/projects/treebase/develop">TreeBASE
+ subversion repository</a> at SourceForge under a BSD license.
+ Documentation on installing and running TreeBASE can be
+ found at the <a href="https://sourceforge.net/apps/mediawiki/treebase/index.php?title=Main_Page">
+ TreeBASE wiki</a>.
+ </p>
+ <h2>Architecture</h2>
+ <p>
+ TreeBASE has a tiered Java-based architecture using the Hibernate and Spring
+ frameworks built on a PostgreSQL database. The following schematic illustrates
+ the content and features of this software stack:
+ </p>
+ <img src="images/architecture.jpeg"/>
+ <ol>
+ <li>
+ TreeBASE stores alignments, character matrices, and trees used for research
+ that is published in peer-reviewed journals and books.
+ </li>
+ <li>
+ Each study has one or more analyses; each analysis has one or more steps;
+ each step associates matrices and trees with algorithms and software.
+ </li>
+ <li>
+ Each row of sequence alignments or coded characters has a taxon label that
+ maps to leaf nodes on associated trees. Trees are hashed to allow topological
+ querying.
+ </li>
+ <li>
+ Each row in a character matrix can be subdivided into one or more row segments;
+ each row segment can have associated specimen, tissue, or gene sequence metadata.
+ </li>
+ <li>
+ Names in the rows of a matrix and in row segment metadata can independently
+ map to a dictionary of name variants, which maps to a taxonomy. This taxonomy will
+ be mapped to a classification tree in the next release.
+ </li>
+ </ol>
+ <h2>Reference</h2>
+ <p>
+ <strong>Blake, J. A., C. J. Bult, M. J. Donoghue, J. Humphries, and C. Fields.</strong>
+ 1994. Interoperability of biological databases: a meeting report.
+ <em>Syst. Biol.</em> <strong>43</strong>:585-589.
+ </p>
+ <p>
+ <strong>Donoghue, M. J.</strong>
+ 1994. Progress and prospects in reconstructing plant phylogeny.
+ <em>Ann. Missouri Bot. Gard.</em> <strong>81</strong>:405-418.
+ </p>
+ <p>
+ <strong>Donoghue, M. J. and D. D. Ackerly.</strong>
+ 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology.
+ <em>Phil. Trans. R. Soc. London B (in press).</em>
+ </p>
+ <p>
+ <strong>Maddison, W. P. and D. R. Maddison.</strong>
+ 1992.
+ <em>MacClade: Interactive Analysis of Phylogeny and Character Evolution, Vers. 3.0.</em>
+ Sunderland, MA: Sinauer Assoc.
+ </p>
+ <p>
+ <strong>Morell, V.</strong>
+ 1996. TreeBASE: the roots of phylogeny.
+ <em>Science</em> <strong>273</strong>: 569.
+ </p>
+ <p>
+ <strong>Piel, W. H.</strong>
+ 2003. "Phyloinformatics and Tree Networks." In:
+ <strong>Wu, C. H., P. Wang, and J. T. L. Wang,</strong> eds.
+ <em>Computational Biology and Genome Informatics</em>. World Scientific Press.
+ </p>
+ <p>
+ <strong>Piel, W. H., M. J. Donoghue, and M. J. Sanderson.</strong>
+ 2002. "TreeBASE: a database of phylogenetic knowledge." Pp. 41-47. In:
+ <strong>Shimura, J., K. L. Wilson, and D. Gordon,</strong> eds.
+ <em>To the interoperable "Catalog of Life" with partners Species 2000 Asia Oceanea.</em>
+ Research Report from the National Institute for Environmental Studies No. 171, Tsukuba, Japan.
+ </p>
+ <p>
+ <strong>Piel, W. H., M. J. Sanderson, and M. J. Donoghue.</strong>
+ 2003. The Small-World Dynamics of Tree Networks and Data Mining in Phyloinformatics.
+ <em>Bioinformatics</em>, <strong>19</strong>(9): 1162-1168.
