Merge pull request #217 from eppic-team/newpub

Adding new publication and fixing docs
eppic-team · May 1, 2018 · 472e8bd · 472e8bd
2 parents 5bfb708 + 712659b
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diff --git a/eppic-cli/README.md b/eppic-cli/README.md
@@ -5,11 +5,11 @@ http://www.eppic-web.org
 
 If you use this software for your research, please cite:
 
-> Duarte JM, Srebniak A, Schärer MA and Capitani G, Protein interface 
-> classification by evolutionary analysis, BMC Bioinformatics 2012 13:334 
-> doi:10.1186/1471-2105-13-334 
+> Bliven S, Lafita A, Parker A, Capitani G, Duarte JM (2018) 
+> Automated evaluation of quaternary structures from protein crystals. 
+> PLoS Comput Biol 14(4): e1006104. https://doi.org/10.1371/journal.pcbi.1006104 
 >
-> http://www.biomedcentral.com/1471-2105/13/334
+> http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006104
 
 The software is released under the GNU General Public License (GPL).
 
@@ -68,7 +68,7 @@ EPPIC is a java program that should work in any Unix like system.
 It has only been tested in Linux but there is no reason why it should
 not work in MacOSX.
 
-You need Java 1.7 or newer. Most systems will have java already 
+You need Java 1.8 or newer. Most systems will have java already 
 installed. Otherwise get it by installing the OpenJDK package in 
 Linux or downloading java from http://java.com/en/download/index.jsp
 

diff --git a/eppic-wui/src/main/java/ch/systemsx/sybit/crkwebui/client/about/gui/windows/AboutWindow.java b/eppic-wui/src/main/java/ch/systemsx/sybit/crkwebui/client/about/gui/windows/AboutWindow.java
@@ -43,16 +43,6 @@ public AboutWindow(WindowData windowData)
 				"</tr>" +
 				"<tr>" +
 				"<td></td>" +
-				"<td>" +
-				"Crystallography and Structural Bioinformatics Group<br>" +
-				"Laboratory of Biomolecular Research<br>" +
-				"Paul Scherrer Institut<br>" +
-				"Villigen PSI<br>" +
-				"Switzerland" +
-				"</td>" +
-				"</tr>" +
-				"<tr>" +
-				"<td></td>" +
 				"<td>This server is intended for research purposes only. " +
 				"It is a non-profit service to the scientific community, " +
 				"provided on an \"as is\" basis without any warranty, expressed or implied. " +

diff --git a/.../src/main/java/ch/systemsx/sybit/crkwebui/client/commons/appdata/AppProperties.properties b/.../src/main/java/ch/systemsx/sybit/crkwebui/client/commons/appdata/AppProperties.properties
@@ -61,7 +61,7 @@ input_pdb_code_radio=PDB code
 input_pdb_input_type=
 input_citation=If you use this service for your research please cite
 input_citation_link_tooltip=Click to open publication
-input_citation_link_text=Duarte et al., BMC Bioinformatics 2012
+input_citation_link_text=Bliven et al., PLoS Computational Biology 2018
 input_news_header=NEWS
 		
 parameters_allignment=Alignment
@@ -205,7 +205,7 @@ navigation_panel_change_viewer_link_label=3D Viewer
 bottom_panel_disclaimer_link_label=Disclaimer
 bottom_panel_about_link_label=About us
 bottom_panel_contact_link_label=Contact
-bottom_panel_about_link=https://www.psi.ch/lbr/capitani-guido
+bottom_panel_about_link=http://www.rcsb.org
 bottom_panel_contact_email=eppic@systemsx.ch
 bottom_panel_status_error_refresh_page=Please refresh the page
 

diff --git a/eppic-wui/src/main/resources/META-INF/email.properties b/eppic-wui/src/main/resources/META-INF/email.properties
@@ -26,5 +26,5 @@ To see the results please go to your job's unique URL:\n\n\
   %s#id/%s \n\n\
 This URL is not public and only known to you. Your job will be stored in our server for at least a month. After that the URL will not work anymore. \n\n\
 Thanks for using the EPPIC service. If you find the service useful please cite our paper: \n\n\
-  http://www.biomedcentral.com/1471-2105/13/334 \n\n\
+  http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006104 \n\n\
 The EPPIC team
diff --git a/eppic-wui/src/main/resources/META-INF/server.properties b/eppic-wui/src/main/resources/META-INF/server.properties
@@ -55,7 +55,7 @@ max_file_upload_size=50
 pdb_link_url=http://www.pdb.org/pdb/explore/explore.do?structureId=
 uniprot_link_url=http://www.uniprot.org/uniprot/
 uniparc_link_url=http://www.uniprot.org/uniparc/
-publication_link_url=http://www.biomedcentral.com/1471-2105/13/334
+publication_link_url=http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006104
 wikipedia_link_url=http://en.wikipedia.org/wiki/
 
 use_precompiled=true

diff --git a/eppic-wui/src/main/webapp/downloads.html b/eppic-wui/src/main/webapp/downloads.html
@@ -55,7 +55,6 @@ <h2>Downloading mmCIF files of interfaces or assemblies</h2>
 			<p>
 				<code>http://www.eppic-web.org/ewui/ewui/fileDownload?type=assembly&amp;id=&lt;PDB_code&gt;&amp;assemblyId=&lt;Assembly_id&gt;&amp;coordsFormat=cif</code>
 			</p>
-		</p>
 		<p>
 			Please note that the server uses gzip encoding. Thus if you use wget, you will need the following syntax:
 		</p>
@@ -147,10 +146,10 @@ <h2>Datasets</h2>
 		</p>
 
