[MOBY-guts] biomoby commit
Eddie Kawas
kawas at pub.open-bio.org
Wed Oct 19 22:00:26 UTC 2005
kawas
Wed Oct 19 18:00:26 EDT 2005
Update of /home/repository/moby/moby-live/Java/docs/taverna/guide
In directory pub.open-bio.org:/tmp/cvs-serv21367
Modified Files:
index.html
Added Files:
InstallingLocalMOBYCentral.html
Log Message:
added an installing mobycentral link
moby-live/Java/docs/taverna/guide InstallingLocalMOBYCentral.html,NONE,1.1 index.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html 2005/10/18 20:12:36 1.1
+++ /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html 2005/10/19 22:00:26 1.2
@@ -1,200 +1,400 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
-"http://www.w3.org/TR/html4/loose.dtd">
-<html>
-<head>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
-<title>The 'new' BioMoby plugin For Taverna</title>
-</head>
-
-<body>
-<h1>How to use the BioMoby plugin in Taverna 1.3</h1>
-<blockquote>
- <h3>Introduction</h3>
- <blockquote>
- <p>We updated the BioMoby plugin so that we could add functionality that we believed was missing.</p>
- <p>In the past, users of the plugin were forced to start every Moby based workflow with the root Moby<br>
- datatype. In other words, you were able to utilize a local widget called 'create_moby_data', however, <br>
- the Moby data really was just the root datatype in disguise.</p>
- <p>In addition, in Taverna releases prior to version 1.2, the BioMoby services were always limited to one <br>
- input and one output. This worked for many of the Moby services, but for those wishing to create a<br>
- workflow that initally utilized a service with more inputs, that option just wasn't available.</p>
- </blockquote>
- <h3>New Features</h3>
- <blockquote>
- <p>The updated BioMoby plugin contains many new features. Some of these features include the following:</p>
- <ul>
- <li>The ability to work with any datatype in the MobyCentral Object ontology</li>
- <li>The ability to utilize services with more than 1 input or output</li>
- <li>The ability to obtain useful information regarding the datatypes or services</li>
- <li>The addition of Moby collection support (currently handles only collections as inputs, not outputs) </li>
- <li>The ability to completely add a Moby data type with all of its sub components to a workflow </li>
- </ul>
- <p>To start using these new features, please follow the short tutorial below! </p>
- </blockquote>
- <h3>Tutorial</h3>
- <blockquote>
- <h4>Creating a BioMoby Scavenger</h4>
- <blockquote>
- <p>Creating a new BioMoby scavenger has never been easier! In fact, if you are familar with Taverna,<br>
- then adding a BioMoby scavenger is just like adding any other scavenger.</p>
- <p>Starting from the 'Available Services' window, you will need to context click the folder labeled <br>
- 'Available Processors'. Below is a image illustrating the 'Available Services' window.</p>
- <p><img src="./availableServices.png" alt="Available Services Window" width="399" height="112"></p>
- <p>Performing a context click on the selected folder reveals the following menu. Notice how<br>
- we chose to add new BioMoby scavenger.</p>
- <p><img src="./availableProcessorsContextC.png" alt="Scavengers that we can choose from" width="395" height="388"> </p>
- <p>Upon making our selection, we will be prompted to enter certain information that will allow Taverna<br>
- to create our scavenger. The information that we need to provide includes the URL of the BioMoby<br>
- central registry that we would like to use, as well as the URL of the RDF document describing the<br>
- BioMoby datatype ontology.</p>
- <p><img src="./AddRegEndpoint.png" alt="Enter your registry details" width="630" height="75"></p>
- <p>You may now be scratching your head, and are wondering why you have never heard of this RDF document.<br>
- Currently, this location is undocumented in the Moby API, and the API will be supplemented with this information<br>