+ </p>
+ <p>
+ <strong>Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson,
+ J. M. Porter, C. Von Dohlen, M. F. Wojciechowski & M. J. Donoghue.
+ </strong> 1993. The growth of phylogenetic information and the need for a phylogenetic database.
+ <em>Syst. Biol.</em> <strong>42</strong>:562-568.
+ </p>
+ <p>
+ <strong>Sanderson, M. J. and M. J. Donoghue.</strong>
+ 1996. The relationship between homoplasy and confidence in a phylogenetic tree. In:
+ <em>Homoplasy and the Evolutionary Process</em> (<strong>M. Sanderson and L. Hufford</strong>, eds.).
+ San Diego: Academic Press.
+ </p>
+ <p>
+ <strong>Sanderson, M. J., M. J. Donoghue, W. Piel, and T. Eriksson.</strong>
+ 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive
+ tool for browsing the phylogeny of life.
+ <em>American Journal of Botany</em>, <strong>81</strong>(6): 183.
+ </p>
+ <p>
+ <strong>Shan, H., K. G. Herbert, W. H. Piel, D. Shasha and J. T. L. Wang.</strong>
+ 2002. A Structure-Based Search Engine for Phylogenetic Databases.
+ <em>Proceedings of the 14th International Conference on Scientific and Statistical
+ Database Management (SSDBM 2002),</em> Edinburgh, Scotland, pp. 7-10.
+ </p>
+ <p>
+ <strong>Swofford, D. L.</strong>
+ 1993.
+ <em>PAUP: Phylogenetic Analysis Using Parsimony, Vers. 3.1.1.</em> Washington, DC: Smithsonian Institution.
+ </p>
+ <p>
+ <strong>Wang, J. T. L., H. Shan, D. Shasha, and W. H. Piel.</strong>
+ 2003. TreeRank: A Similarity Measure for Nearest Neighbor Searching in Phylogenetic Databases.
+ <em>Proceedings of the 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003),</em> Cambridge, MA, pp. 171-180.
+ </p>
+ <p>
+ <strong>Wang, J. T. L., H. Shan, D. Shasha and W. H. Piel.</strong>
+ 2005. Fast Structural Search in Phylogenetic Databases.
+ <em>Evolutionary Bioinformatics Online</em>, <strong>1</strong>: 37-46.
+ </p>
+ </div>
+</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,109 +1,122 @@
-<div class="gutter">
-<h2>URL API</h2>
-<p>
- The TreeBASE2 website provides users with simple ways to navigate the underlying data
- programmatically. This page describes the stateless web service interface and URL architecture
- that can be used to search the web site and obtain data in a variety of formats with rich semantics.
-</p>
-<h3>PhyloWS support</h3>
-<p>
- The site structure described here is designed to be compliant with the emerging
- <a href="http://evoinfo.nescent.org/PhyloWS">PhyloWS</a> standard. One of the tenets of the
- standard is that URLs contain a <strong>/phylows/</strong> delimiter below which the standard
- recommends a <a href="https://www.nescent.org/wg_evoinfo/PhyloWS/REST">simple API</a> to derefence
- phylogenetic data by their accession numbers. In the examples below, the url fragments come
- immediately below the <strong>/phylows/</strong> delimiter (everything between the
- <strong>http://</strong> and <strong>phylows</strong> is considered
- subject to change, likely to be stabilized using <a href="http://purl.org">purl</a> addresses).
