Author: gnaylor
Date: Thu Jul 14 18:34:50 2016
New Revision: 1752720
URL: http://svn.apache.org/viewvc?rev=1752720&view=rev
Log:
Add section headers and attrib for 2 quotes
Modified:
incubator/taverna/site/trunk/content/introduction/related-projects.md
Modified: incubator/taverna/site/trunk/content/introduction/related-projects.md
URL:
http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/introduction/related-projects.md?rev=1752720&r1=1752719&r2=1752720&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/introduction/related-projects.md
(original)
+++ incubator/taverna/site/trunk/content/introduction/related-projects.md Thu
Jul 14 18:34:50 2016
@@ -16,17 +16,19 @@ Notice: Licensed to the Apache Softwa
specific language governing permissions and limitations
under the License.
-The Taverna team are currently involved or collaborating on several projects
sponsoring the development
+## New Projects
+The Taverna team are currently involved in or collaborating on several
projects sponsoring the development
of new tools and the improvement of Taverna:
- [SEEK][103] â the SEEK platform is a web-based resource for sharing
heterogeneous scientific research datasets, models or simulations, processes
and research outcomes.
- - [BioVeL][1] â establishing an international e-Laboratory to allow
biodiversity scientists to jointly tackle
+ - [BioVeL][1] â establishing an international e-Laboratory to allow
biodiversity scientists to jointly tackle
diverse research challenges using Taverna, myExperiment and BioCatalogue
- - [Wf4Ever][2] â providing methods and tools required to ensure the
long-term preservation of
+ - [Wf4Ever][2] â providing methods and tools required to ensure the
long-term preservation of
scientific workflows
- - [SCAPE][3] â large scale and computation intense automated digital
preservation and quality assurance
+ - [SCAPE][3] â large scale and computation intense automated digital
preservation and quality assurance
workflows on a cloud infrastructure
+## Specific e-Science projects
We are also involved in various projects set out to solve particular e-Science
problems using Taverna:
- [ChemTaverna][4] â workflows for chemoinformatics
@@ -35,22 +37,24 @@ We are also involved in various projects
- [REFINE][8] â text mining and visualisation
- [HELIO][9] â services and workflows for HelioPhysics
-An outreach project designed to expose scientists to the possible uses of
e-Science and to aid them in
+## Outreach project
+An outreach project is designed to expose scientists to the possible uses of
e-Science and to aid them in
adopting the available tools and techniques:
- - [ENGAGE][10] â JISC initiative for exploiting the benefits of
e-Infrastructure by developing and deploying
- new software solutions on available UK e-Infrastructure; funded a
development project to facilitate
+ - [ENGAGE][10] â JISC initiative for exploiting the benefits of
e-Infrastructure by developing and deploying
+ new software solutions on available UK e-Infrastructure; funded a
development project to facilitate
the use of Taverna for [Shared Genomics][11]
+## Previous projects
There are also a large number of Taverna-related projects that the team have
been involved with in the past:
- [HELIO][12] â the Heliophysics Integrated Observatory
- - [TSB grant][13] â to address NHS requirements for accessing and comparing
large amounts of information and
+ - [TSB grant][13] â to address NHS requirements for accessing and comparing
large amounts of information and
find common genetic links when testing new treatments (in partnership
with Eagle Genomics)
- - [Taverna-Galaxy][14] â a tool for automatic generation and exposure of
Taverna workflows as Galaxy tools.
+ - [Taverna-Galaxy][14] â a tool for automatic generation and exposure of
Taverna workflows as Galaxy tools.
Galaxy is an open, web-based platform for data intensive biomedical research
- - [e-LICO][15] â a virtual laboratory for interdisciplinary collaborative
workflows in data mining and
+ - [e-LICO][15] â a virtual laboratory for interdisciplinary collaborative
workflows in data mining and
data-intensive sciences
- [NeISS][16] â Taverna workflows for social (population and traffic)
simulations in portals
- [caGrid project][17] â support for running cancer-research workflows
@@ -58,79 +62,80 @@ There are also a large number of Taverna
- [ISpider][19] â proteomics workflows
- [MIASGrid][20] â medical imaging
+## Project descriptions
<a name="biovel"></a>
-##BioVeL##
+### BioVeL
-The Biodiversity Virtual eâLaboratory (BioVeL) project,
- led by the School of Computer Science and Informatics at Cardiff University,
+The Biodiversity Virtual eâLaboratory (BioVeL) project,
+ led by the School of Computer Science and Informatics at Cardiff University,
has â¬5 million in funding and is seeking to provide a vital service that
will improve the way scientists share,
- analyse and present information in the growing area of biodiversity science.