- at a later time. At the time that this tutorial was written, there was only one location known for this RDF document<br>
- and it is the default one in Taverna (shown above)
- .</p>
- <p>Once the information has been inputted into the text boxes, the Moby services and datatypes will now be available<br>
- as processors in the 'Available Services' window.</p>
- <p><img src="./processorsView.png" alt="The service and datatype ontologies are illustrated" width="398" height="173"> </p>
- <p>If you would like to work with your own custom Mobycentral registry and not that of the default, <em>http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl</em>, then it is recommended that you edit the <strong>/taverna-workbench-1.3/conf/mygrid.properties </strong>file. In this file, modify the value for the property <em><strong>taverna.defaultbiomoby </strong></em>replacing the URL with that of your custom registry. </p>
- </blockquote>
- <h4>Creating a workflow</h4>
- <blockquote>
- <p><em>Workflow used in this tutorial may be downloaded <a href="tutorialWorkflow.xml">here.</a> <br>
- Workflow input used in this tutorial may be downloaded <a href="tutorialWorkflowInput.xml">here.</a> </em></p>
- <p>Creating a workflow with the new BioMoby plugin is as easy as it was using the previous plugin. There are, of course, <br>
- a few
- differences. When creating workflows, it is no longer necessary to use the local widget 'create_moby_data'.<br>
- When you are ready to instantiate a Moby datatype, all that is necessary is for you to choose the datatype from the list<br>
- of 'Available Processors' under the 'Moby Objects' folder.</p>
- <p>As an example, we will add the Moby datatype called DNASequence to our workflow. In order to do this, we must <br>
- navigate the datatype ontology to find DNASequence. We can find DNASequence by traversing the 'Moby Objects'<br>
- tree in the following order:
- Object, VirtualSequence, GenericSequence, NucleotideSequence and finally DNASequence.<br>
- Now that we have found the processor that we were looking for, let's add it to the workflow.</p>
- <p><img src="./addDNAtoModel.png" alt="Adding the datatype DNASequence to the workflow" width="375" height="202"></p>
- <p>'DNASequence' has now been added to the workflow diagram. To reveal what inputs and outputs this processor<br>
- utilizes, we need to ask Taverna to show us all of the ports in the workflow diagram.</p>
- <p><img src="./dnasequence.png" alt="DNASequence and all of its ports" width="483" height="295"></p>
- <p>Notice how 'DNASequence' takes as input a namespace, an id, an article name, and 2 Moby datatypes: String and <br>
- Integer. Since 'String' and 'Integer' are Moby datatypes contained within a 'DNASequence', they have been conveniently<br>
- added to the workflow and linked appropriately. </p>
- <p>Our workflow diagram
-looks something like the following:</p>
- <p><img src="./completeDnasequence.png" alt="A DNASequence with all of its sub components connected to it" width="644" height="208"></p>
- <p>A complex BioMoby datatype. 'DNASequence', and all of its subcomponents have now been added to our workflow.<br>
- Next we will add a BioMoby service processor that handles our complex datatype.</p>
- <p>We will add the service 'runFasta' from the authority 'www.pcm.uam.es'. This service runs the fasta tool on the input<br>
- sequence
- . From the list of processors, we will navigate to www.pcm.uam.es and then choose the service that we are<br>
- interested in, i.e. 'runFasta'.</p>
- <p><img src="./addingMelting.png" alt="Adding the runFasta processor" width="346" height="192"> </p>
- <p>The next thing to do is to connect the input of the 'runFasta' processor to the output of 'DNASequence'. It should be noted <br>
- that there are 2 inputs to the processor 'runFasta': 'GenericSequence(_ANON_)' and 'input'. The port labelled 'input' serves to<br>
- support workflows created prior to Taverna 1.2 and should be used when you create workflows utilizing the Local Widgets<br>
- 'create_moby_data'.
