D2.1.35 - EMBRACE

stizzahaddockSoftware and s/w Development

Dec 14, 2013 (3 years and 7 months ago)

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LHSG
-
CT
-
2004
-
512092




EMBRACE


A European Model for Bioinformatics Research and Community
Education



Network of Excellenc
e


Life Sciences, Genomics and Biotechnology for Health





2.1.35 Public standard interface to Spoctopus






Due date of deliverable:

31.1.2010

Actual submission date:

15.3.2010



Start date of project:


1.2.200
5


Duration: 6
6

months





Organisation nam
e of lead contractor for this deliverable: STO

EMBRACE WP2


Deliverable 2.1.31

Public standard interface to Spoctopus


Background and Introduction

Given the amino acid sequence of a putative alpha
-
helical membrane protein, Spoctopus
predicts the topology

of the protein, i.e. a specification of the membrane spanning
segments and their IN/OUT orientation relative to the membrane. This Spoctopus
algorithm is based on the octopus program, which is a part of the Topcons predictor suite
(Deliverable 2.2.28). Ho
wever, in contrast to these programs, Spoctopus also predicts
signal peptides.


This WSDL service provides the following named operations:

runSpoctopusDefault


Definitions

SOAP: This is a protocol for exchanging XML messages over a network. It allows one
computer (a client) to send a request message to another computer (a server) and for the
server to send a reply back to the client.


Web service: A web service is a software system designed to allow inter
-
computer
interaction over a network. It has an inte
rface described by a computer
-
readable
definition language called WSDL (web services description language). Other computers
interact with a web service, in a manner prescribed by the interface, using messages.
These messages, for this deliverable, are encl
osed in a SOAP envelope and are conveyed
by HTML. Software applications can use web services to exchange data over a network.


Component: A component is a reusable building block, which performs some well
-
defined function within a process, such as a workfl
ow. A key feature of components is
that they are atomic i.e. they cannot be split into smaller units.


Workflow: This is a set of components and relations between them, used to define a
complex process from simple building blocks. Relations may be in the f
orm of data links,
which allow the output of one component to be used as the input of another, or control
links, which state some conditions on the execution of a component.


Protocol


The prediction services have been exposed as web services using the Web

Service
Description language (WSDL) and SOAP::Lite, as outlined in the Embrace technology
recommendation (D3.1.1).
Web Service Description Language is a language for
describing the interface of a Web service. It describes the structure of the data sent t
o and
received from the service, the different operations supported on the service, how to
communicate with the service, and finally where the service is located. All the messages
and description languages are based on XML.

The SOAP::Lite [1] framework, as

its name implies, is an implementation of SOAP and
Web services specifications for the Perl programming language.

This implementation allows writing either clients or servers. On one hand,
a
client means
an application written in Perl that can connect to,

and interact with a Web service with
the definition that is given in its WSDL: the client will just send a request to the service
and get back a response. On the other hand,
a
server means simply the Web service, and
its underlying application. This appli
cation will be published via a Web service and can
then be addressed via its URL (which uniquely identifies the application).


Access to the web service



The service for this deliverable is accessible from Stockholm University. Access is
provided from the

URL
http://wsdl.sbc.su.se/wsdl/
spoctopus.wsdl.


Uses of the service


Users of the application will typically build them into workflows. A Pcons.net prediction
workflow component can be built into workflows usin
g the Taverna [2] software
(
http://taverna.sourceforge.net
), by adding a WSDL
-
scavenger pointing to the above
wsdl
-
URL. Taverna allows the construction of arbitrarily complex workflows using a
graphical inter
face. After the workflows have been constructed it then allows users to run
(enact) the workflow.


The service is also registered in the Embrace registry at
www.embraceregistry.net


Example
input

Input to Sp
octopus is a sequence file.


References


1.

SOAP::Lite. Available at
www.soaplite.com

2.

Taverna: A tool for the composition and enactment of bioinformatics workflows
(2004).
Oinn,T. et al. Bioinformatics Journal 20 (17),

pp 3045
-
3054

3.

SPOCTOPUS: a combined predictor of signal peptides and membrane protein
topology.

Viklund, et al.
Bioinformatics 24 (24) : 2928
-
2929.