+ analyse and present information in the growing area of biodiversity science.
The project includes the application of Taverna, [myExperiment][21] and the
[BioCatalogue][22].
-Biodiversity science is the study of plants and animals that inhabit our
planet and the environments they
- live in.
-Amid growing concerns over the extinction rate of certain species as their
natural habitats are increasingly
- destroyed, and with biodiversity becoming as important as climate change on
the political agenda,
+Biodiversity science is the study of plants and animals that inhabit our
planet and the environments they
+ live in.
+Amid growing concerns over the extinction rate of certain species as their
natural habitats are increasingly
+ destroyed, and with biodiversity becoming as important as climate change on
the political agenda,
this new research project could not be more timely.
-Biodiversity Virtual eâLaboratory (BioVeL) will establish an international
e-Laboratory â
- the first of its kind in Europe â that will allow biodiversity scientists
to jointly tackle diverse
+Biodiversity Virtual eâLaboratory (BioVeL) will establish an international
e-Laboratory â
+ the first of its kind in Europe â that will allow biodiversity scientists
to jointly tackle diverse
research challenges.
-Experts from Cardiff University along with 15 partners from institutions
across Europe,
- hope that when completed, the BioVeL e-Laboratory will, for the first time,
- give scientists access to multiple data, analysis and computing resources
for biodiversity science through
+Experts from Cardiff University along with 15 partners from institutions
across Europe,
+ hope that when completed, the BioVeL e-Laboratory will, for the first time,
+ give scientists access to multiple data, analysis and computing resources
for biodiversity science through
a robust e-Science infrastructure.
-Ranked by the European Commission (EC) as top of its class from more than 60
proposals,
- BioVeL is funded under the ECâs FP7 e-Infrastructures programme to support
the creation of the
+Ranked by the European Commission (EC) as top of its class from more than 60
proposals,
+ BioVeL is funded under the ECâs FP7 e-Infrastructures programme to support
the creation of the
European Research Area.
For further information on the BioVeL project, visit
[http://www.biovel.eu/][23]
<a name="scape"></a>
-##SCAPE##
+### SCAPE
-[SCAPE][24] (SCAlable Preservation Environments) is an EU-funded FP7 project
aimed at building a scalable
- platform for planning and execution of computation intensive processes for
ingestion or migration of
+[SCAPE][24] (SCAlable Preservation Environments) is an EU-funded FP7 project
aimed at building a scalable
+ platform for planning and execution of computation intensive processes for
ingestion or migration of
large data sets in order to help automate digital preservation.
-The data sets involved are either heterogeneous data collections (collections
of objects of different type),
- contain data objects that are themselves large or complex in structure or
contain a huge amount of digital
- objects.
-The sheer volume of data archives makes it impossible to use the current
service-oriented architectures to
+The data sets involved are either heterogeneous data collections (collections
of objects of different type),
+ contain data objects that are themselves large or complex in structure or
contain a huge amount of digital
+ objects.
+The sheer volume of data archives makes it impossible to use the current
service-oriented architectures to
ensure access to digital information over time.
-In this project, preservation processes will be realised as data pipelines and
described formally as automated,
- quality-assured preservation Taverna workflows. The workflows will invoke
various services for planning
- and execution of institutional preservation and quality assurance
strategies.
-The workflows will be deployed on a large scale (using Hadoop MapReduce
clouds) and executed over large,
+In this project, preservation processes will be realised as data pipelines and
described formally as automated,
+ quality-assured preservation Taverna workflows. The workflows will invoke
various services for planning
+ and execution of institutional preservation and quality assurance
strategies.
+The workflows will be deployed on a large scale (using Hadoop MapReduce
clouds) and executed over large,
distributed and heterogeneous collections of complex digital objects.
-The workflows will enable reproducibility of preservation processes and
collect provenance data over the
+The workflows will enable reproducibility of preservation processes and
collect provenance data over the
entire digital objectâs lifecycle.
-The execution of workflows will be controlled by a policy-based âplanning
and watchâ system, which will
- ensure the workflows are in line with state-of-the art in digital object
representation, file formats,
+The execution of workflows will be controlled by a policy-based âplanning
and watchâ system, which will
+ ensure the workflows are in line with state-of-the art in digital object
representation, file formats,
rendering tools, etc. and detect and report any errors in a preservation
process.
