<div id="content">\r
<h2 id="headtitle">JABAWS FUNDING</h2>\r
<p>\r
-The primary funding for JABAWS development is provided by the BBSRC Bioinformatics and Biological Resources Grant: \r
+The current funding for JABAWS development is provided by the BBSRC Bioinformatics and Biological Resources Grant: \r
"The Dundee Resource for Protein Structure Prediction and Sequence Analysis" 2013 to 2018 (BB/J019364/1) to Prof. \r
-Geoff Barton. Further support comes from Wellcome Trust Strategic Grant: 100476.\r
+Geoff Barton.<br/>\r
+Further support comes from Wellcome Trust Strategic Grant: 100476.\r
</p>\r
\r
<p>\r
collection of web services for bioinformatics, and currently provides services that make it easy \r
to access well-known multiple sequence alignment and protein disorder prediction programs \r
(see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.\r
- Future versions of JABAWS will incorporate many other tools.\r
+ Future versions of JABAWS will incorporate other tools.\r
</p>\r
<h4>Getting JABAWS</h4>\r
<p>\r
- JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and \r
+ JABAWS consists of a server and a client, but unlike most bioinformatics web service systems, you can download and \r
run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS \r
Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your \r
lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure \r
<li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>\r
<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>\r
<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>\r
- <li>Clients can submit jobs to any JABAWS servers that you might want to access, such as the one running on your local computer, \r
+ <li>Clients can submit jobs to any JABAWS servers that they might want to access, such as the one running on your local computer, \r
your lab's server, or the publicly available services at the <a href="http://www.compbio.dundee.ac.uk/">University of Dundee</a>.</li>\r
<li>Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.</li>\r
- <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>\r
+ <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>\r
</ul>\r
\r
\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>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
+ 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
<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
+ <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>\r
<li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>\r
<li>Documentation has been updated</li>\r
</ul>\r
page, and you can use this to automatically generate service bindings for your program. If you use Java \r
you may wish to use our <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev">client package</a> to access JABAWS. \r
This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which \r
- is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify \r
+ is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify \r
working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.\r
</p>\r
</div><!-- content end-->\r
the hardware click continue.\r
<img src="images/aws_launch_instance.gif" alt="select hardware" width="872" height="590" />\r
</li>\r
- <li>You should not need to customize anything on this page, continue to the next.\r
+ <li>You should not need to customize anything on this page, continue to the next page.\r
<img src="images/aws_launch_instance2.gif" alt="keys" width="872" height="592" />\r
</li>\r
<li> At the "Create a key pair" step, choose "Proceed without a key pair" unless you want to access JABAWS server via SSH. \r
<img src="images/aws_launch_instance3.gif" width="872" height="592" />\r
</li>\r
<li>Create a new security group with a single HTTP (80) port as shown below. You may want to add SSH (22) port if \r
- you are planning to manage your instance via SSH. For starting/stopping your JABAWS instance SSH is not necessary, \r
+ you are planning to manage your instance via SSH. For starting/stopping your JABAWS instance, SSH is not necessary, \r
you can do this from the Amazon Webservices Console (AWS).\r
<img src="images/aws_launch_instance_sec_group.gif" alt="ese" width="856" height="588" />\r
</li>\r
<li>At this point you should have JABAWS instance up and running. Your AWS console should look something like this:\r
<img src="images/aws_launch_instance_done.gif" width="812" height="848" />\r
</li>\r
- <li>Now you can consume JABAWS web services by accessing the public DNS address of your JABAWS server instance. \r
+ <li>Now you can run JABAWS web services by accessing the public DNS address of your JABAWS server instance. \r
For instance, to register it with Jalview, just add the new JABAWS web server. Prefix your instance public \r
DNS address with http:// e.g. type: http://<public DNS>. The JABAWS instance on the screenshot can be \r
accessed on http://ec2-46-137-50-196.eu-west-1.compute.amazonaws.com.\r
<td>JABAWS command line client </td>\r
</tr>\r
</table>\r
-<p>Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />\r
+<p>Additional utility libraries that this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />\r
Please refer to a <a href="dm_javadoc/index.html">data model javadoc</a> for a detailed description of each class and its methods. </p>\r
\r
\r
<p class="attention">\r
For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client \r
source code is available from the <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev">download page</a>. Please note that for now all \r
-the examples are in Java other languages will follow given a sufficient demand. </p>\r
+the examples are in Java, other languages will follow if there is sufficient demand. </p>\r
<p>\r
Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal \r
web service deployed in the University of Dundee. </p>\r
<p class="code">1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
2) String jobId = msaws.align(fastalist); <br />\r
