[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Tue Oct 10 14:02:12 UTC 2006
kawas
Tue Oct 10 10:02:12 EDT 2006
Update of /home/repository/moby/moby-live/Java/docs/taverna/guide
In directory dev.open-bio.org:/tmp/cvs-serv22876/Java/docs/taverna/guide
Modified Files:
index.html
Log Message:
moby-live/Java/docs/taverna/guide index.html,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html 2006/08/21 19:47:17 1.12
+++ /home/repository/moby/moby-live/Java/docs/taverna/guide/index.html 2006/10/10 14:02:12 1.13
@@ -2,37 +2,39 @@
"http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
+<link rel="stylesheet" href="../../images/stylesheet.css" type="text/css">
<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 (Updated September 2006) <a name="top"></a></h1>
+<h1>How to use the BioMoby plugin in Taverna (Updated October 2006) <a name="top"></a></h1>
<blockquote>
<h3>Table of Contents</h3>
<blockquote>
- <pre><a href="#introduction">Introduction</a>
-
-
-
-<a href="#new_features">New Features</a>
-
-
-
-<a href="#tutorial">Tutorial</a><blockquote><li><a href="#scavenger">Creating a BioMoby Scavenger</a></li>
- <li><a href="#workflow">Creating a workflow</a></li>
- <li><a href="#datatype">Obtaining information on a Moby Datatype</a></li>
- <li><a href="#service">Obtaining information on a Moby Service</a></li>
- <li><a href="#secondarys">Using secondary parameters</a></li>
- <li><a href="#parsing">Obtaining the 'data' from a Moby service</a></li>
- </blockquote>
-<a href="#whats_next">What's Next</a>
-
-
-<a href="#faq">FAQ</a>
-
-
-<a href="#questions">Comments / Questions</a></pre>
+ <ul>
+ <li><a href="#introduction">Introduction</a></li>
+ <li>
+ <a href="#new_features">New Features</a> </li>
+ <li><a href="#tutorial">Tutorial</a></li>
+ </ul>
+ <ol>
+ <blockquote><li><a href="#scavenger">Creating a BioMoby Scavenger</a></li>
+ <li><a href="#workflow">Creating a workflow</a></li>
+ <li><a href="#datatype">Obtaining information on a Moby Datatype</a></li>
+ <li><a href="#service">Obtaining information on a Moby Service</a></li>
+ <li><a href="#secondarys">Using secondary parameters</a></li>
+ <li><a href="#parsing">Obtaining the 'data' from a Moby service</a></li>
+ </blockquote>
+ </ol>
+ <ul>
+ <li><a href="#whats_next">What's Next</a> </li>
+ <li> <a href="#faq">FAQ</a></li>
+ <li>
+
+
+ <a href="#questions">Comments / Questions</a> </li>
+ </ul>
</blockquote>
<h3>Introduction<a name="introduction"></a></h3>
<blockquote>
@@ -206,10 +208,10 @@
<ul>
<li><em>Find Services that Consume NCBI_BLAST_Text('blast') - brief search</em>:<br>
</li>
- <pre>Searches for all services that consume NCBI_BLAST_Text</pre>
+ <pre class="script">Searches for all services that consume NCBI_BLAST_Text</pre>
<li><em>Find Services that Consume NCBI_BLAST_Text('blast') - semantic search</em></li>
- <pre>Searches for all services that either consume NCBI_BLAST_Text
+ <pre class="script">Searches for all services that either consume NCBI_BLAST_Text
or it parent datatype.
For more infomation on this behaviour, <a href="http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/ObjectStructure.html" target="_blank">click here.</a></pre>
</ul>
@@ -295,15 +297,15 @@
<br>
There are 3 different types of output ports that Moby services utilize and 2 different types of input ports (excluding the legacy ports<br>
'input' and 'output'.<br>
- <pre>
+ <pre class="script">
<em><strong>Moby Service Output</strong></em> ----Connects to ---> <em><strong>Moby Service Input</strong></em>
- 1 Simple Simple<br>
- 2 Simple Collection<br>
- 3 Collection Simple<br>
- 4 Collection Collection<br>
- 5 CollectionAsSimples Simples<br>
- 6 CollectionAsSimples Collection<br>
+ 1 Simple Simple
+ 2 Simple Collection
+ 3 Collection Simple
+ 4 Collection Collection
+ 5 CollectionAsSimples Simples
+ 6 CollectionAsSimples Collection
</pre>
A <em><strong>Simple</strong></em> is a datatype that is not contained within a collection, i.e. do not have a name that contains '(Collection -'.<br>
A <em><strong>CollectionAsSimples</strong></em> is an output port that contains a Taverna style List of the individuals in a Moby Collection.<br>
@@ -325,7 +327,7 @@
<br><li><strong>Why do some services have have '_ANON_' or 'Collection - MobyCollection' in there name?<a name="faq3"></a></strong> <br>
<br>
These are names automatically generated for services that incorrectly registered with a Mobycentral registry.<br>
- You should attempt to contact the service provider so that they may fix this service.<br>
+ You should attempt to contact the service provider so that they may fix and proplerly register these services.<br>
<br>
</li>
<li><strong>If all I want to do is run a Moby service, do I have to specify article names?<a name="faq4"></a></strong><br>
@@ -346,8 +348,7 @@
<img src="email.png" alt="email" width="468" height="60"> </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>
+<hr>
</blockquote>
</blockquote>
</body>
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