-###SCAPE and Taverna in use###
+**SCAPE and Taverna in use**
by Schlarb Sven, [email protected], Austrian National Library
-SCAPE consists of testbeds that have three application areas: Digital
Repositories,
- from the library community, Web Content, from the web archiving community,
and Research Data Sets,
- from the scientific community.
-The testbeds are used to evaluate solutions developed by the SCAPE project
against defined institutional
- data sets in order to validate their applicability to real life application
scenarios,
+SCAPE consists of testbeds that have three application areas: Digital
Repositories,
+ from the library community, Web Content, from the web archiving community,
and Research Data Sets,
+ from the scientific community.
+The testbeds are used to evaluate solutions developed by the SCAPE project
against defined institutional
+ data sets in order to validate their applicability to real life application
scenarios,
such as large scale data repository ingest-workflows or data archive
maintenance.
-Taverna is being used to develop concept workflows locally, to study the
feasibility of differing approaches.
-Taverna server is used for remote execution of workflows,
+Taverna is being used to develop concept workflows locally, to study the
feasibility of differing approaches.
+Taverna server is used for remote execution of workflows,
with the Tool service in use as the main integration pattern.
-In the context of how Taverna technology is currently used from a research
perspective it is being used
- as a tool for ETL (Extraction/Transform/Load) and creating query-able data
tables from large
+In the context of how Taverna technology is currently used from a research
perspective it is being used
+ as a tool for ETL (Extraction/Transform/Load) and creating query-able data
tables from large
digital object collections. Content analysis and quality assurance are also
performed using Taverna.
Austrian National Library
@@ -139,82 +144,82 @@ Max Kaiser, Head of Department of Resear
Bettina Kann, Head of Digital Library
<a name="ChemTaverna"></a>
-##ChemTaverna##
+### ChemTaverna
-ChemTaverna is a pilot project currently being undertaken to investigate the
application of Taverna in
+ChemTaverna is a pilot project currently being undertaken to investigate the
application of Taverna in
cheminformatics by scientists at the School of Chemistry, University of
Southampton in collaboration
with developers at the [Manchester Interdisciplinary Biocentre][25] (MIB).
-A range of cheminformatics services are available for use in the Taverna
Workbench â
- their [descriptions and example workflows][26] showing how they can be used
in data analyses are available
- on-line.
-All cheminformatics services can be imported to the Workbench in one go in the
form of the
+A range of cheminformatics services are available for use in the Taverna
Workbench â
+ their [descriptions and example workflows][26] showing how they can be used
in data analyses are available
+ on-line.
+All cheminformatics services can be imported to the Workbench in one go in the
form of the
[Chemistry Service Set][27] , which is available from myExperiment as a
Service Set Pack.
-The results from cheminformatics workflows will be shared by means of blogs to
provide a notebook record
- of data analyses.
-The ChemTaverna project will also investigate how laboratory instrumentation
can be controlled in workflows
+The results from cheminformatics workflows will be shared by means of blogs to
provide a notebook record
+ of data analyses.
+The ChemTaverna project will also investigate how laboratory instrumentation
can be controlled in workflows
for use in closed-loop optimization experiments to enhance the performance
of analytical instruments.
-[UsefulChem][28] project, an Open Notebook Science project in chemistry led by
the Bradley Laboratory at
- Drexel University, have created many useful chemistry workflows using
Taverna.
+[UsefulChem][28] project, an Open Notebook Science project in chemistry led by
the Bradley Laboratory at
+ Drexel University, have created many useful chemistry workflows using
Taverna.
The workflows are described at Jean-Claude Bradleyâs [UsefulChem blog][29].
<a name="ondex"></a>
-##ONDEX##
+### ONDEX
-[ONDEX][30] is currently an opensource suite of software that âenables data
from diverse biological data sets
- to be linked, integrated and visualisedâ.
-This [BBSRC][31] funded project aims to support ONDEX and its integration with
more general bioinformatics
+[ONDEX][30] is currently an opensource suite of software that âenables data
from diverse biological data sets
+ to be linked, integrated and visualisedâ.
+This [BBSRC][31] funded project aims to support ONDEX and its integration with
more general bioinformatics
tools, such as those developed by the myGrid team.
-The existing ONDEX functionality is being exposed as Web services.