 		<ul>
-			<li><a href="../downloads/DCxtal.txt"  target="_blank">DCxtal set</a>: a set of
+			<li><a href="https://github.com/eppic-team/datasets/blob/master/data/DCxtal.txt"  target="_blank">DCxtal set</a>: a set of
 				crystal contacts with large interface areas (&gt;1000Å<sup>2</sup>)
 			</li>
-			<li><a href="../downloads/DCbio.txt"  target="_blank">DCbio set</a>: a set of
+			<li><a href="https://github.com/eppic-team/datasets/blob/master/data/DCbio.txt"  target="_blank">DCbio set</a>: a set of
 				biologically relevant interfaces with relatively small interface
 				areas (&lt;2000Å<sup>2</sup>)</li>
 		</ul>
@@ -179,7 +178,7 @@ <h2>Datasets</h2>
 			oligomeric structures. It can also be downloaded as text file here:
 		</p>
 		<ul>
-			<li><a href="../downloads/TMPbio.txt"  target="_blank">TMPbio set</a>: a set of
+			<li><a href="https://github.com/eppic-team/datasets/blob/master/data/TMPbio.txt"  target="_blank">TMPbio set</a>: a set of
 				biological interfaces spanning the transmembrane region, from both
 				alpha and beta TMP subclasses</li>
 		</ul>
@@ -198,38 +197,33 @@ <h2>Datasets</h2>
 			XtalMany and BioMany can be downloaded as text files here:
 		</p>
 		<ul>
-			<li><a href="../downloads/ManyXtal.txt"  target="_blank">XtalMany set</a>: a large
+			<li><a href="https://github.com/eppic-team/datasets/blob/master/data/ManyXtal.txt"  target="_blank">XtalMany set</a>: a large
 				dataset of crystal contacts</li>
 		</ul>
 		<ul>
-			<li><a href="../downloads/ManyBio.txt"  target="_blank">BioMany set</a>: a large
+			<li><a href="https://github.com/eppic-team/datasets/blob/master/data/ManyBio.txt"  target="_blank">BioMany set</a>: a large
 				dataset of biological interfaces</li>
 		</ul>
 
-
+		<p>
+			In <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006104" target="_blank">Bliven et al. 2018</a> we
+			used a dataset of assemblies extracted from the bioassembly annotations in the PDB (only the 1st bioassembly "PDB1" was used).
+			Bioassemblies with good consensus within their 70% sequence clusters were taken, see full details in
+			<a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006104" target="_blank">paper</a>.
+		</p>
+		<ul>
+			<li><a href="https://github.com/eppic-team/datasets/blob/master/data/benchmark-pdb1_clusters.csv" target="_blank">
+				Consensus assemblies (PDB1 clusters)</a> </li>
+		</ul>
 
 		<p>
 			Please note that the original publications also contain the datasets including
 			our full annotations. However we cannot update those if we find any mistakes.
-			The downloadable datasets here represent the most up-to-date and best
+			The datasets linked here represent the most up-to-date and best
 			validated sets. Please use these ones preferentially to the ones available in the
 			original publications.
 		</p>
-		<p>
-			For completeness this is a full changelog of any mistakes that we have found
-			since publication:
 
-		</p>
-		<ul>
-			<li>
-			DCbio set: 3f3e was removed because it is a membrane protein and additionally the experimental evidence
-			was not sufficiently clear; 1ytq was removed because it has a clear domain swap
-			</li>
-			<li>
-			TMPbio set: the relevant interface for 2wsw is 2, as listed in the publication. The downloadable dataset
-			file has been corrected accordingly
-			</li>
-		</ul>
 
