Author: gnaylor
Date: Thu Jul 14 18:46:38 2016
New Revision: 1752723
URL: http://svn.apache.org/viewvc?rev=1752723&view=rev
Log:
Fix formatting of HELIO publications and Galaxy try it out
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=1752723&r1=1752722&r2=1752723&view=diff
==============================================================================
--- incubator/taverna/site/trunk/content/introduction/related-projects.md
(original)
+++ incubator/taverna/site/trunk/content/introduction/related-projects.md Thu
Jul 14 18:46:38 2016
@@ -229,8 +229,10 @@ The project runs from January 2007 to Ju
> coordinate access to the resources needed by the community, and will
> 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
+
+**Publications**
Workflows for Heliophysics, Blanc, A., Brooke, J., Fellows, D., Soldati, M.,
Pérez-Suárez, D., Marassi, A.,
Santin, A., [Journal of Grid Computing][45].
@@ -250,7 +252,8 @@ Workflows for Heliophysics, Blanc, A., B
>The principal investigator is David De Roure.
->ENGAGE funded a development project to facilitate the use of Taverna for
[Shared Genomics][53].<small>[mGrid, ENGAGE][105]</small>
+>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
@@ -304,9 +307,9 @@ For Taverna-Galaxy users
- You can [search/browse][63] Taverna workflows from the [myExperiment][64]
workflow repository, and
- Just let your Galaxy administrator know which Taverna workflows you want
installed in Galaxy
-Try it out
+**Try it out**
- The [NBIC Galaxy Server][65] provides a demo platform to run some
pre-installed Taverna workflows in Galaxy
+The [NBIC Galaxy Server][65] provides a demo platform to run some
pre-installed Taverna workflows in Galaxy
**Taverna-Galaxy in use**
@@ -550,3 +553,539 @@ The workflows covered two domains:
[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/
+ ## Current 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
+ diverse research challenges using Taverna, myExperiment and
BioCatalogue
+ - [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
+ 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
+ - [ONDEX][5] â integration of biological data
+ - [Shared Genomics][6] â the use of the [Taverna
Server](/documentation/server) to run genetic data workflows
+ - [REFINE][8] â text mining and visualisation
+ - [HELIO][9] â services and workflows for HelioPhysics
+
+ ## 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
+ 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
+ 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.
+ 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
+ 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
+ - [e-Fungi][18] â Web services for comparative genomics
+ - [ISpider][19] â proteomics workflows
+ - [MIASGrid][20] â medical imaging
+
+ ## Project descriptions
+ <a name="biovel"></a>
+ ### BioVeL
+
+ 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.
+ 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,
+ 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
+ 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
+ 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
+ European Research Area.
+
+ For further information on the BioVeL project, visit
[http://www.biovel.eu/][23]
+
+ <a name="scape"></a>
+ ### 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
+ 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
+ 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,
+ distributed and heterogeneous collections of complex digital objects.
+
+ 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,
+ rendering tools, etc. and detect and report any errors in a preservation
process.
+
+ **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,
+ 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,
+ 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
+ digital object collections. Content analysis and quality assurance are
also performed using Taverna.
+
+ Austrian National Library
+
+ Max Kaiser, Head of Department of Research and Development
+ Bettina Kann, Head of Digital Library
+
+ <a name="ChemTaverna"></a>
+ ### ChemTaverna
+
+ 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
+ [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
+ 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.
+ The workflows are described at Jean-Claude Bradleyâs [UsefulChem blog][29].
+
+ <a name="ondex"></a>
+ ### 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
+ 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
+ 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 project runs from April 2008 to March 2011.
+
+ <a name="shared-genomics"></a>
+ ### 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
+ 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
+ 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
+ in a more efficient manner. This work builds on the Taverna Server.
+
+ <a name="refine"></a>
+ ### 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
+ 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
+ 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 project runs from January 2007 to June 2010.