-</p>
-<h3>Site sections</h3>
-<p>The data on the TreeBASE2 website are organized in four subsections:</p>
-<ul>
- <li><strong>taxon/</strong> <em>operational taxonomic units, taxonomic mappings and outlinks</em></li>
- <li><strong>matrix/</strong> <em>character state matrices, morphological character definitions</em></li>
- <li><strong>tree/</strong> <em>contains trees and tree nodes</em></li>
- <li><strong>study/</strong> <em>full submission records, including citation and analysis records</em></li>
-</ul>
-<p>
- Within those four sections, every item in the TreeBASE2 database can be de-referenced by appending
- the item's full identifier to the right section name. For example, <strong>tree/TB2:Tr2227</strong>
- represents a tree (and returns a simple RDF file to describe the tree). For some classes of objects,
- these short addresses can be passed a <strong>format</strong>
- parameter to specify in which data format to represent the object:
- <a href="/treebase-web/phylows/study/TB2:S1787?format=html">study/TB2:S1787?format=html</a>.
- Identifiers that match any of the following expressions can be represented as <strong>nexml</strong>,
- <strong>nexus</strong>, <strong>rdf</strong> or <strong>html</strong> (i.e. in a web page):
-</p>
-<ul>
- <li><strong>matrix/TB2:M[0-9]+</strong> <em>character state matrix</em></li>
- <li><strong>tree/TB2:Tr[0-9]+</strong> <em>phylogenetic tree</em></li>
- <li><strong>study/TB2:S[0-9]+</strong> <em>study record</em></li>
-</ul>
-<h3>NeXML support</h3>
-<p>
- The <strong>nexml</strong> and the <strong>rdf</strong> download options both use output
- generated by the java support libraries available from the
- <a href="http://nexml.org/nexml/java">nexml website</a>. The website uses the nexml annotation
- feature extensively to transmit all the metadata stored by the database. Nexml annotations
- are <a href="http://www.w3.org/TR/xhtml-rdfa-primer/">RDFa</a> compliant element structures
- that use <a href="http://www.w3.org/TR/curie/">CURIE</a> strings to identify metadata properties,
- and @content attributes to store the property value. For example, this (simplified) annotation:
- <strong>
- <meta content="uBio:2538170" property="tb:identifier.ubio"/>
- </strong>
- means that the element that encloses it has a special kind of identifier attached to it, namely
- one that TreeBASE recognizes as originating in <a href="/treebase-web/phylows/taxon/uBio:2538170">uBio</a>.
-</p>
-<p>
- The salient part is
- the CURIE string predicate <strong>tb:identifier.ubio</strong>, which is one of a
- <a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">long list</a> of
- proposed predicates that are written in TreeBASE's NeXML output and can be used as
- <a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> search predicates. The predicates
- proposed (and now experimentally transmitted) are intended to be subclasses of predicates
- from commonly used vocabularies. For example, <strong>tb:identifier.ubio</strong> inherits from
- <a href="http://dublincore.org/documents/dcmi-terms/#terms-identifier">dcterms:identifier</a> and
- so any of the latter's semantics apply to the former, which is refined to indicate that the
- value is a uBio namebank ID.
-</p>
-<h3>Searching</h3>
-<p>
- The TreeBASE website can be searched using a subset of constructs from the
- <a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> specification. Specifically,
- the predicates
- <a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">listed here with
- an asterisk</a> can be used in statements in the site section they apply to, such that, for example
- a taxon can be retrieved by its ncbi ID like so:
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.identifier.ncbi=<em><ncbi taxon id></em></strong>
+<div id="contentRight">
+ <div class="gutter">
+ <h1>Data Access</h1>
+ <h2>URL API</h2>
+ <p>
+ The TreeBASE2 website provides users with simple ways to navigate the underlying data
+ programmatically. This page describes the stateless web service interface and URL architecture
+ that can be used to search the web site and obtain data in a variety of formats with rich semantics.
+ </p>
+ <h3>PhyloWS support</h3>
+ <p>
+ The site structure described here is designed to be compliant with the emerging
+ <a href="http://evoinfo.nescent.org/PhyloWS">PhyloWS</a> standard. One of the tenets of the
+ standard is that URLs contain a <strong>/phylows/</strong> delimiter below which the standard
+ recommends a <a href="https://www.nescent.org/wg_evoinfo/PhyloWS/REST">simple API</a> to derefence
+ phylogenetic data by their accession numbers. In the examples below, the url fragments come
+ immediately below the <strong>/phylows/</strong> delimiter (everything between the
+ <strong>http://</strong> and <strong>phylows</strong> is considered
+ subject to change, likely to be stabilized using <a href="http://purl.org">purl</a> addresses).
