Author: gnaylor
Date: Tue Jul 12 19:20:23 2016
New Revision: 1752334
URL: http://svn.apache.org/viewvc?rev=1752334&view=rev
Log:
Add/fix headings; list service types; minor rewrites
Modified:
incubator/taverna/site/trunk/content/introduction/services-in-taverna.md
Modified:
incubator/taverna/site/trunk/content/introduction/services-in-taverna.md
URL:
http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/introduction/services-in-taverna.md?rev=1752334&r1=1752333&r2=1752334&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/introduction/services-in-taverna.md
(original)
+++ incubator/taverna/site/trunk/content/introduction/services-in-taverna.md
Tue Jul 12 19:20:23 2016
@@ -16,25 +16,26 @@ Notice: Licensed to the Apache Softwa
specific language governing permissions and limitations
under the License.
-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.
+## Overview
+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.
-Taverna can invoke generic [WSDL-style Web services][1].
+- **WSDL-style Web services.** Taverna can invoke generic [WSDL-style Web
services][1].
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 [Web service developersâ documentation][2] if you are
planning on developing Web services
accessible from Taverna.
-Taverna can also access other types of Web services, such as [BioMoby][3],
[BioMart][4] and [SoapLab][5]
+- **Other Web services.** Taverna can also access other types of Web services,
such as [BioMoby][3], [BioMart][4] and [SoapLab][5]
services.
-In addition, Taverna can invoke local Java services ([Beanshell][6] scripts),
local Java API ([API Consumer][7]),
+- **Java, R scripts, spreadsheets, and browsers.** In addition, Taverna can
invoke local Java services ([Beanshell][6] scripts), local Java API ([API
Consumer][7]),
R scripts on an R server ([Rshell][8] scripts), import data from a [cvs or
Excel spreadsheet][9] and interact
with users in a browser.
-Taverna can also [interact][10] with a running workflow from your Web browser,
+- **Workflows and workflow fragments.** Taverna can also [interact][10] with a
running workflow from your Web browser,
and has the ability to incorporate workflow fragments (reusable
[components][11]) as services in a workflow.
A full list of service types is in the [User Manual][12].
@@ -42,52 +43,63 @@ A full list of service types is in the [
Please see the [BioCatalogue][13] 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 [the
BioCatalogue team][14].
+---
##Domain and shim services##
Services accessible from Taverna can be broadly categorised into domain
services and shim services.
- - Domain (scientific) services perform scientific function(s) and are often
provided by third-party suppliers.
+ - **Domain (scientific) services** perform scientific function(s) and are
often provided by third-party suppliers.
They cannot usually be changed by individual users.
- - Shim services are created during workflow design,
- to specifically connect the inputs and outputs of closely related
services in order to achieve
+
+ - **Shim services** are created during workflow design
+ specifically to connect the inputs and outputs of closely related
services 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.
+ 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.
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.
+If a service needs explicitly to be mentioned in the method, then it is not a
shim.
+---
##Service providers##
-Nearly all services accessible by Taverna are neither owned nor provided by
us.
+Most services accessible by Taverna are not owned or 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,
+Taverna only provides commonly used shim services, e.g. to concatenate
strings, read content from a file,
etc.
-Service suppliers can often be large government-funded bodies such as the
[NCBI][15] (United States),
+###Large suppliers
+Service suppliers are often large government-funded bodies such as the
[NCBI][15] (United States),
[EMBL-EBI][16] (Europe) or [DNA Databank of Japan][17].
-Each is responsible in providing data to the global scientific community.
+Each is responsible for 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.
+ hosting, and maintenance.
+In addition to programmatic access to their services, these suppliers also
maintain Web-form based access.
+###Smaller suppliers
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
+Developers of services from these small establishments may have limited
knowledge of Web services and
related standards when compared to their knowledge of
programming/scripting.
-Such circumstances have required myGrid to develop tools like [Soaplab][18]
that help alleviate this limitation
+Such circumstances required myGrid (pre-Apache Taverna) to develop tools like
[Soaplab][18] that help alleviate this limitation
of small-scale providers by allowing simple deployment of the tool at hand.
+### Other considerations
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
+
+---
+##Creating a service accessible from Taverna
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[link
text][19].
+ please have a look at the [documentation for Web service developers][19].
[1]: /documentation/glossary#wsdl
