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Posted to commits@taverna.apache.org by br...@apache.org on 2015/03/02 10:48:39 UTC
svn commit: r1663233 -
/incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md
Author: brenninc
Date: Mon Mar 2 09:48:38 2015
New Revision: 1663233
URL: http://svn.apache.org/r1663233
Log:
Added CCPN
Modified:
incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md
Modified: incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md
URL: http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md?rev=1663233&r1=1663232&r2=1663233&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md (original)
+++ incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md Mon Mar 2 09:48:38 2015
@@ -119,6 +119,65 @@ They developed a Web-based player of Tav
Target application area is the system biology field,
in particular analysis of the kinetic models of biological systems.
+<a name="ccpn"><'a>
+##CCPN
+
+**CCPN use of Taverna**
+by Rasmus Fogh r.h.fogh@bioc.cam.ac.uk, Feb 2013
+
+[WeNMR](http://www.wenmr.eu/) (Worldwide e-Infrastructure for NMR and structural biology)
+ is a virtual research community project that is funded as part of the 7th EU framework.
+The infrastructure lies within the fields of structural biology, NMR and SAXS.
+Its purpose is twofold: It provides an infrastructure for sharing documentation, outreach and communications.
+It also offers web portals where structural biology programs can be run, supports a grid infrastructure
+ for running associated relevant jobs and provides software that presents programs on the web portals and
+ pipes data between them for uploading and downloading.
+
+Our contribution to the WeNMR project is the development of a dual use Workflow Management System (WMS) as shown in Fig.1.
+Its two methods of use are as a:
+
+ - means to launch, manage, and gather results generated by structural biology calculations,
+ making use of programs present on the WeNMR portals,
+ in effect to serve as an entry port for WeNMR and associated calculations in general.
+
+ - data tracking, management and access control system for structural biology laboratories.
+
+
+
+<p align="center">Fig. 1</p>
+
+Taverna is being used to encapsulate and combine protocols on our system,
+ so that the systems are available to, and can be combined with,
+ workflow components from other sources,
+ and to combine different protocols on our system into pipelines.
+The current test project is to develop a system to run four different structure calculation programs
+ from a single job start specification and collating the results into a single combined data source.
+
+Whether Taverna is being used in a scientific role is down to the definition of its role within the project.
+We are developing scientific software,
+ which will be used to perform actual scientific research and analysis by end users â
+ we tend to categorise our role as that of methods developers for structural biology.
+Whether that categorises the role as computer science, structural biology,
+ or software engineering depends on the point of view.
+
+The *methods* are established programs for calculating (mainly) macromolecular structures
+ from Nuclear Magnetic Resonance data, and are therefore used as the primary process for obtaining results.
+These types of calculation require the use of several different programs, sequentially, to process them.
+Passing the data and results from one program to another has been a problem for many years.
+CCPN has long been working on data exchange standards, data conversion software and integration with different programs,
+ and is now working explicitly on setting up pipelines.
+There is an ever-increasing demand for high-throughput calculations that allow the use of alternative programs and
+ that inexperienced users are able to utilise with ease.
+It is to meet these demands that Taverna is being used as a tool that enables the setup of flexible,
+ easy-to-use pipelines.
+
+About me:
+
+I am currently working at the University of Cambridge, Department of Biochemistry,
+ under Professor Ernest Laue.
+As part of my role I am attached to the [CCPN project](http://www.ccpn.ac.uk/),
+ led by Professor Vuister (University of Leicester), formerly led by Professor Laue.
+
<a name="planet"></a>
##PLANET