+ </p>
+ <h3>Site sections</h3>
+ <p>The data on the TreeBASE2 website are organized in four subsections:</p>
+ <ul>
+ <li><strong>taxon/</strong> <em>operational taxonomic units, taxonomic mappings and outlinks</em></li>
+ <li><strong>matrix/</strong> <em>character state matrices, morphological character definitions</em></li>
+ <li><strong>tree/</strong> <em>contains trees and tree nodes</em></li>
+ <li><strong>study/</strong> <em>full submission records, including citation and analysis records</em></li>
+ </ul>
+ <p>
+ Within those four sections, every item in the TreeBASE2 database can be de-referenced by appending
+ the item's full identifier to the right section name. For example, <strong>tree/TB2:Tr2227</strong>
+ represents a tree (and returns a simple RDF file to describe the tree). For some classes of objects,
+ these short addresses can be passed a <strong>format</strong>
+ parameter to specify in which data format to represent the object:
+ <a href="/treebase-web/phylows/study/TB2:S1787?format=html">study/TB2:S1787?format=html</a>.
+ Identifiers that match any of the following expressions can be represented as <strong>nexml</strong>,
+ <strong>nexus</strong>, <strong>rdf</strong> or <strong>html</strong> (i.e. in a web page):
+ </p>
+ <ul>
+ <li><strong>matrix/TB2:M[0-9]+</strong> <em>character state matrix</em></li>
+ <li><strong>tree/TB2:Tr[0-9]+</strong> <em>phylogenetic tree</em></li>
+ <li><strong>study/TB2:S[0-9]+</strong> <em>study record</em></li>
+ </ul>
+ <h3>NeXML support</h3>
+ <p>
+ The <strong>nexml</strong> and the <strong>rdf</strong> download options both use output
+ generated by the java support libraries available from the
+ <a href="http://nexml.org/nexml/java">nexml website</a>. The website uses the nexml annotation
+ feature extensively to transmit all the metadata stored by the database. Nexml annotations
+ are <a href="http://www.w3.org/TR/xhtml-rdfa-primer/">RDFa</a> compliant element structures
+ that use <a href="http://www.w3.org/TR/curie/">CURIE</a> strings to identify metadata properties,
+ and @content attributes to store the property value. For example, this (simplified) annotation:
+ <strong>
+ <meta content="uBio:2538170" property="tb:identifier.ubio"/>
+ </strong>
+ means that the element that encloses it has a special kind of identifier attached to it, namely
+ one that TreeBASE recognizes as originating in <a href="/treebase-web/phylows/taxon/uBio:2538170">uBio</a>.
+ </p>
+ <p>
+ The salient part is
+ the CURIE string predicate <strong>tb:identifier.ubio</strong>, which is one of a
+ <a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">long list</a> of
+ proposed predicates that are written in TreeBASE's NeXML output and can be used as
+ <a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> search predicates. The predicates
+ proposed (and now experimentally transmitted) are intended to be subclasses of predicates
+ from commonly used vocabularies. For example, <strong>tb:identifier.ubio</strong> inherits from
+ <a href="http://dublincore.org/documents/dcmi-terms/#terms-identifier">dcterms:identifier</a> and
+ so any of the latter's semantics apply to the former, which is refined to indicate that the
+ value is a uBio namebank ID.