3) Alignment alignment = msaws.getResult(jobId);</p>\r
-<p>Line one loads FASTA sequence from the file<br />\r
- Line two submits them to web service represented by msaws proxy <br />\r
+<p>Line one loads FASTA sequence from the file.<br />\r
+ Line two submits them to web service represented by msaws proxy. <br />\r
Line three retrieves the alignment from a web service. This line will block the execution until the result is available. \r
Use this with caution. In general, you should make sure that the calculation has been completed before attempting \r
retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. \r
5) Alignment alignment = msaws.getResult(jobId);</p>\r
<p>Line one obtains the lists of presets supported by a web service.<br />\r
Line two return a particular Preset \r
- by its name<br />\r
+ by its name.<br />\r
Lines three to five are doing the same job as in the first <a href="#defalign"> aligning sequences example</a>.</p>\r
<h3><a name="customalign" id="customalign"></a>Aligning with custom parameters</h3>\r
<p class="code"> 1) RunnerConfig options = msaws.getRunnerOptions();<br />\r
9) String jobId = msaws.customAlign(fastalist, arguments);<br />\r
10) Alignment alignment = msaws.getResult(jobId);</p>\r
<p>Line one obtains the <span class="hightlight">RunnerConfig</span> object that holds information on supported parameters and their values<br />\r
- Line two retrieve a particular parameter from the holder by its name<br />\r
+ Line two retrieve a particular parameter from the holder by its name.<br />\r
Lines three sets a value to this parameter which will be used in the calculation. <br />\r
- Line four and five do the same but for another parameter<br />\r
- Line 6 makes a List to hold the parameters <br />\r
- Line seven puts the parameters into that list<br />\r
+ Line four and five do the same but for another parameter.<br />\r
+ Line 6 makes a List to hold the parameters. <br />\r
+ Line seven puts the parameters into that list.<br />\r
Line eight \r
- and ten is the same as in previous examples<br />\r
- Line nine submit an alignment request with the sequences and the parameters <br />\r
+ and ten is the same as in previous examples.<br />\r
+ Line nine submit an alignment request with the sequences and the parameters. <br />\r
The names of all the parameters supported by a web service e.g. "PAM300" can be obtained \r
using <span class="hightlight">options.getArguments() </span>method. Further details on the methods \r
available from <span class="hightlight">RunnerConfig</span> object are available from the \r
<h3><a name="compex" id="compex"></a>A complete client example </h3>\r
<p>\r
Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using \r
-one of the Clustal web service preset. Three is also a <a href="Example_template.pdf">PDF version</a> of \r
+one of the Clustal web service presets. There is also a <a href="Example_template.pdf">PDF version</a> of \r
this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, \r
the alternatives given in the code are line commented // comment. You may want to remove line style comments to \r
test alternatives of the functions. All you need for this to work is a \r
<p>\r
JABAWS are the standard <a href="http://jax-ws.java.net/">JAX-WS</a> SOAP web services, which are <a href="http://www.ws-i.org/">WS-I</a> \r
basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can \r
-generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our client library as \r
+generate portable artifacts to work with JABAWS from Java. However if programming in Java, we recommend using our client library as \r
it provides a handful of useful methods in addition to plain data types. </p>\r
<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>\r
</div><!-- content end-->\r
<li><a href="#exec_stat_conf">Configuring JABAWS execution statistics</a></li>\r
</ul>\r
<h3><a name="usage_sum"></a>Summary of Usage </h3>\r
-<p>JABAWS comes with a web application for visualizing usage statistics. The screenshot below shows the main page of this application. Each month is a link to the detailed usage statistics for this month described later. Please note however, that the links to the detailed monthly statistics are only available for authenticated users in the role <span class="hightlight">admin</span>. There is a link at the bottom of the page that would let you login, if you have not done so. </p>\r
-<p>If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, e.g. empty. </p>\r
+<p>JABAWS comes with a web application for visualizing usage statistics. The screenshot below shows the main page of this application. The individual month is linked to detailed usage statistics (described later). Please note, that the links to the detailed monthly statistics are only available for authenticated users in the role <span class="hightlight">admin</span>. There is a link at the bottom of the page that lets you login, if you have not done so. </p>\r
+<p>If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, i.e. empty. </p>\r
<p>If you have deployed a JABAWS WAR file, then please see the <a href="#conf_tomcat_user">configuring privileged access for Tomcat web application server</a> section for further details. </p>\r
<p><img src="images/usage_statistics_main.gif" alt="JABAWS usage statistics" width="608" height="318" /></p>\r
<p>The table contains the number of jobs processed by JABAWS per month, for the whole period when the statistics was collected</p>\r
<p>For each month the table contains the following information.</p>\r
<ul>\r
- <li>Month - the period of time for which statistics is displayed. For example Jan 2011 means period of time from the first of January to the first of February.</li>\r
+ <li>Month - the period of time for which statistics is displayed. For example Jan 2011 means period of time from the first of January to the first of February</li>\r
<li>Total - the total number of jobs accepted by JABAWS</li>\r