-These may then be used in workflow systems such as Taverna. Taverna workflows
are also used to increase the
+The existing ONDEX functionality is being exposed as Web services.
+These may then be used in workflow systems such as Taverna. Taverna workflows
are also used to increase the
functionality of ONDEX.
-The partners are the [University of Manchester][32] ([Carole Goble][33] and
Robert Stevens),
-[University of Newcastle][34] (Anil Wipat), [Rothamsted Research][35] (C
Rawlings),
-[the National Centre for Text Mining][36] and [Manchester Centre of
Integrative Systems Biology][37].
+The partners are the [University of Manchester][32] ([Carole Goble][33] and
Robert Stevens),
+[University of Newcastle][34] (Anil Wipat), [Rothamsted Research][35] (C
Rawlings),
+[the National Centre for Text Mining][36] and [Manchester Centre of
Integrative Systems Biology][37].
The project runs from April 2008 to March 2011.
<a name="shared-genomics"></a>
-##Shared Genomics##
+### Shared Genomics
-Shared Genomics project, in partnership with Microsoft, aims to develop
accessible High Power Computing
- infrastructure to support the analysis of large genetic data. An essential
part of the work is the
- integration of results with metadata retrieved from knowledge repositories.
-This work will build upon the myGrid achievements in the association of
metadata with data and the description
+Shared Genomics project, in partnership with Microsoft, aims to develop
accessible High Power Computing
+ infrastructure to support the analysis of large genetic data. An essential
part of the work is the
+ integration of results with metadata retrieved from knowledge repositories.
+This work will build upon the myGrid achievements in the association of
metadata with data and the description
of the semantics of services.
-The project is based at the North West Institute for BioHealth Informatics
(NIBHI),
- a collaborative venture between the major universities in the North West of
England,
- industrial partners such as Astra Zeneca, and the North West Development
Agency.
-The principal investigator is Iain Buchan. The project is funded for £600k
and runs from March 2008 to
+The project is based at the North West Institute for BioHealth Informatics
(NIBHI),
+ a collaborative venture between the major universities in the North West of
England,
+ industrial partners such as Astra Zeneca, and the North West Development
Agency.
+The principal investigator is Iain Buchan. The project is funded for £600k
and runs from March 2008 to
February 2010.
Enable Taverna workflows in a Shared Genomics causality workbench
-This is an ENGAGE funded project to enable Taverna workflows using Shared
Genomics services to be called
+This is an ENGAGE-funded project to enable Taverna workflows using Shared
Genomics services to be called
in a more efficient manner. This work builds on the Taverna Server.
<a name="refine"></a>
-##REFINE##
+### REFINE
-[REFINE][38], Tools for the text mining-based visualisation of the provenance
of
- biochemical networks, is a BBSRC funded project to find solutions for the
terminology
+[REFINE][38], Tools for the text-mining-based visualisation of the provenance
of
+ biochemical networks, is a BBSRC funded project to find solutions for the
terminology
problem in systems biology, by developing techniques for recognising
synonym terms.
-The REFINE project involves the use of text mining tools.
-Their application will be influenced by the experience of the myGrid team and
Taverna Workbench users in
+The REFINE project involves the use of text-mining tools.
+Their application will be influenced by the experience of the myGrid team and
Taverna Workbench users in
this area.
-The principal investigator is [Sophia Ananiadou][40], Director of the National
Centre for Text Mining
- ([NaCTeM][41]) at the [University of Manchester][42].
+The principal investigator is [Sophia Ananiadou][40], Director of the National
Centre for Text Mining
+ ([NaCTeM][41]) at the [University of Manchester][42].
The project runs from January 2007 to June 2010.
<a name="helio"></a>
-##HELIO##
+### HELIO
-[HELIO][43], the Heliophysics Integrated Observatory, is a three year EU
funded project that started in
+[HELIO][43], the Heliophysics Integrated Observatory, is a three year EU
funded project that started in
June 2009.
> The Heliophysics Integrated Observatory, HELIO, will deploy a
@@ -222,73 +227,73 @@ The project runs from January 2007 to Ju
> community of researchers in heliophysics. HELIO will provide the most
> comprehensive integrated information system in this domain; it will
> coordinate access to the resources needed by the community, and will
-> provide access to services to mine and analyse the data.
+> provide access to services to mine and analyse the data. <small>[HELIO
Project Information][104]</small>
The project [partners][44] include institutions from France, Ireland, Italy,
Switzerland, the UK and the USA.