+ </p>
+ <h3>Searching</h3>
+ <p>
+ The TreeBASE website can be searched using a subset of constructs from the
+ <a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> specification. Specifically,
+ the predicates
+ <a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">listed here with
+ an asterisk</a> can be used in statements in the site section they apply to, such that, for example
+ a taxon can be retrieved by its ncbi ID like so:
+ </p>
+ <div style="background-color:;padding:10px">
+ <strong>taxon/find?query=tb.identifier.ncbi=<em><ncbi taxon id></em></strong>
+ </div>
+ <p>
+ or by its name like so:
+ </p>
+ <div style="background-color:;padding:10px">
+ <strong>taxon/find?query=tb.title.taxon=<em><name></em></strong>
+ </div>
+ <p>
+ or using an exact match
+ (<strong>==</strong>) or a case-insensitive one (<strong>=/ignoreCase</strong>). These statements
+ can be combined with boolean <strong>and</strong>, <strong>or</strong> and <strong>not</strong>.
+ For example:
+ </p>
+ <div style="background-color:;padding:10px">
+ <strong>study/find?query=dcterms.contributor=Huelsenbeck or dcterms.contributor=Ronquist</strong>
+ </div>
+ <p>
+ Finally, searching can be modified to project the results from one section info those of another. The
+ effect is roughly the same as switching between tabs in the search section: if the results are a
+ list of tree and you click on the matrix search tab, the trees are converted to the set of matrices
+ on which the trees are based. This behaviour can be used by specifying the
+ <strong>recordSchema=<section></strong> argument, i.e.:
+ </p>
+ <div style="background-color:;padding:10px">
+ <strong>taxon/find?query=dcterms.title=="Homo sapiens"&recordSchema=tree</strong>
+ </div>
+ <p>
+ returns all the trees that have <em>Homo sapiens</em> in them.
+ By default, all these queries return a web page, but with a <strong>format=rss1</strong> argument
+ the search results are listed in an RDF compatible RSS1.0 file, i.e.:
+ </p>
+ <div style="background-color:;padding:10px">
+ <strong>taxon/find?query=tb.title.taxon=<em><name></em>&format=rss1</strong>
+ </div>
+ <p>
+ The returned results in RSS1.0 use the short urls of the form <strong><section>/<id></strong>, whose
+ returned resource descriptions (like <a href="/treebase-web/phylows/tree/TB2:Tr2227">
+ this</a> one) need to be scanned to discover suitable serialization formats.
+ </p>
</div>
- or by its name like so:
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.title.taxon=<em><name></em></strong>
- </div>
- or using an exact match
- (<strong>==</strong>) or a case-insensitive one (<strong>=/ignoreCase</strong>). These statements
- can be combined with boolean <strong>and</strong>, <strong>or</strong> and <strong>not</strong>.
- For example:
- <div style="background-color:;padding:10px">
- <strong>study/find?query=dcterms.contributor=Huelsenbeck or dcterms.contributor=Ronquist</strong>
- </div>
- Finally, searching can be modified to project the results from one section info those of another. The
- effect is roughly the same as switching between tabs in the search section: if the results are a
- list of tree and you click on the matrix search tab, the trees are converted to the set of matrices
- on which the trees are based. This behaviour can be used by specifying the
- <strong>recordSchema=<section></strong> argument, i.e.:
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=dcterms.title=="Homo sapiens"&recordSchema=tree</strong>
- </div>
- returns all the trees that have <em>Homo sapiens</em> in them.
- By default, all these queries return a web page, but with a <strong>format=rss1</strong> argument
- the search results are listed in an RDF compatible RSS1.0 file, i.e.:
- <div style="background-color:;padding:10px">
- <strong>taxon/find?query=tb.title.taxon=<em><name></em>&format=rss1</strong>
- </div>
- The returned results in RSS1.0 use the short urls of the form <strong><section>/<id></strong>, whose
- returned resource descriptions (like <a href="/treebase-web/phylows/tree/TB2:Tr2227">
- this</a> one) need to be scanned to discover suitable serialization formats.