- For our workflow, we will connect the complex datatype 'DNASequence' to the input port labeled<br>
- 'DNASequence(sequence)' of the 'runFasta' processor.</p>
- <p><img src="./dnaConnectedMelting.png" alt="DNASequence datatype connected to the Melting service" width="580" height="226"> </p>
- <p>We are almost done! The only things that are missing now are the workflow inputs and the workflow outputs. We will create<br>
- the following inputs:</p>
- <ul>
- <li>namespace - this input will connect to the 'namespace' input port of 'DNASequence' </li>
- <li>id - this input will connect to the 'id' input port of 'DNASequence' </li>
- <li>sequence - this input will connect to the 'value' input port of 'String' </li>
- <li>length - this input will connect to the 'value' input port of 'Integer' </li>
- </ul>
- <p>We will also create a workflow output called 'output'. This workflow output will be connected to the <br>
- output port, 'FASTA_Text(_ANON_)' of the processor 'runFasta'.</p>
- <p>Once these connections have been made, you should have something similar to the image below. Note that the image is only showing<br>
- those ports that are bound to inputs or outputs. </p>
- <p><img src="./workflowComplete.png" alt="A completed workflow Diagram" width="609" height="467"></p>
- <p>So there we have a completed workflow based on BioMoby Services and datatypes. If you wish to run this<br>
- workflow, some suitable values for the workflow inputs are as follows:</p>
- <ul>
- <li>namespace - NCBI_gi</li>
- <li>id - 646464</li>
- <li>sequence - tatata </li>
- <li>length - 6 </li>
- </ul>
- <p>The output from this data is shown below.</p>
- <p><img src="./results.png" alt="The results from running our workflow" width="643" height="387"> </p>
- </blockquote>
- <h4>Obtaining information on a Moby datatype</h4>
- <blockquote>
- <p>One of the neatest things added to the plugin was the ability to obtain information regarding BioMoby datatypes. For<br>
- instance, you can find out what services a particular datatype can be used as input or output. In addition, you can find<br>
- the descriptions of those services.</p>
- <p>As an example, imagine that we wanted to discover what services the Moby datatype 'Integer' feeds into. To do this, we<br>
- can use our existing workflow. From the 'Advanced model explorer' window, context click on the processor called 'Integer'<br>
- and choose 'Moby Object Details'.</p>
- <p><img src="./contextObjectDetails.png" alt="Finding out more about a particular Moby Datatype" width="394" height="444"> </p>
- <p>As soon as you choose 'Moby Object Details', a pop up window appears and embedded in that window<br>
- is a tree like structure. <em>Note that this window can take up to a minute to appear depending on your <br>
- internet connection and the data type chosen. </em>At the root of the tree is the datatype that we chose to <br>
- know more about, in our case
- 'Integer', and 2 sub trees labeled 'Feeds into' and 'Produced by'. In the <br>
- 'Feeds into' sub tree, you will find out
- what BioMoby services consume the datatype in question, sorted by <br>
- authority. </p>
- <p>When you navigate the sub tree
- and mouse over the service name, a tool tip appears giving you the <br>
- description of the service. </p>
- <p><img src="./objectTooltip.png" alt="Tool tip provided to describe the service that consumes our datatype" width="462" height="116"></p>
- <p>In addition, you can context click the service name, in this case
- PupaSNP,
- and a menu is shown:</p>
- <p><img src="objectContextMenu.png" alt="Moby Object Details Context Menu" width="389" height="220"></p>
- <p>From this menu, you can choose to either add the selected service to the workflow or view more a more detailed<br>
- service description. Below, the window that appears upon choosing to 'Find out about PupaSNP':</p>
- <p><img src="serviceDescription.png" alt="Moby Service Description" width="468" height="327"></p>
- <p> </p>
- <p>The sub tree
- 'Produced by' offers similar information, except about services that produce the datatype in question. <br>
- The context menu is not available for children of the 'Produced by' node. </p>
- <p> </p>
- </blockquote>
- <h4>Obtaining information on a Moby service</h4>
- <blockquote>
- <p>As with Moby datatypes, information about services is also available. For a particular service, we can determine<br>
- what are the inputs and outputs. And if you wish, you may add the input datatypes to the workflow.In addition, <br>
- we can also discover what namespaces a particular input or output
- is valid in.</p>
- <p>Using the workflow that we created above, we can discover what inputs and outputs 'runFasta' utilize. To determine this,<br>
- we need to context click on the 'runFasta' processor from the 'Advanced model explorer', just as we had done before<br>