Publications
-Workflows for Heliophysics, Blanc, A., Brooke, J., Fellows, D., Soldati, M.,
Pérez-Suárez, D., Marassi, A.,
+Workflows for Heliophysics, Blanc, A., Brooke, J., Fellows, D., Soldati, M.,
Pérez-Suárez, D., Marassi, A.,
Santin, A., [Journal of Grid Computing][45].
[http://link.springer.com/article/10.1007%2Fs10723-013-9256-5][46]
<a name = "engage"></a>
-##ENGAGE##
+### ENGAGE
-The ENGage Academic Groups with E-infrastructure ([ENGAGE][47]) project is a
[JISC][48]
- funded initiative involving the
- [National Grid Service][49] (NGS) and the Universities of
[Southampton][50],
+>The ENGage Academic Groups with E-infrastructure ([ENGAGE][47]) project is a
[JISC][48]
+ funded initiative involving the
+ [National Grid Service][49] (NGS) and the Universities of [Southampton][50],
[Manchester][51] and [Edinburgh][52].
-âThe overall aim of the project is to improve the experience of research
users of UK e-Infrastructure,
- and promote the use of UK e-Infrastructure to a wider set of users by
engaging with different research
+>âThe overall aim of the project is to improve the experience of research
users of UK e-Infrastructure,
+ and promote the use of UK e-Infrastructure to a wider set of users by
engaging with different research
communities.â
-The principal investigator is David De Roure.
+>The principal investigator is David De Roure.
-ENGAGE funded a development project to facilitate the use of Taverna for
[Shared Genomics][53].
+>ENGAGE funded a development project to facilitate the use of Taverna for
[Shared Genomics][53].<small>[mGrid, ENGAGE][105]</small>
<a name = "tsb"></a>
-##TSB grant##
+### TSB grant
-This £500,000 project is part-funded by the UKâs national innovation
agency,
- the Technology Strategy Board (TSB) and is carried out by [Eagle
Genomics][54],
- a leading open-source bioinformatics service provider,
- in collaboration with the myGrid/Taverna team and Cytocell Ltd., with
assistance from [NGRL][55],
- based at the Central Manchester University Hospitals NHS Foundation Trust,
+This £500,000 project is part-funded by the UKâs national innovation agency,
+ the Technology Strategy Board (TSB) and is carried out by [Eagle
Genomics][54],
+ a leading open-source bioinformatics service provider,
+ in collaboration with the myGrid/Taverna team and Cytocell Ltd., with
assistance from [NGRL][55],
+ based at the Central Manchester University Hospitals NHS Foundation Trust,
and the [NIHR Manchester Biomedical Research Centre][56].
-The project will build upon the success of the Taverna Workflow Management
System in next generation
- sequencing to enable medical researchers who are developing and testing new
treatments to compare large
+The project will build upon the success of the Taverna Workflow Management
System in next generation
+ sequencing to enable medical researchers who are developing and testing new
treatments to compare large
amounts of information analysed and stored on a cloud and find common
genetic links.
-The technology will also help clinicians to look at an individual patientâs
genetic make-up to aid diagnosis
+The technology will also help clinicians to look at an individual patientâs
genetic make-up to aid diagnosis
and ongoing treatment.
-Rather than simply testing a patient for one suspected condition,
+Rather than simply testing a patient for one suspected condition,
using the cloud technology could allow clinicians to test for a much wider
range of complaints.
-Currently, the NHS IT systems do not have the resources to cope with the huge
demands required.
+Currently, the NHS IT systems do not have the resources to cope with the huge
demands required.
The cloud system can be accessed from a separate site, away from hospitals,
freeing up space.
-Eagle Genomics will work with the Taverna team to adapt Taverna to allow
non-IT experts to easily add and
+Eagle Genomics will work with the Taverna team to adapt Taverna to allow
non-IT experts to easily add and
extract information and share it with their colleagues.
[Read mode about the project][57].
<a name = "taverna-galaxy"></a>
-##Taverna 2-Galaxy##
+### Taverna 2-Galaxy
-[Galaxy][58] is an open, Web-based platform for data intensive biomedical
research.
-Taverna 2-Galaxy integration is a first step towards making Galaxy and Taverna
2 more interoperable.
-It allows the automatic generation of Galaxy tools from Taverna 2 workflows.
-The tools can then be installed as usual in a Galaxy server and allow the
Taverna workflows to become part
+[Galaxy][58] is an open, Web-based platform for data intensive biomedical
research.