+
+ <a name="helio"></a>
+ ### HELIO
+
+ [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
+ > distributed network of services that will address the needs of a broad
+ > 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. <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.,
+ Santin, A., [Journal of Grid Computing][45].
+ [http://link.springer.com/article/10.1007%2Fs10723-013-9256-5][46]
+
+ <a name = "engage"></a>
+ ### 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],
+ [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
+ communities.â
+
+ >The principal investigator is David De Roure.
+
+ >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
+
+ 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
+ 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
+ and ongoing treatment.
+
+ 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.
+ 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
+ extract information and share it with their colleagues.
+
+ [Read mode about the project][57].
+
+ <a name = "taverna-galaxy"></a>
+ ### 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
+ 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.
+ They will also need a [Taverna Server][61] that will run the Taverna
2-Galaxy tools.
+
+ Also check out the Taverna-Galaxy [wiki][62].
+ For Taverna-Galaxy users
+
+ - You can now include Taverna workflows as part of your Galaxy workflows
+ - The Taverna workflow will be made available as a Galaxy tool
+ - You can [search/browse][63] Taverna workflows from the [myExperiment][64]
workflow repository, and
+ - Just let your Galaxy administrator know which Taverna workflows you want
installed in Galaxy
+
+ 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**
+
+ 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
+
+ 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 name = "neiss"></a>
+ ### 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)),
+ [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
+ 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
+ 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.
+
+ <a name = "cagrid"></a>
+ ### caGrid
+
+ [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,
+ 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
+ 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
+ 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].
+ 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
+ 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 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].
+
+ **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 project.
+
+ <a name = "e-fungi"></a>
+
+ ### 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.
+ 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 project ran from October 2004 to June 2008.
+
+ <a name = "ispider"></a>
+
+ ### 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].
+ The project ran from July 2004 to June 2007.
+
+ 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
+ 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
+ [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,
+ [gpmDB][96], [PedroDB][97], PepSeeker and [Pride][98].
+
+ <a name = "miasgrid"></a>
+ ### 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 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 workflows made use of [MATLAB][101] and also interaction with users.
+
+ The workflows covered two domains:
+
+ - The analysis of MRI scans of knees to detect changes in cartilage
+ - The [description and searching][102] of a database of mammograms
+
+
+ [1]: #biovel
+ [2]: http://www.wf4ever-project.org/home
+ [3]: #scape
+ [4]: #ChemTaverna
+ [5]: #ondex
+ [6]: #shared-genomics
+ [8]: #refine
+ [9]: #helio
+ [10]: #engage
+ [11]: #shared-genomics