- with the Moby datatype processors above, and choose 'Moby Service Details'.</p>
- <p><img src="./serviceContextClick.png" alt="Context clicking a Moby service to retrieve additional information" width="419" height="416"></p>
- <p>A pop window appears and embedded in it is a tree that has as its root the name of the Moby<br>
- service. The children of the root node are 2 sub trees, 'Inputs' and 'Outputs'. The items under<br>
- these sub trees simply illustrate what datatypes the service consumes and produces.</p>
- <p><img src="./serviceTooltip.png" alt="The window showing the service details and a tooltip describing the output of the service" width="401" height="150"> </p>
- <p>Similarly to the 'Moby Object Details', you can either add the input datatype to the workflow or<br>
- obtain additional information on the datatype:</p>
- <p><img src="msdAddToWorkflow.png" alt="Moby Service Details Context Menu" width="446" height="182"></p>
- <p> </p>
- </blockquote>
- </blockquote>
- <h3>What's Next</h3>
- <blockquote>
- <p>In the future, we hope to add even more functionality to the plugin. Below are some of the features that<br>
- we have thought about:</p>
- <ul>
- <li>Adding collection support that behaves as stated in the BioMoby API</li>
- <li>Adding the ability to parse Moby datatypes and pass this parsed data onto other non Moby services.</li>
- <li>Adding the ability to add Moby services from the 'Moby Object Details' window.</li>
- </ul>
- <p>If there are specific features that you would like us to consider, please contact the BioMoby development<br>
- team. </p>
- </blockquote>
- <h3>Comments / Questions</h3>
- <blockquote>
- <p>If you have any questions or comments, please feel free to contact Eddie Kawas @<br>
- <strong>edward</strong>[<em>DoT</em>]<strong>kawas</strong>[<em>AT</em>]<strong>gmail</strong>[<em>DoT</em>]<strong>com</strong></p>
- <p>If you have any suggestions regarding new features or you would like to report a bug,<br>
- please let me know.</p>
- <p> </p>
- <p> </p>
- </blockquote>
-</blockquote>
-</body>
-</html>
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+
+"http://www.w3.org/TR/html4/loose.dtd">
+
+<html>
+
+<head>
+
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+
+<title>The 'new' BioMoby plugin For Taverna</title>
+
+</head>
+
+
+
+<body>
+
+<h1>How to use the BioMoby plugin in Taverna 1.3</h1>
+
+<blockquote>
+
+ <h3>Introduction</h3>
+
+ <blockquote>
+
+ <p>We updated the BioMoby plugin so that we could add functionality that we believed was missing.</p>
+
+ <p>In the past, users of the plugin were forced to start every Moby based workflow with the root Moby<br>
+
+ datatype. In other words, you were able to utilize a local widget called 'create_moby_data', however, <br>
+
+ the Moby data really was just the root datatype in disguise.</p>
+
+ <p>In addition, in Taverna releases prior to version 1.2, the BioMoby services were always limited to one <br>
+
+ input and one output. This worked for many of the Moby services, but for those wishing to create a<br>
+
+ workflow that initally utilized a service with more inputs, that option just wasn't available.</p>
+
+ </blockquote>
+
+ <h3>New Features</h3>
+
+ <blockquote>
+
+ <p>The updated BioMoby plugin contains many new features. Some of these features include the following:</p>
+
+ <ul>
+
+ <li>The ability to work with any datatype in the MobyCentral Object ontology</li>
+
+ <li>The ability to utilize services with more than 1 input or output</li>
+
+ <li>The ability to obtain useful information regarding the datatypes or services</li>
+
+ <li>The addition of Moby collection support (currently handles only collections as inputs, not outputs) </li>
+
+ <li>The ability to completely add a Moby data type with all of its sub components to a workflow </li>
+
+ </ul>
+
+ <p>To start using these new features, please follow the short tutorial below! </p>
+
+ </blockquote>
+
+ <h3>Tutorial</h3>
+
+ <blockquote>
+
+ <h4>Creating a BioMoby Scavenger</h4>
+
+ <blockquote>
+
+ <p>Creating a new BioMoby scavenger has never been easier! In fact, if you are familar with Taverna,<br>
+
+ then adding a BioMoby scavenger is just like adding any other scavenger.</p>
+
+ <p>Starting from the 'Available Services' window, you will need to context click the folder labeled <br>
+
+ 'Available Processors'. Below is a image illustrating the 'Available Services' window.</p>
+
+ <p><img src="./availableServices.png" alt="Available Services Window" width="399" height="112"></p>
+
+ <p>Performing a context click on the selected folder reveals the following menu. Notice how<br>
+
+ we chose to add new BioMoby scavenger.</p>
+
+ <p><img src="./availableProcessorsContextC.png" alt="Scavengers that we can choose from" width="395" height="388"> </p>
+
+ <p>Upon making our selection, we will be prompted to enter certain information that will allow Taverna<br>
