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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/01/30 08:01:42 UTC
svn commit: r938341 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/introduction/services-in-taverna.html
Author: buildbot
Date: Fri Jan 30 07:01:41 2015
New Revision: 938341
Log:
Staging update by buildbot for taverna
Added:
websites/staging/taverna/trunk/content/introduction/services-in-taverna.html
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
Propchange: websites/staging/taverna/trunk/cgi-bin/
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--- websites/staging/taverna/trunk/content/introduction/services-in-taverna.html (added)
+++ websites/staging/taverna/trunk/content/introduction/services-in-taverna.html Fri Jan 30 07:01:41 2015
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+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+ <meta http-equiv="X-UA-Compatible" content="IE=edge">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <title>Apache Taverna - Services in Taverna</title>
+
+ <meta http-equiv="Content-Type" content="text/html;charset=UTF-8">
+ <meta property="og:image" content="/img/taverna-logo-145x134.png" />
+
+ <link rel="shortcut icon" href="/favicon.ico">
+ <link rel="icon" type="image/png" sizes="145x134" href="/img/taverna-logo-145x134.png">
+ <link rel="apple-touch-icon" sizes="145x134" href="/img/taverna-logo-145x134.png">
+
+ <link rel="stylesheet" href="/lib/bootstrap/css/bootstrap.min.css">
+ <link rel="stylesheet" href="/lib/bootstrap/css/bootstrap-theme.min.css">
+ <link rel="stylesheet" href="/css/sticky-footer-navbar.css">
+ <link rel="stylesheet" href="/css/taverna.css">
+
+
+
+
+ <!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. -->
+
+ <!-- JSON-LD markup for Google Structured Data -->
+
+ <!-- generic JSON-LD for this page -->
+ <script type="application/ld+json">
+ {
+ "@context" : "http://schema.org",
+ "@type" : ["CreativeWork"],
+ "@id": "",
+ "name" : "Services in Taverna",
+ "publisher" : {
+ "@type" : "Organization",
+ "url" : "http://www.apache.org/",
+ "name" : "The Apache Software Foundation (ASF)"
+ },
+ "license": {
+ "@type": "CreativeWork",
+ "@id": "http://www.apache.org/licenses/LICENSE-2.0",
+ "url": "http://www.apache.org/licenses/LICENSE-2.0",
+ "name": "Apache License, Version 2.0"
+ }
+ }
+</script>
+
+ </head>
+
+ <body>
+
+ <!-- Static navbar -->
+ <nav class="navbar navbar-default" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="/"><img src="/img/taverna-logo-145x134.png" alt="">Apache Taverna</a>
+
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li class="dropdown">
+ <a class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Introduction<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/introduction/">Introduction</a></li>
+ <li><a href="/introduction/taverna-features.html">Taverna features</a></li>
+ <li><a href="/introduction/why-use-workflows.html">Why use workflows?</a></li>
+ <li><a href="/introduction/what-is-in-silico-experimentation.html">What is âin silicoâ experimentation?</a></li>
+ </ul>
+ </li>
+ <li><a href="/about/">About</a></li>
+ <li class="dropdown">
+ <a href="/download/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Download<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/download/">Apache Taverna 3.x</a></li>
+ <li><a href="/download/pre-apache.html">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li><a href="/doc/">Documentation</a></li>
+ <li><a href="/code/">Code</a></li>
+ <li><a href="/contact/">Contact</a></li>
+ </ul>
+
+ <form >
+
+
+ <!--<input type="submit" id="submit" value="Search">-->
+ </form>
+
+ <form class="navbar-form navbar-right" role="search"
+ name="search" id="search" action="http://www.google.com/search" method="get">
+ <input value="taverna.incubator.apache.org" name="sitesearch" type="hidden"/>
+ <div class="form-group input-group">
+ <input type="text" name="q" id="query" placeholder="Search" class="form-control">
+ <span class="input-group-btn">
+ <button type="submit" class="btn btn-default">Search</button>
+ </span>
+ </div>
+ </form>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">ASF<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="http://www.apache.org/">Apache Software Foundation</a></li>
+ <li><a href="http://www.apache.org/foundation/how-it-works.html">How it works</a></li>
+ <li><a href="http://www.apache.org/foundation/thanks.html">Thanks</a></li>
+ <li><a href="http://www.apache.org/foundation/sponsorship.html">Become a Sponsor</a></li>
+ <li><a href="http://incubator.apache.org/projects/taverna.html">Taverna Incubation Status</a></li>
+ </ul>
+ </li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container-->
+ </nav>
+
+
+ <div id="page" class="container">
+ <h1>Services in Taverna</h1>
+ <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
+
+Taverna is transitioning to the Apache Incubator.
+This webpage reflects material not yet released under Apache Incubator.
+Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
+</div>
+
+
+ <div id="content"><p>Taverna can access a large number of services in the fields of bioinformatics, astronomy, chemoinformatics,
+ health informatics and others. Although many examples of using Taverna lie in the bioinformatics domain,
+ Taverna is actually domain independent.