+Taverna 2-Galaxy integration is a first step towards making Galaxy and Taverna
2 more interoperable.
+It allows the automatic generation of Galaxy tools from Taverna 2 workflows.
+The tools can then be installed as usual in a Galaxy server and allow the
Taverna workflows to become part
of a Galaxy pipeline. It has been developed by Kostas Karasavvas of
[NBIC][59].
-Users do not need to install Taverna 2-Galaxy themselves.
-It is available as part of the myExperiment [Web site][60].
-While browsing Taverna 2 workflows the user will see an additional link
âDownload as Galaxy Toolâ in the
- download section of the workflow.
-The tool can then be installed into Galaxy in the usual manner by the Galaxy
administrator.
+Users do not need to install Taverna 2-Galaxy themselves.
+It is available as part of the myExperiment [Web site][60].
+While browsing Taverna 2 workflows the user will see an additional link
âDownload as Galaxy Toolâ in the
+ download section of the workflow.
+The tool can then be installed into Galaxy in the usual manner by the Galaxy
administrator.
They will also need a [Taverna Server][61] that will run the Taverna 2-Galaxy
tools.
Also check out the Taverna-Galaxy [wiki][62].
@@ -303,138 +308,138 @@ Try it out
The [NBIC Galaxy Server][65] provides a demo platform to run some
pre-installed Taverna workflows in Galaxy
-Taverna-Galaxy in use
+**Taverna-Galaxy in use**
-Dr Casey Bergman and his group of Life Sciences researchers from the [Bergman
Lab][66] @ University of Manchester
+Dr Casey Bergman and his group of Life Sciences researchers from the [Bergman
Lab][66] @ University of Manchester
working on eukaryotic genome biology have successfully installed and used
the integrated Taverna-Galaxy tools.
See [their blog][67] about their experiences in installing and running
Taverna-Galaxy.
<a name = "e-lico"></a>
-##e-LICO##
+### e-LICO
The goal of the [e-LICO project][68] is to build a virtual laboratory for
interdisciplinary collaborative research in data mining and data-intensive
sciences. The proposed e-lab will comprise three layers: the e-science and data
mining layers will form a generic research environment that can be adapted to
different scientific domains by customizing the application layer.
The foundation of the e-science layer is a suite of open source components
from the myGrid e-science platform (one of which is the next generation Taverna
Workbench). To build the e-LICO infrastructure, these components will be
extended with tools for content creation (e.g. semantic annotation, ontology
engineering), as well as mechanisms for multiple levels and modes of
collaboration in experimental research.
-A [video tutorial][69] explains how to build data mining workflows.
+A [video tutorial][69] explains how to build data-mining workflows.
<a name = "neiss"></a>
-##NeISS##
+### NeISS
-The National e-Infrastructure for Social Simulation is a [JISC][70]-funded
project to undertake a coordinated
- programme of producing services and furthering uptake through community
engagement to create a sustainable,
- long-term platform for social simulation with potential for major strategic
impact,
- both in the UK and internationally.
-The project involves [Leeds University][71], [Manchester University][72]
- (including
[NCeSS](http://en.wikipedia.org/wiki/National_Centre_for_e-Social_Science)),
+The National e-Infrastructure for Social Simulation is a [JISC][70]-funded
project to undertake a coordinated
+ programme of producing services and furthering uptake through community
engagement to create a sustainable,
+ long-term platform for social simulation with potential for major strategic
impact,
+ both in the UK and internationally.
+The project involves [Leeds University][71], [Manchester University][72]
+ (including
[NCeSS](http://en.wikipedia.org/wiki/National_Centre_for_e-Social_Science)),
[Stirling University][74], Glasgow University, UCL, Southampton University,
STFC Daresbury Laboratory.
Within the project, the Taverna team are working on:
- - the integration of the Taverna functionality into a portal, i.e. providing
JSR 168/286 compliant
+ - the integration of the Taverna functionality into a portal, i.e. providing
JSR 168/286 compliant
components that provide access to enactment, management, monitoring and
creation of workflows.
- - the re-purposing of services from [myExperiment][75], facilitating their
integration into a portal.
- An important focus will be the incorporation of social networking
functionality to provide extended
+ - the re-purposing of services from [myExperiment][75], facilitating their
integration into a portal.
+ An important focus will be the incorporation of social networking
functionality to provide extended
archiving and documentation capability for social simulations.