+
+ to create our scavenger. The information that we need to provide includes the URL of the BioMoby<br>
+
+ central registry that we would like to use, as well as the URL of the RDF document describing the<br>
+
+ BioMoby datatype ontology.</p>
+
+ <p><img src="./AddRegEndpoint.png" alt="Enter your registry details" width="630" height="75"></p>
+
+ <p>You may now be scratching your head, and are wondering why you have never heard of this RDF document.<br>
+
+ Currently, this location is undocumented in the Moby API, and the API will be supplemented with this information<br>
+
+ at a later time. At the time that this tutorial was written, there was only one location known for this RDF document<br>
+
+ and it is the default one in Taverna (shown above)
+
+ .</p>
+
+ <p>Once the information has been inputted into the text boxes, the Moby services and datatypes will now be available<br>
+
+ as processors in the 'Available Services' window.</p>
+
+ <p><img src="./processorsView.png" alt="The service and datatype ontologies are illustrated" width="398" height="173"> </p>
+
+ <p>If you would like to work with your own custom Mobycentral registry and not that of the default, <em>http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl</em>, then it is recommended that you edit the <strong>/taverna-workbench-1.3/conf/mygrid.properties </strong>file. In this file, modify the value for the property <em><strong>taverna.defaultbiomoby </strong></em>replacing the URL with that of your custom registry. </p>
+ <p>If you would like to host your own local custom registry, please <a href="./InstallingLocalMOBYCentral.html" target="_blank">click here</a>. </p>
+ </blockquote>
+
+ <h4>Creating a workflow</h4>
+
+ <blockquote>
+
+ <p><em>Workflow used in this tutorial may be downloaded <a href="tutorialWorkflow.xml">here.</a> <br>
+
+ Workflow input used in this tutorial may be downloaded <a href="tutorialWorkflowInput.xml">here.</a> </em></p>
+
+ <p>Creating a workflow with the new BioMoby plugin is as easy as it was using the previous plugin. There are, of course, <br>
+
+ a few
+
+ differences. When creating workflows, it is no longer necessary to use the local widget 'create_moby_data'.<br>
+
+ When you are ready to instantiate a Moby datatype, all that is necessary is for you to choose the datatype from the list<br>
+
+ of 'Available Processors' under the 'Moby Objects' folder.</p>
+
+ <p>As an example, we will add the Moby datatype called DNASequence to our workflow. In order to do this, we must <br>
+
+ navigate the datatype ontology to find DNASequence. We can find DNASequence by traversing the 'Moby Objects'<br>
+
+ tree in the following order:
+
+ Object, VirtualSequence, GenericSequence, NucleotideSequence and finally DNASequence.<br>
+
+ Now that we have found the processor that we were looking for, let's add it to the workflow.</p>
+
+ <p><img src="./addDNAtoModel.png" alt="Adding the datatype DNASequence to the workflow" width="375" height="202"></p>
+
+ <p>'DNASequence' has now been added to the workflow diagram. To reveal what inputs and outputs this processor<br>
+
+ utilizes, we need to ask Taverna to show us all of the ports in the workflow diagram.</p>
+
+ <p><img src="./dnasequence.png" alt="DNASequence and all of its ports" width="483" height="295"></p>
+
+ <p>Notice how 'DNASequence' takes as input a namespace, an id, an article name, and 2 Moby datatypes: String and <br>
+
+ Integer. Since 'String' and 'Integer' are Moby datatypes contained within a 'DNASequence', they have been conveniently<br>
+
+ added to the workflow and linked appropriately. </p>
+
+ <p>Our workflow diagram
+
+looks something like the following:</p>
+
+ <p><img src="./completeDnasequence.png" alt="A DNASequence with all of its sub components connected to it" width="644" height="208"></p>
+
+ <p>A complex BioMoby datatype. 'DNASequence', and all of its subcomponents have now been added to our workflow.<br>
+
+ Next we will add a BioMoby service processor that handles our complex datatype.</p>
+
+ <p>We will add the service 'runFasta' from the authority 'www.pcm.uam.es'. This service runs the fasta tool on the input<br>
+
+ sequence
+
+ . From the list of processors, we will navigate to www.pcm.uam.es and then choose the service that we are<br>
+
+ interested in, i.e. 'runFasta'.</p>
+
+ <p><img src="./addingMelting.png" alt="Adding the runFasta processor" width="346" height="192"> </p>
+
+ <p>The next thing to do is to connect the input of the 'runFasta' processor to the output of 'DNASequence'. It should be noted <br>
+
+ that there are 2 inputs to the processor 'runFasta': 'GenericSequence(_ANON_)' and 'input'. The port labelled 'input' serves to<br>
+
+ support workflows created prior to Taverna 1.2 and should be used when you create workflows utilizing the Local Widgets<br>
+
+ 'create_moby_data'.