-</p>
</div>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml 2010-03-12 00:02:30 UTC (rev 547)
@@ -859,6 +859,7 @@
<prop key="/login.html">filenameController</prop>
<prop key="/urlAPI.html">filenameController</prop>
<prop key="/people.html">filenameController</prop>
+ <prop key="/technology.html">filenameController</prop>
<prop key="/user/viewXML.html">filenameController</prop>
<prop key="/test/phylowidget.html">filenameController</prop>
Modified: trunk/treebase-web/src/main/webapp/common/footer.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/footer.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/footer.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,8 +1,30 @@
<%@ include file="/common/taglibs.jsp" %>
-<p style="text-align:center"><!-- Revision <%= org.cipres.treebase.Version.VCSID %> -->
-<br />
- <a href="http://validator.w3.org/check?uri=referer"><img src="<fmt:message key="icons.xhtml" />" alt="XHTML" title="Validate page markup" class="iconButton" style="vertical-align:middle"/></a>
- <a href="http://jigsaw.w3.org/css-validator/check/referer"><img src="<fmt:message key="icons.css"/>" alt="CSS" title="Validate page styles" class="iconButton" style="vertical-align:middle"/></a><br />
- <a href="http://www.nescent.org/"><img src="<c:url value="/images/nescent_logo.gif"/>" alt="NESCent" width="101" height="83" border="0" /></a>
-</p>
\ No newline at end of file
+<p class="footerLogo"><!-- Revision <%= org.cipres.treebase.Version.VCSID %> -->
+ <a href="http://www.nescent.org/">
+ <img
+ src="<c:url value="/images/nescent_logo.png"/>"
+ alt="NESCent"
+ width="83"
+ height="83"
+ border="0" />
+ </a>
+</p>
+<p style="text-align:center">
+ <a href="http://validator.w3.org/check?uri=referer">
+ <img
+ src="<fmt:message key="icons.xhtml" />"
+ alt="XHTML"
+ title="Validate page markup"
+ class="iconButton"
+ style="vertical-align:middle"/>
+ </a>
+ <a href="http://jigsaw.w3.org/css-validator/check/referer">
+ <img
+ src="<fmt:message key="icons.css"/>"
+ alt="CSS"
+ title="Validate page styles"
+ class="iconButton"
+ style="vertical-align:middle"/>
+ </a>
+</p>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/common/header.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/header.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/header.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,4 +1,8 @@
<%@ include file="/common/taglibs.jsp"%>
-<h1><a href="<c:url value="/home.html"/>"><img src="<c:url value="/images/logo.gif"/>" alt="TreeBase Logo" width="523" height="112" border="0" /></a></h1>
-
+<h1>
+ <a href="<c:url value="/home.html"/>">
+ <img src="<c:url value="/images/logo.gif"/>" alt="TreeBase Logo" width="523" height="112" border="0" />
+ </a>
+</h1>
+<img src="images/gradient.jpg" style="width:100%;height:10px"/>
Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,20 +1,22 @@
<%@ include file="/common/taglibs.jsp"%>
-
-<div class="gutter">
- <div id="navcontainer">
- <ul id="navlist">
- <li><a href="<c:url value="/search/studySearch.html"/>"><fmt:message key="nav.search.treebase"/></a></li>
- <li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>
- <li><span style="font-weight:bold;border-bottom: 1px solid #CCC;padding:3px;display:block"><fmt:message key="nav.about"/></span>
- <ul id="innerNavlist">
- <li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
- <li><a href="#"><fmt:message key="nav.technology"/></a></li>
- <li><a href="<c:url value="/people.html"/>"><fmt:message key="nav.people"/></a></li>
- <li><a href="#"><fmt:message key="nav.partnerships"/></a></li>
- </ul>
- </li>
- <li><a href="<c:url value="/urlAPI.html"/>"><fmt:message key="nav.dataaccess"/></a></li>
- <li><a href="#"><fmt:message key="nav.contact"/></a></li>
- </ul>
+<div>
+ <div class="gutter" id="sidebarLeftGutter">
+ <div id="navcontainer">
+ <ul id="navlist">
+ <li><a href="<c:url value="/search/studySearch.html"/>"><fmt:message key="nav.search.treebase"/></a></li>