-[Documentation on wrapping Taverna workflows in a portal and the code][76] is
available from our
- (Pre Apache) wiki.
+[Documentation on wrapping Taverna workflows in a portal and the code][76] is
available from our
+ (Pre-Apache) wiki.
<a name = "cagrid"></a>
-##caGrid##
+### caGrid
-[caGrid][77] is part of [caBIG][78] (cancer Biomedical Informatics Grid),
+[caGrid][77] is part of [caBIG][78] (cancer Biomedical Informatics Grid),
a US project to carry out eScience and bioinformatics in cancer research.
-The Taverna team were funded by the US National Cancer Institute (NCI) to help
integrate Taverna with caGrid,
+The Taverna team were funded by the US National Cancer Institute (NCI) to help
integrate Taverna with caGrid,
so that Taverna can find and use (secured and non-secured) caBIG data and
analytical services found on caGrid.
-The team wrapped a selection of typical non-caBIG services used by Taverna
users so that they are annotated
+The team wrapped a selection of typical non-caBIG services used by Taverna
users so that they are annotated
and comply with caBIGâs Silver-level compatibility requirements.
-The team also implemented a plugin for Taverna 2.1.2 that enables semantic
search for caGrid services
+The team also implemented a plugin for Taverna 2.1.2 that enables semantic
search for caGrid services
described by the caGridâs Index Service and adding them as component to
workflows.
-More details about the project and the deliverables can be found on the
projectâs [Wiki pages][79] and
- NCIâs Gforge project pages. Source code of the Taverna plugins is
available from the [SVN repository][80].
+More details about the project and the deliverables can be found on the
projectâs [Wiki pages][79] and
+ NCIâs Gforge project pages. Source code of the Taverna plugins is
available from the [SVN repository][80].
The project ran from September 2008 to November 2009.
-The work on the caGrid project follows on from caGridâs previous adoption of
Taverna when the Taverna and
- caGrid collaborated in 2007 to develop a Taverna 1.7.0 GT4 processor as a
plugin based upon the
- Tavernaâs WSDL processor.
-This work has been updated for Taverna 2.x and there are two plugins
available: [caGrid plugin][81]
- (for invoking caGrid services) and [caGrid remote execution plugin][82]
(for remote execution of
+The work on the caGrid project follows on from caGridâs previous adoption of
Taverna when the Taverna and
+ caGrid collaborated in 2007 to develop a Taverna 1.7.0 GT4 processor as a
plugin based upon the
+ Tavernaâs WSDL processor.
+This work has been updated for Taverna 2.x and there are two plugins
available: [caGrid plugin][81]
+ (for invoking caGrid services) and [caGrid remote execution plugin][82]
(for remote execution of
caGrid workflows on a server).
-The functionality of the Taverna 1.7.0 caGrid plugin was shown at a caGrid
meeting in late 2008 where
+The functionality of the Taverna 1.7.0 caGrid plugin was shown at a caGrid
meeting in late 2008 where
the associated poster won an outstanding poster [award][83].
The installation and use of the Taverna 1.7.0 caGrid plugin is described on
the caGrid [wiki][84].
-###Publications###
+**caGrid Publications**
-The [paper][85] âCombining the Power of Taverna and caGrid: Scientific
Workflows that Enable Web-Scale
- Collaborationâ has been written by Wei Tan, Ian Foster and Ravi Madduri
to describe some of the work done on
+The [paper][85] âCombining the Power of Taverna and caGrid: Scientific
Workflows that Enable Web-Scale
+ Collaborationâ has been written by Wei Tan, Ian Foster and Ravi Madduri
to describe some of the work done on
the project.
<a name = "e-fungi"></a>
-##e-Fungi##
+### e-Fungi
-e-Fungi was a BBSRC funded project to produce an e-Science infrastructure for
comparative functional
- genomics in fungal species.
-Parts of the e-Fungi project include the development of a data warehouse and
analysis libraries that are
- exposed as Web services.
+e-Fungi was a BBSRC funded project to produce an e-Science infrastructure for
comparative functional
+ genomics in fungal species.
+Parts of the e-Fungi project include the development of a data warehouse and
analysis libraries that are
+ exposed as Web services.
These Web services can be used within the Taverna Workbench for the creation
of workflows.
-The principal investigators were Professor Norman Paton, Professor Oliver,
- Dr Rattray and Dr Hubbard of the University of Manchester.