+
+ For our workflow, we will connect the complex datatype 'DNASequence' to the input port labeled<br>
+
+ 'DNASequence(sequence)' of the 'runFasta' processor.</p>
+
+ <p><img src="./dnaConnectedMelting.png" alt="DNASequence datatype connected to the Melting service" width="580" height="226"> </p>
+
+ <p>We are almost done! The only things that are missing now are the workflow inputs and the workflow outputs. We will create<br>
+
+ the following inputs:</p>
+
+ <ul>
+
+ <li>namespace - this input will connect to the 'namespace' input port of 'DNASequence' </li>
+
+ <li>id - this input will connect to the 'id' input port of 'DNASequence' </li>
+
+ <li>sequence - this input will connect to the 'value' input port of 'String' </li>
+
+ <li>length - this input will connect to the 'value' input port of 'Integer' </li>
+
+ </ul>
+
+ <p>We will also create a workflow output called 'output'. This workflow output will be connected to the <br>
+
+ output port, 'FASTA_Text(_ANON_)' of the processor 'runFasta'.</p>
+
+ <p>Once these connections have been made, you should have something similar to the image below. Note that the image is only showing<br>
+
+ those ports that are bound to inputs or outputs. </p>
+
+ <p><img src="./workflowComplete.png" alt="A completed workflow Diagram" width="609" height="467"></p>
+
+ <p>So there we have a completed workflow based on BioMoby Services and datatypes. If you wish to run this<br>
+
+ workflow, some suitable values for the workflow inputs are as follows:</p>
+
+ <ul>
+
+ <li>namespace - NCBI_gi</li>
+
+ <li>id - 646464</li>
+
+ <li>sequence - tatata </li>
+
+ <li>length - 6 </li>
+
+ </ul>
+
+ <p>The output from this data is shown below.</p>
+
+ <p><img src="./results.png" alt="The results from running our workflow" width="643" height="387"> </p>
+
+ </blockquote>
+
+ <h4>Obtaining information on a Moby datatype</h4>
+
+ <blockquote>
+
+ <p>One of the neatest things added to the plugin was the ability to obtain information regarding BioMoby datatypes. For<br>
+
+ instance, you can find out what services a particular datatype can be used as input or output. In addition, you can find<br>
+
+ the descriptions of those services.</p>
+
+ <p>As an example, imagine that we wanted to discover what services the Moby datatype 'Integer' feeds into. To do this, we<br>
+
+ can use our existing workflow. From the 'Advanced model explorer' window, context click on the processor called 'Integer'<br>
+
+ and choose 'Moby Object Details'.</p>
+
+ <p><img src="./contextObjectDetails.png" alt="Finding out more about a particular Moby Datatype" width="394" height="444"> </p>
+
+ <p>As soon as you choose 'Moby Object Details', a pop up window appears and embedded in that window<br>
+
+ is a tree like structure. <em>Note that this window can take up to a minute to appear depending on your <br>
+
+ internet connection and the data type chosen. </em>At the root of the tree is the datatype that we chose to <br>
+
+ know more about, in our case
+
+ 'Integer', and 2 sub trees labeled 'Feeds into' and 'Produced by'. In the <br>
+
+ 'Feeds into' sub tree, you will find out
+
+ what BioMoby services consume the datatype in question, sorted by <br>
+
+ authority. </p>
+
+ <p>When you navigate the sub tree
+
+ and mouse over the service name, a tool tip appears giving you the <br>
+
+ description of the service. </p>
+
+ <p><img src="./objectTooltip.png" alt="Tool tip provided to describe the service that consumes our datatype" width="462" height="116"></p>
+
+ <p>In addition, you can context click the service name, in this case
+
