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-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
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<td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
- <td class="bg"><img src="images/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
+ <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
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<p> JABAWS currently provides access to the following programs:</p>\r
<p>Multiple Sequence Alignement </p>\r
<ul>\r
- <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>\r
- <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.52)</li>\r
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>\r
- <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
- <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
- <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
+ <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>\r
+ <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.52)</li>\r
+ <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>\r
+ <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
+ <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
+ <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
+ <li><a href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>\r
+ <li><a href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</li>\r
</ul>\r
<p>Protein Secondary structure prediction</p>\r
<ul>\r
<li><span style="color:black; font-weight:normal; text-align:left;">RNAalifold from <a href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a></span> (2.0) </li>\r
</ul>\r
\r
-All these codes including Jronn and AAcon are available at the <a href="http://www.compbio.dundee.ac.uk/download">Download</a> section (registration is required).\r
+All these codes including Jronn and AAcon are available at the <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
+section (registration is required).\r
\r
-<h3><a name="jaba2.1"/></a>What is new in JABAWS 2.1? </h3>\r
-<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong><p>JABAWS 2.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2.0</a>. These are listed below:</p>\r
+\r
+\r
+<h3><a name="jaba2.1"/>What is new in JABAWS 2.1? </h3>\r
+<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong>\r
+<p>Several new web services are available in this version of JABAWS:</p>\r
+<ul>\r
+ <li>Two multiple sequence aligners: MSAprobs and GLprobs. Both services return the standard Alignment object</li>\r
+ <li>RNAalifoldWS returns RNAStructScoreManager which is the standard ScoreManager objects with several additional methods.</li>\r
+ <li>\r
+ JpredWS returns the JpredAligment object which is the standard Alignment with additional methods for extracting \r
+ Jpred predictions. These predictions are supplied as additional sequences in the aligment.\r
+ </li>\r
+</ul>\r
+\r
+<p>Some bugs have been fixed and several improvements have been done:</p>\r
+<ul>\r
+ <li>WS status servlet returns version and some additional information on each web service</li>\r
+ <li>a bug with path to help in the client</li>\r
+ <li>Fix two bug with the Google Analytics library: no-stop due to running thread</li>\r
+ <li>GoogleAnalytics gets proper JABAWS version</li>\r
+</ul>\r
+\r
+\r
+<strong>JABAWS Version 2.0.1 (Released 2nd Jul 2013)</strong><p>JABAWS 2.0.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2.0</a>. These are listed below:</p>\r
<ul>\r
<li>Disembl returned swapped strings for HOTLOOPS and REM465</li>\r
<li>Jronn failed to process jobs with more than 3 sequences</li>\r
- <li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>\r
+ <li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>\r
<li>Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores \r
in one call</li>\r
<li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties</li>\r
git://source.jalview.org / jabaws.git / blobdiff