<li>Incomplete - the number of jobs for which the result file was not found or was empty excluding cancelled</li>\r
<li>Cancelled - the number of jobs cancelled by the user</li>\r
</ul>\r
<p>The summary for each column is displayed in the last row of the table.</p>\r
<h3><a name="helpUsageStats"></a>Authentication</h3>\r
-<p>Authentication lets you see the detailed usage statistics. If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, e.g. empty. In other cases you need to ask your system administrator for it. </p>\r
+<p>Authentication lets you see the detailed usage statistics. If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, i.e. empty. In other cases you need to ask your system administrator for it. </p>\r
<h3><a name="detailed_usage"></a>Detailed Usage Statistic </h3>\r
<p>Detailed execution statistics for each month is available for authenticated users only. </p>\r
<p><img src="images/usage_statistics_month.gif" alt="JABAWS one month usage statistics" width="670" height="902" /></p>\r
-<p>Each table contains the number of jobs processed by JABAWS during the period of time specified in the title.</p>\r
+<p>Each table contains the number of jobs processed by JABAWS during the period of time specified in the title:</p>\r
<ul>\r
- <li>The "All Jobs" table contains the summary of all jobs.</li>\r
- <li>"Local Jobs" table - contains the summary of the jobs calculated by the local engine.</li>\r
- <li>"Cluster Jobs" table - contains the summary of the jobs calculated by the cluster.</li>\r
+ <li>The "All Jobs" table contains the summary of all jobs</li>\r
+ <li>"Local Jobs" table - contains the summary of the jobs calculated by the local engine</li>\r
+ <li>"Cluster Jobs" table - contains the summary of the jobs calculated by the cluster</li>\r
</ul>\r
-Each table contains the following information for each web service\r
+Each table contains the following information for each web service:\r
<ul>\r
<li>Total - the total number of jobs accepted by a particular JABA service</li>\r
<li>Incomplete - the number of jobs for which the result file was not found or was empty excluding cancelled</li>\r
<li>Abandoned - the number of jobs which result(s) were not collected</li>\r
</ul>\r
<h3><a name="job_list"></a>Job List </h3>\r
-<p>Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view the application server may need to be configured. Please see <a href="#exec_stat_conf">Configuring JABAWS execution statistics</a> section for further details. </p>\r
+<p>Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view, the application server may need to be configured. Please see <a href="#exec_stat_conf">Configuring JABAWS execution statistics</a> section for further details. </p>\r
<p><img src="images/usage_statistics_details.gif" alt="JABAWS - job list" width="917" height="198" /> </p>\r
-<p>Columns </p>\r
+<p>Columns: </p>\r
<ul>\r
<li>JobID - the JABAWS job id, unique for every job</li>\r
<li>Cluster JobID - cluster job id</li>\r
<li>Finish time (s)- job's finish time and date</li>\r
<li>isCancelled - whether the job was cancelled</li>\r
<li>isCollected - whether the job was collected. False for the jobs that has been initiated but which results has never been retrieved</li>\r
- <li>isFinished - whether the job has finished. This does not necessarily mean that the job has produced the result. The job can sometime finish in failure.</li>\r
+ <li>isFinished - whether the job has finished. This does not necessarily mean that the job has produced the result. The job can sometime finish in failure</li>\r
</ul>\r
<h3><a name="job_dir"></a>JABAWS Job Directory Content </h3>\r
<p><img src="images/usage_statistics_job_details.gif" alt="JABAWS- job details" width="716" height="420" /></p>\r
<p>procError.txt and procOutput.txt files contains the content of the standard out and standard error streams of the process. </p>\r
<p>result.txt file contains the results. </p>\r
<p>input.txt file contains input into the process. </p>\r
-<p>There are maybe other files depending on the nature of the job, but the one described above will present in most cases. In this example, stat.log file stories the execution statistics generated by the process (clustal executable in this example).</p>\r
+<p>There are maybe other files depending on the nature of the job, but the one described above will be present in most cases. In this example, stat.log file stories the execution statistics generated by (clustal executable in this example) process.</p>\r
<p> If you have deployed JABAWS WAR file or made changes to JABAWS configuration you may need to make a few changes to the Tomcat configuration to be able to see the content of the job directory. Please see <a href="#exec_stat_conf">Configuring JABAWS execution statistics</a> section for further details. </p>\r
<h3><a name="exec_stat_conf"></a>Configuring JABAWS execution statistics</h3>\r
-<p>JABAWS execution statistics is a multi-component system. First is a crawler which job is to collect and preprocess the statistics from the job temporary directories and record the collected statistics into the database. The second part of the system is a web application which job is to visualise the statistics from the database. </p>\r
+<p>JABAWS execution statistics is a multi-component system. First is a crawler whose job is to collect and preprocess the statistics from the job temporary directories and record the collected statistics into the database. The second part of the system is a web application whose job is to visualise the statistics from the database. </p>\r
<p>It is possible to enable/disable the statistics collector by changing the following properties in the conf/Cluster.engine.properties and conf/Local.engine.properties files. </p>\r
<p class="box"># Enable/disable cluster statistics collector true = enable, false = disable <br/>\r
cluster.stat.collector.enable=false\r
git://source.jalview.org / jabaws.git / commitdiff