+ PupaSNP,
+
+ and a menu is shown:</p>
+
+ <p><img src="objectContextMenu.png" alt="Moby Object Details Context Menu" width="389" height="220"></p>
+
+ <p>From this menu, you can choose to either add the selected service to the workflow or view more a more detailed<br>
+
+ service description. Below, the window that appears upon choosing to 'Find out about PupaSNP':</p>
+
+ <p><img src="serviceDescription.png" alt="Moby Service Description" width="468" height="327"></p>
+
+ <p> </p>
+
+ <p>The sub tree
+
+ 'Produced by' offers similar information, except about services that produce the datatype in question. <br>
+
+ The context menu is not available for children of the 'Produced by' node. </p>
+
+ <p> </p>
+
+ </blockquote>
+
+ <h4>Obtaining information on a Moby service</h4>
+
+ <blockquote>
+
+ <p>As with Moby datatypes, information about services is also available. For a particular service, we can determine<br>
+
+ what are the inputs and outputs. And if you wish, you may add the input datatypes to the workflow.In addition, <br>
+
+ we can also discover what namespaces a particular input or output
+
+ is valid in.</p>
+
+ <p>Using the workflow that we created above, we can discover what inputs and outputs 'runFasta' utilize. To determine this,<br>
+
+ we need to context click on the 'runFasta' processor from the 'Advanced model explorer', just as we had done before<br>
+
+ with the Moby datatype processors above, and choose 'Moby Service Details'.</p>
+
+ <p><img src="./serviceContextClick.png" alt="Context clicking a Moby service to retrieve additional information" width="419" height="416"></p>
+
+ <p>A pop window appears and embedded in it is a tree that has as its root the name of the Moby<br>
+
+ service. The children of the root node are 2 sub trees, 'Inputs' and 'Outputs'. The items under<br>
+
+ these sub trees simply illustrate what datatypes the service consumes and produces.</p>
+
+ <p><img src="./serviceTooltip.png" alt="The window showing the service details and a tooltip describing the output of the service" width="401" height="150"> </p>
+
+ <p>Similarly to the 'Moby Object Details', you can either add the input datatype to the workflow or<br>
+
+ obtain additional information on the datatype:</p>
+
+ <p><img src="msdAddToWorkflow.png" alt="Moby Service Details Context Menu" width="446" height="182"></p>
+
+ <p> </p>
+
+ </blockquote>
+
+ </blockquote>
+
+ <h3>What's Next</h3>
+
+ <blockquote>
+
+ <p>In the future, we hope to add even more functionality to the plugin. Below are some of the features that<br>
+
+ we have thought about:</p>
+
+ <ul>
+
+ <li>Adding collection support that behaves as stated in the BioMoby API</li>
+
+ <li>Adding the ability to parse Moby datatypes and pass this parsed data onto other non Moby services.</li>
+
+ <li>Adding the ability to add Moby services from the 'Moby Object Details' window.</li>
+
+ </ul>
+
+ <p>If there are specific features that you would like us to consider, please contact the BioMoby development<br>
+
+ team. </p>
+
+ </blockquote>
+
+ <h3>Comments / Questions</h3>
+
+ <blockquote>
+
+ <p>If you have any questions or comments, please feel free to contact Eddie Kawas @<br>
+
+ <strong>edward</strong>[<em>DoT</em>]<strong>kawas</strong>[<em>AT</em>]<strong>gmail</strong>[<em>DoT</em>]<strong>com</strong></p>
+
+ <p>If you have any suggestions regarding new features or you would like to report a bug,<br>
+
+ please let me know.</p>
+
+ <p> </p>
+
+ <p> </p>
+
+ </blockquote>
+
+</blockquote>
+
+</body>
+
+</html>
+
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