+ [12]: #helio
+ [13]: #tsb
+ [14]: #taverna-galaxy
+ [15]: #e-lico
+ [16]: #neiss
+ [17]: #cagrid
+ [18]: #e-fungi
+ [19]: #ispider
+ [20]: #miasgrid
+ [21]: http://www.myexperiment.org/
+ [22]: http://www.biocatalogue.org/
+ [23]: http://www.biovel.eu/
+ [24]: http://www.scape-project.eu/
+ [25]: http://www.mib.ac.uk/
+ [26]: /introduction/chemistry-web-services
+ [27]: http://www.myexperiment.org/packs/135.html
+ [28]: http://usefulchem.wikispaces.com/
+ [29]: http://usefulchem.blogspot.com/
+ [30]: http://www.ondex.org/
+ [31]: http://www.bbsrc.ac.uk/
+ [32]: http://www.manchester.ac.uk/
+ [33]: https://sites.google.com/site/carolegoble/
+ [34]: http://www.ncl.ac.uk/
+ [35]: http://www.rothamsted.ac.uk/
+ [36]: http://www.nactem.ac.uk/
+ [37]: http://www.mcisb.org/
+ [38]: http://www.nactem.ac.uk/pathtext/
+ [40]: http://www.nactem.ac.uk/staff/sophia.ananiadou/
+ [41]: http://www.nactem.ac.uk/
+ [42]: http://www.manchester.ac.uk/
+ [43]: http://www.helio-vo.eu/
+ [44]: http://www.helio-vo.eu/aboutus/helio_consortium.php
+ [45]: http://link.springer.com/journal/10723
+ [46]: http://link.springer.com/article/10.1007%2Fs10723-013-9256-5
+ [47]: http://www.engage.ac.uk/
+ [48]: http://www.jisc.ac.uk/
+ [49]: http://www.ngs.ac.uk/
+ [50]: http://www.soton.ac.uk/
+ [51]: http://www.manchester.ac.uk/
+ [52]: http://www.edinburgh.ac.uk/
+ [53]: #shared-genomics
+ [54]: http://www.eaglegenomics.com/
+ [55]: http://www.ngrl.org.uk/
+ [56]: http://www.manchesterbrc.org/index.php
+ [57]:
http://www.eaglegenomics.com/genetics-cloud-to-create-new-opportunities-for-researchers-and-clinicians
+ [58]: http://galaxy.psu.edu/
+ [59]: http://www.nbic.nl/
+ [60]: http://www.myexperiment.org/
+ [61]: /documentation/server
+ [62]: https://trac.nbic.nl/elabfactory/wiki/eGalaxy
+ [63]: http://www.myexperiment.org/workflows
+ [64]: http://www.myexperiment.org/
+ [65]: http://galaxy.nbic.nl/
+ [66]: http://bergmanlab.smith.man.ac.uk/
+ [67]: http://bergmanlab.smith.man.ac.uk/?p=943
+ [68]: http://www.e-lico.eu/
+ [69]: http://www.vimeo.com/10345778
+ [70]: http://www.jisc.ac.uk/
+ [71]: http://www.leeds.ac.uk/
+ [72]: http://www.manchester.ac.uk/
+ [74]: http://www.stir.ac.uk/
+ [75]: http://www.myexperiment.org/
+ [76]: http://www.mygrid.org.uk/dev/wiki/display/portals/NeISS+Project
+ [77]: http://www.cagrid.org/
+ [78]: http://cabig.cancer.gov/
+ [79]: http://www.mygrid.org.uk/dev/wiki/display/caGrid/Home
+ [80]: https://gforge.nci.nih.gov/svnroot/taverna-cagrid/
+ [81]:
http://www.taverna.org.uk/documentation/taverna-plugins/taverna-2-x-plugins#cagrid_plugin
+ [82]:
http://www.taverna.org.uk/documentation/taverna-plugins/taverna-2-x-plugins#cagrid_remote_execution_plugin
+ [83]:
http://www.mygrid.org.uk/2008/09/outstanding-poster-award-at-the-cabig-ncri-conference/
+ [84]:
http://cagrid.org/display/knowledgebase/How+to+Create+CaGrid+Workflow+Using+Taverna
+ [85]: http://dx.doi.org/10.1109/MIC.2008.120
+ [86]: http://www.ispider.manchester.ac.uk/
+ [87]: http://www.bbsrc.ac.uk/
+ [88]: https://sites.google.com/site/carolegoble/
+ [89]: http://www.manchester.ac.uk/
+ [90]: http://www.mygrid.org.uk/tools/service-management/feta/
+ [91]: http://www.myexperiment.org/
+ [92]: http://www.mygrid.org.uk/tools/service-management/mygrid-ontology/
+ [93]: http://www.ogsadai.org.uk/
+ [94]: http://link.springer.com/chapter/10.1007%2F978-3-540-24741-8_58
+ [95]: http://www.doc.ic.ac.uk/automed/
+ [96]: http://gpmdb.thegpm.org/
+ [97]: http://pedro.cs.manchester.ac.uk/
+ [98]: http://www.ebi.ac.uk/pride/
+ [99]: http://www.robots.ox.ac.uk/~irc/grid_mias-grid.html
+ [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/
+ [104]: http://helio-dev.cs.technik.fhnw.ch/heliovo/project-info.html
+ [105]: http://www.mygrid.org.uk/projects/engage/