+ <li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>
+ <li><span class="navlistHeading"><fmt:message key="nav.about"/></span>
+ <ul id="innerNavlist">
+ <li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
+ <li><a href="<c:url value="/technology.html"/>"><fmt:message key="nav.technology"/></a></li>
+ <li><a href="<c:url value="/people.html"/>"><fmt:message key="nav.people"/></a></li>
+ <li><a href="#"><fmt:message key="nav.partnerships"/></a></li>
+ </ul>
+ </li>
+ <li><a href="<c:url value="/urlAPI.html"/>"><fmt:message key="nav.dataaccess"/></a></li>
+ <li><a href="#"><fmt:message key="nav.contact"/></a></li>
+ </ul>
+ </div>
</div>
-</div>
+ <img src="<c:url value="images/footer_bg.gif"/>" style="width:100%"/>
+</div>
\ No newline at end of file
Added: trunk/treebase-web/src/main/webapp/images/TreeBASE.png
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/TreeBASE.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/architecture.jpeg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/architecture.jpeg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/gradient.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/gradient.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/nescent_logo.png
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/nescent_logo.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/anon.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/anon.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/krice.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/krice.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: trunk/treebase-web/src/main/webapp/styles/displaytag.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/displaytag.css 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/styles/displaytag.css 2010-03-12 00:02:30 UTC (rev 547)
@@ -15,8 +15,6 @@
width: 80%;
}
-
-
table.list {
border: 1px solid #808080;
border-collapse: collapse;
@@ -24,18 +22,18 @@
width: 100%;
background: white;
}
+
table.list td {
- padding-left: 3px;
+ padding-left: 3px
}
-
table.list th {
background-color: silver;
padding: 2px;
padding-left: 3px;
border-bottom: 1px solid black;
text-align: left;
- color: black;
+ color: black;
white-space: nowrap
}
@@ -162,4 +160,4 @@
table.detail th {
text-align: right;
padding: 0px 3px 0px 0px;
-}
+}
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css 2010-03-12 00:02:30 UTC (rev 547)
@@ -1,31 +1,32 @@
body {
margin: 0;
padding: 0;
- font-family: Verdana, sans-serif;
- font-size: small;
+ font-family: "Helvetica Neue", GillSans, helvetica, "lucida sans", arial, sans-serif;
+ font-size: 80%;
+ line-height: 1.5em
}
/* Link Styles
*******************************************************************************************/
-#content a:link {
+#content a:link, #contentRight a:link {
color: #003366;
text-decoration: none;
font-weight: bold
}
-#content a:visited {
+#content a:visited, #contentRight a:visited {
color: #3863a4;
text-decoration: none;
font-weight: bold
}
-#content a:hover {
+#content a:hover, #contentRight a:hover {
border-bottom: 2px solid orangered;
font-weight: bold
}
-#content a:active {
+#content a:active, #contentRight a:active {
text-decoration: underline;
font-weight: bold
}
@@ -34,44 +35,59 @@
*******************************************************************************************/
h1, h2, h3 {
- color: #003366;
+ color: #003366
}
#content h2 {
- background: #BED1E5 url(../img/off_bg.gif) repeat-x left top;
+ background: #BED1E5 url("../images/off_bg.gif") repeat-x left top;
padding: 5px !important
}
+#contentRight h1 {
+ margin: 0px;
+ padding: 15px;
+ border-top: 1px solid silver;
+ background-image: url("../images/footer_bg.gif")
+}
+
+#contentRight h2, #contentRight h3, #contentRight p {
+ padding-left: 15px !important;
+ padding-right: 15px !important;
+ padding-top: 15px !important
+}
+
+#contentRight h2 {
+ border-top: 1px solid silver
+}
+
/* Page Structure/Layout
***************************...
[truncated message content] |