+This means that Taverna can be applied to a wide range of fields â even music and food sciences.</p>
+<p>Taverna can invoke generic <a href="/documentation/glossary.html#wsdl">WSDL-style Web services</a>.
+You do not need to alter a service in any way;
+you simply need to give Taverna the URL address of the serviceâs WSDL document.
+Please refer to our <a href="/developers/web-service-developers.html">Web service developersâ documentation</a> if you are planning on developing Web services
+ accessible from Taverna.</p>
+<p>Taverna can also access other types of Web services, such as <a href="/documentation/glossary.html#biomoby">BioMoby</a>, <a href="/documentation/glossary.html#biomart">BioMart</a> and <a href="/documentation/glossary.html#soaplab">SoapLab</a>
+ services.</p>
+<p>In addition, Taverna can invoke local Java services (<a href="/documentation/glossary.html#beanshell">Beanshell</a> scripts), local Java API (<a href="/documentation/glossary.html#api_consumer">API Consumer</a>),
+ R scripts on an R server (<a href="/documentation/glossary.html#rshell">Rshell</a> scripts), import data from a <a href="/documentation/glossary.html#spreadsheet_import">cvs or Excel spreadsheet</a> and interact
+ with users in a browser.</p>
+<p>Taverna can also <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Interaction+service">interact</a> with a running workflow from your Web browser,
+ and has the ability to incorporate workflow fragments (reusable <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Component+services">components</a>) as services in a workflow.</p>
+<p>A full list of service types is in the <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Service+types">User Manual</a>.</p>
+<p>Please see the <a href="http://biocatalogue.org/">BioCatalogue</a> for details of the services we are currently aware of that work with Taverna.
+If you would like to add your services to this list, please contact <a href="http://www.biocatalogue.org/contact">the BioCatalogue team</a>.</p>
+<h2 id="domain-and-shim-services">Domain and shim services</h2>
+<p>Services accessible from Taverna can be broadly categorised into domain services and shim services.</p>
+<ul>
+<li>Domain (scientific) services perform scientific function(s) and are often provided by third-party suppliers.
+ They cannot usually be changed by individual users.</li>
+<li>Shim services are created during workflow design,
+ to specifically connect the inputs and outputs of closely related services in order to achieve
+ interoperation between domain services.
+ This typically involves changing one serviceâs output into a different format for another service to accept. An example might include changing the output from tab to comma separated values. Taverna comes with a library of frequently used shim services. A new workflow, however, often brings about the need to develop a new shim or modify an existing one.</li>
+</ul>
+<p>A rule of thumb for distinguishing a domain service from a shim service is that a workflow,
+ when the shims services are invisible, is equivalent to the methods section of a scientific paper.
+If a service needs to be explicitly mentioned in the method, then it is not a shim.</p>
+<h2 id="service-providers">Service providers</h2>
+<p>Nearly all services accessible by Taverna are neither owned nor provided by us.
+The majority of services are provided by third-party institutes and research facilities,
+ all of which can be accessed from within Taverna.
+Taverna only provides most commonly used shim services, e.g. to concatenate strings, read content from a file,
+ etc.</p>
+<p>Service suppliers can often be large government-funded bodies such as the <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> (United States),
+ <a href="http://www.ebi.ac.uk/">EMBL-EBI</a> (Europe) or <a href="http://www.ddbj.nig.ac.jp/">DNA Databank of Japan</a>.
+Each is responsible in providing data to the global scientific community.
+These major providers generally have dedicated human resources for service development, API documentation,
+ hosting and maintenance.
+In addition to programmatic access to their services these also maintain Web-form based access.</p>
+<p>A large proportion of suppliers of services and workflows are much smaller in scale â
+ this includes individuals or small laboratories that have developed a tool, algorithm, database,
+ or workflow that they wish to share with others.
+Developers of services from these small establishments may have limited knowledge on Web services and
+ related standards when compared to their knowledge of programming/scripting.
+Such circumstances have required myGrid to develop tools like <a href="http://www.ebi.ac.uk/soaplab/">Soaplab</a> that help alleviate this limitation
+ of small-scale providers by allowing simple deployment of the tool at hand.</p>
+<p>All these service providers are independent of, and usually ignorant of, their consumers.
+Thus, the suppliers and consumers in the open market are loosely coupled and asynchronous.
+Other services are private and local to the scientist (workflow designer),
+ or developed specifically for a workflow to make it work.
+Creating a service accessible from Taverna</p>
+<p>If you are planning on creating a service that should be accessible from Taverna,
+ please have a look at the documentation for Web service developers<a href="/developers/web-service-developers.html">link text</a>.</p></div>
+
+ </div>
+
+ <footer class="footer">
+ <div class="container">
+ <p id="copyright" class="text-muted">
+ Copyright © 2014 The Apache Software Foundation, Licensed under the
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a>.
+ Apache and the Apache feather logo are trademarks of The Apache Software Foundation.
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