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7 <title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>
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20 <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>
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21 <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>
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31 <div id="supermenu">
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32 <a class="newa" href="index.html">Home</a>
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33 <a class="newa" href="quick_start.html">Getting Started</a>
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34 <a class="newpressed" href="man_about.html">Manual</a>
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37 <a class="newpressed" href="man_about.html">About</a>
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38 <a class="newa" href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>
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39 <a class="newa" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>
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40 <a class="newa" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>
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41 <a class="newa" href="man_configuration.html" >Configure JABAWS</a>
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42 <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>
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43 <a class="newa" href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>
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44 <a class="newa" href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>
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45 <a class="newa" href="man_server_dev.html" >Develop JABAWS</a>
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52 <h2 id="headtitle">JABAWS MANUAL</h2>
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56 <li><a href="#wisjaba">What is JABAWS?</a></li>
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57 <li><a href="#wjaba">JABAWS Benefits</a></li>
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58 <li><a href="#alprog">JABA Web Services Programs </a></li>
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59 <li><a href="#jaba2.1">What is new in JABAWS 2.1?</a> </li>
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60 <li><a href="#jabaclient">What is JABAWS Client</a>?</li>
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61 <li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>
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62 <li><a href="#cmdclient">Programmatic access to JABAWS</a></li>
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67 <h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>
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69 JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a
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70 collection of web services for bioinformatics, and currently provides services that make it easy
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71 to access well-known multiple sequence alignment and protein disorder prediction programs
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72 (see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.
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73 Future versions of JABAWS will incorporate other tools.
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75 <h4>Getting JABAWS</h4>
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77 JABAWS consists of a server and a client, but unlike most bioinformatics web service systems, you can download and
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78 run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS
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79 Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your
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80 lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure
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81 but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested
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82 in writing your own client, the JABAWS command line client is what you need.
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87 <h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>
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89 <li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>
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90 <li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>
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91 <li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>
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92 <li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>
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93 <li>Clients can submit jobs to any JABAWS servers that they might want to access, such as the one running on your local computer,
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94 your lab's server, or the publicly available services at the <a href="http://www.compbio.dundee.ac.uk/">University of Dundee</a>.</li>
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95 <li>Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.</li>
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96 <li>Wide range of configuration options to control size of jobs accepted by a server, and the command line options available for the program run by a service.</li>
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101 <h3><a name="alprog" id="alprog"/>JABA Web Services Programs </h3>
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102 <p> JABAWS currently provides access to the following programs:</p>
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103 <p>Multiple Sequence Alignement </p>
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105 <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>
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106 <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.52)</li>
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107 <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>
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108 <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>
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109 <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>
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110 <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
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111 <li><a href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>
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112 <li><a href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</li>
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114 <p>Protein Secondary structure prediction</p>
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116 <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/www-jpred">Jpred</a></span> (3.0.3) </li>
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119 <p>Protein disorder prediction</p>
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121 <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>
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122 <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://iupred.enzim.hu">IUPred</a></span> (1.0) </li>
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123 <li><span style="color:black; font-weight:normal; text-align:left;">Jronn - Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>
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124 <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://globplot.embl.de/">GlobPlot</a></span> (2.3) </li>
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126 <p>Amino Acid conservation</p>
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128 <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a></span> (1.0) </li>
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130 <p>Secondary structure for an RNA aligment</p>
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132 <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>
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135 All these codes including Jronn and AAcon are available at the <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a>
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136 section (registration is required).
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140 <h3><a name="jaba2.1"/>What is new in JABAWS 2.1? </h3>
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141 <strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong>
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142 <p>Several new web services are available in this version of JABAWS:</p>
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144 <li>Two multiple sequence aligners (MSAprobs and GLprobs), both services return the standard Alignment object</li>
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145 <li>RNAalifoldWS returns RNAStructScoreManager, which is the standard ScoreManager objects with several additional methods</li>
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147 JpredWS returns the JpredAligment object, which is the standard alignment with additional methods for extracting
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148 Jpred predictions. These predictions are supplied as additional sequences in the aligment
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152 <p>Some bugs have been fixed and several improvements have been done:</p>
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154 <li>WS status servlet returns version and some additional information on each web service</li>
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155 <li>a bug with path to help in the client</li>
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156 <li>Fix two bug with the Google Analytics library: no-stop due to running thread</li>
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157 <li>GoogleAnalytics gets proper JABAWS version</li>
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161 <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>
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163 <li>Disembl returned swapped strings for HOTLOOPS and REM465</li>
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164 <li>Jronn failed to process jobs with more than 3 sequences</li>
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165 <li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>
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166 <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
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168 <li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties</li>
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169 <li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>
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170 <li>Documentation has been updated</li>
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172 <a name="jaba2"/><strong>JABAWS Version 2 (Released 16th Dec 2011)</strong><p>Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use.</p><p>It contains:</p>
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173 <ul><li>updates for all multiple sequence alignment services</li>
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174 <li>four new protein disorder prediction services</li>
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175 <li>Clustal Omega multiple sequence alignment web service</li>
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176 <li>amino acid conservation service</li>
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177 <li>web services execution statistics visualization </li>
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178 <li>web services status check from a web page</li>
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179 <li>VirtualBox support was dropped in favour of VMware</li>
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180 <li>new WAR package for Mac users</li>
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181 <li>Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud</li>
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182 <li>Improved web services client API</li>
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183 <li>Simplified WAR package installation</li>
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188 <h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>
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190 A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web
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191 services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web
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192 services on any instance of JABAWS Server available over the web. The basic client is useful if you would like
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193 to test or execute the programs provided by theJABAWS server in your own scripts, but you do not want to handle
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194 any web service specific details. The client is an open source software, so you can also use the source code to
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195 as an example how to manipulate with JABAWS web services in your own code.
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196 <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good
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197 example of a graphical JABAWS client. This client uses the same functionality as the command line client, but
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198 instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.
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203 <h3><a name="jalviewsup"></a>JABAWS versions compatibility and Jalview support </h3>
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205 JABAWS version 2.1 is fully backward compatible with JABAWS v1.0 and v2.0. This means all JABAWS 1.0 and 2.0 and
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206 2.0.1 clients should also be able to use JABAWS 2.1 services. To access the analysis web services introduced in
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207 JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.
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212 <h3><a name="cmdclient" id="cmdclient"></a>Programmatic access to JABAWS </h3>
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214 JABAWS web services are WS-I basic profile compliant, which means they can be accessed using any programming language
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215 or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home
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216 page, and you can use this to automatically generate service bindings for your program. If you use Java
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217 you may wish to use our <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev">client package</a> to access JABAWS.
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218 This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which
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219 is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify
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220 working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.
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222 </div><!-- content end-->
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223 <div id="copyright">Last update: 30 April 2014<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>
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