 	</div>
 </body>
diff --git a/eppic-wui/src/main/webapp/faq.html b/eppic-wui/src/main/webapp/faq.html
@@ -60,9 +60,9 @@ <h4>Is it open-source? Is it published open-access?</h4>
 			<h4>How should I cite EPPIC?</h4>
 			<p>
 				The main paper describing the EPPIC method is <a
-					href="http://www.biomedcentral.com/1471-2105/13/334"
-					target="_blank"> Duarte JM, Srebniak A, Schaerer MA, Capitani
-					G, BMC Bioinformatics 2012</a>. As well as citing the paper it is
+					href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006104"
+					target="_blank"> Bliven S, Lafita A, Parker A, Capitani G, Duarte JM,
+				PLoS Computational Biology 2018</a>. As well as citing the paper it is
 				important that one cites the <strong>EPPIC software version</strong>
 				(top right below the logo in results page) and even more important
 				the <strong>UniProt database version</strong> (monthly releases)
@@ -293,7 +293,11 @@ <h4>How does EPPIC work?</h4>
 				indicators based on the sequence entropy of homolog sequences. Both
 				aim at detecting differential selection pressure between interface
 				core and rim or rest of surface. For further information please
-				refer to <a href="http://www.biomedcentral.com/1471-2105/13/334"
+				refer to <a
+					href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006104"
+					target="_blank"> Bliven S, Lafita A, Parker A, Capitani G, Duarte JM,
+				PLoS Computational Biology 2018</a>
+				and <a href="http://www.biomedcentral.com/1471-2105/13/334"
 					target="_blank"> Duarte JM, Srebniak A, Schaerer MA, Capitani
 					G, BMC Bioinformatics 2012</a>.
 			</p>

diff --git a/eppic-wui/src/main/webapp/footer.html b/eppic-wui/src/main/webapp/footer.html
@@ -9,7 +9,7 @@
 	<div class="eppic-iframe-footer-left">
 		<p>
 			Please cite this <a
-				href="http://www.biomedcentral.com/1471-2105/13/334" target="_blank">paper</a>
+				href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006104" target="_blank">paper</a>
 			if you use this service.
 		</p>
 		<p>

diff --git a/eppic-wui/src/main/webapp/help.html b/eppic-wui/src/main/webapp/help.html
@@ -35,6 +35,7 @@ <h1>The EPPIC server</h1>
 					<li><a href="#seq-clusters">Searching similar structures</a></li>
 					<li><a href="#known-issues">Known issues</a></li>
 					<li><a href="#misc">Miscellaneous</a></li>
+					<li><a href="#funding">Funding</a></li>
 				</ul>
 			</div>
 
@@ -678,6 +679,19 @@ <h3 id="download-results">Downloading results in XML format</h3>
 		</p>
 
 
+		<h2 id="funding">Funding</h2>
+		<p>
+			Funding to the project came initially from the
+			<a href="https://www.psi.ch" target="_blank">Paul Scherrer Institute</a> (2010-2014) and later
+			from the <a href="http://www.snf.ch/" target="_blank">Swiss National Science Foundation</a> (2013-2016).
+			Since 2016 the <a href="http://www.rcsb.org/pages/about-us/index" target="_blank">RCSB Protein Data Bank</a>
+			has supported the project and enabled its continuation.
+			The RCSB PDB is funded by a grant (DBI-1338415) from the
+			<a href="http://www.nsf.gov/" target="_blank">National Science Foundation</a>, the
+			<a href="http://www.nih.gov/" target="_blank">National Institutes of Health</a>, and the
+			<a href="http://science.energy.gov/" target="_blank">US Department of Energy</a>.
+		</p>
+
 
 	</div>
 </body>
diff --git a/eppic-wui/src/main/webapp/publications.html b/eppic-wui/src/main/webapp/publications.html
@@ -47,10 +47,6 @@ <h2>Main paper describing the EPPIC method and the DCxtal and
 			DOI: <a target="_blank"
 				href="http://www.biomedcentral.com/1471-2105/13/334">10.1186/1471-2105-13-334</a>
 		</p>
-		<p>
-			<i>Please cite this paper if you use any service from this web
-				server</i>
-		</p>
 
 
 
@@ -86,6 +82,23 @@ <h2>PDB-wide assessment</h2>
 		</p>
 
 
+		<h2>Assembly prediction, version 3</h2>
+		<p>
+			<b>Automated evaluation of quaternary structures from protein crystals</b>
+		</p>
+		<p>Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M. Duarte</p>
+		<p>
+			<i>PLoS Computational Biology,</i> 2018, 14(4): e1006104
+		</p>
+		<p>
+			DOI: <a target="_blank"
+					href="https://doi.org/10.1371/journal.pcbi.1006104">10.1371/journal.pcbi.1006104</a>
+		</p>
+		<p>
+			<i>Please cite this paper if you use any service from this web
+				server</i>
+		</p>
+
 
 	</div>
 </body>
diff --git a/eppic-wui/src/main/webapp/releases.html b/eppic-wui/src/main/webapp/releases.html
@@ -14,6 +14,14 @@
 
 		<h1>Release log</h1>
 
+		<h2>3.0.5 - 1st May 2018</h2>
+		<ul class="eppic-iframe-log-list">
+			<li>BioJava dependency updated to next major release 5.0.0.</li>
+			<li>Redundancy in interfaces now handled better for virus capsid entries.</li>
+			<li>Bugfix: PDB files with water-only chains should run correctly now</li>
+			<li>Some bug fixes.</li>
+		</ul>
+
 		<h2>3.0.4 - 9th February 2018</h2>
 		<ul class="eppic-iframe-log-list">
 			<li>Assembly probabilities are now normalised.</li>