+The principal investigators were Professor Norman Paton, Professor Oliver,
+ Dr Rattray and Dr Hubbard of the University of Manchester.
The project ran from October 2004 to June 2008.
<a name = "ispider"></a>
-##iSpider##
+### iSpider
-[iSpider][86] was a [BBSRC][87] funded project to create an informatics
platform for proteomics using Grid-based
- technologies, and to use this to address specific biological problems.
-The grantholders were Dr S. Hubbard, Dr Suzanne Embury, Professor [Carole
Goble][88] CBE,
- Professor Norman Paton, Dr Robert Stevens and Prof Oliver of the
[University of Manchester][89].
+[iSpider][86] was a [BBSRC][87] funded project to create an informatics
platform for proteomics using Grid-based
+ technologies, and to use this to address specific biological problems.
+The grantholders were Dr S. Hubbard, Dr Suzanne Embury, Professor [Carole
Goble][88] CBE,
+ Professor Norman Paton, Dr Robert Stevens and Prof Oliver of the
[University of Manchester][89].
The project ran from July 2004 to June 2007.
-The iSpider project developed three tools that make use of Tavernaâs
functionality and plugability to
+The iSpider project developed three tools that make use of Tavernaâs
functionality and plugability to
support the development of workflows, in particular for proteomics.
Much of the work has been done by Khalid Belhajjame and additional information
can be found in his publications.
A tool for the identification and the characterisation of mismatches in
scientific workflows
-By using the [Feta][90] service registry and extending the capabilities of the
Taverna Workbench,
- this tool provides a means for automatically identifying and characterising
the mismatches that may
+By using the [Feta][90] service registry and extending the capabilities of the
Taverna Workbench,
+ this tool provides a means for automatically identifying and characterising
the mismatches that may
arise between the constituent operations of an in silico experiments.
A tool for automatically inferring service annotations
-This tool allows the derivation, in an automatic fashion,
- of information about the annotations of service parameters using existing
tested-and-tried workflows.
-It has been evaluated using the workflow repository provided by
[myExperiment][91] together with the
+This tool allows the derivation, in an automatic fashion,
+ of information about the annotations of service parameters using existing
tested-and-tried workflows.
+It has been evaluated using the workflow repository provided by
[myExperiment][91] together with the
[myGrid ontology][92].
A system for querying multiple proteomics data sources
-It supports the combined use of Grid data access ([OGSA-DAI][93]), Grid
distributed querying ([OGSA-DQP][94]) and
- data integration ([AutoMed][95]) software tools to support distributed data
analysis.
-This system has been used for providing an integrated access to four
proteomics data sources, namely,
+It supports the combined use of Grid data access ([OGSA-DAI][93]), Grid
distributed querying ([OGSA-DQP][94]) and
+ data integration ([AutoMed][95]) software tools to support distributed data
analysis.
+This system has been used for providing an integrated access to four
proteomics data sources, namely,
[gpmDB][96], [PedroDB][97], PepSeeker and [Pride][98].
<a name = "miasgrid"></a>
-##MIASGrid##
+### MIASGrid
-The MIAS project examined the requirements of Medical Imaging and Signals.
-The [MIASGrid][99] sub-project, took examples of those requirements and
investigated how e-Science and
- the myGrid tools in particular could satisfy them.
+The MIAS project examined the requirements of Medical Imaging and Signals.
+The [MIASGrid][99] sub-project, took examples of those requirements and
investigated how e-Science and
+ the myGrid tools in particular could satisfy them.
The project was funded by the [EPSRC][100] for £494k and ran until April 2006.
-The project produced several workflows that demonstrated the applicability of
Taverna to the handling of
- large amounts of medical image data.
+The project produced several workflows that demonstrated the applicability of
Taverna to the handling of
+ large amounts of medical image data.
The workflows made use of [MATLAB][101] and also interaction with users.
The workflows covered two domains:
@@ -542,4 +547,6 @@ The workflows covered two domains:
[100]: http://www.epsrc.ac.uk/
[101]: http://www.mathworks.com/products/matlab/
[102]: https://www.escholar.manchester.ac.uk/uk-ac-man-scw:1d33210
- [103]: http://www.seek4science.org/
\ No newline at end of file
+ [103]: http://www.seek4science.org/
+ [104]: http://helio-dev.cs.technik.fhnw.ch/heliovo/project-info.html
+ [105]: http://www.mygrid.org.uk/projects/engage/
