More than 350 organizations around the world, both academic and commercial, are known to use Taverna. It is employed in a significant number of differing domains to facilitate novel research or to accelerate, formalise or share existing research. See the domains where Taverna is in use or has been used.
Taverna applications have been implemented or deployed in several domains using a variety of platforms and technologies:
- Standalone workbench (used by the majority of projects)
- As a server
- On a grid or using services on a grid
- On a cloud
- Behind a portal
- Bundled with other products
Summary of Taverna in use¶
The table below shows the distribution of Taverna application domains per deployment infrastructure.
View by chronological order of deployment.
Non-workbench applications¶
As a server¶
Taverna has been used as a service and deployed using Taverna Server by several projects:
- BioVel - establishing an international e-Laboratory to enable scientists to work in biodiversity sciences
- VPH-DARE@IT - using Taverna in research to fight dementia
- VPH-SHARE - online environment for the development, construction and storage of biomedical workflows
- Shared Genomics - using Taverna Server to run genetic data workflows
- HELIO - using Taverna Server to run heliophysics workflows
- caGrid - submit Taverna workflows using caGrid's analytic and data services for execution to a Remote Workflow Execution Service on caGrid
- NeISS - runnig social science workflows deployed on a Taverna server from a portal
On a grid¶
Various projects and institutions use mechanisms to run Taverna workflows on a grid or allow them to access services on a grid:
- TavernaPBS – next generation sequencing analysis using a computational cluster that uses a PBS queuing system and Taverna 2 Workbench
- caGrid – the use of Taverna 2 workflows to link together resources provided by the open source grid software infrastructure developed by the US NCI caBIG aimed at enabling multi-institutional cancer data sharing and analysis in the US
- Europe’s leading grid computing project EGEE, piloted Taverna over EGEE gLite services
- European Model for Bioinformatics Research And Community Education (EMBRACE)
- Know-how Sharing Technology Based on ARC Services and Open Standards (KnowARC) developed prototype to use Taverna as direct interface to Grid resources running ARC
- MOTEUR - running Taverna 1 workflows on EGEE grid
- Netherlands BioInformatics Centre (NBIC)
- Grids for Industrial Product Development (SIMDAT)
- JSDL plugin for Taverna 1.7.x that allows you to submit services within a workflow to a grid using GridSAM
- Taverna and myExperiment on NGS
Learn more about how Taverna workflows can operate over a grid infrastructure
On a cloud¶
Taverna has been used as a service deployed on a cloud by several projects:
- TSB grant - 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)
- Next generation sequencing - using Taverna for the genome Single Nucleotide Polymorphism (SNP) analysis on the Amazon cloud
- SCAPE - large scale and computation intense automated digital preservation and quality assurance workflows on a cloud infrastructure
- National Biomedical Computation Resource (NBCR)'s Opal toolkit - a mechanism to wrap up existing scientific applications rapidly as Web services on a cloud
- e-Science Central - allows e-Science Central workflows to be included as services within a Taverna workflow
- Cloud-based Taverna workflows for NMR-based metabolomics data analysis
- The BioVeL project uses the Taverna Server within the Amazon Cloud by employing a Taverna Server Amazon Machine Image (AMI)
- The VPH-Share project does rapid deployment of Taverna Server in their Cloud platform to execute workflows for clinical physiology. These workflows then use further Cloud instances to run applications that are displayed back to users within the VPH-Share portal the resource and data management are all handled by the workflow inside the Taverna Server instance.
Behind a portal¶
Various projects and tools use portals to allow users to perform actions that run Taverna workflows
“behind the scenes”.
These projects include:
- Automatic Functional Annotation in a distributed Web Service Environment (AFAWE) - a tool for the automatic functional annotation of new genes in plants and other organisms making use of Taverna workflows
- Bioinformatics Workflow Enactment Portal (BioWEP) – running pre-selected Taverna workflows from the BioWEP portal
- PLANET (A Network of European Plant Databases)’s BioFloWeb - using Tavenra workfows for the retrieval of information about Arabidopsis genes from several European databases
- ProDom - using Taverna workflowa to perform searches and comparisons on the content of the ProDom database
- MetWare - provides applications, databases and workflows for metabolomics
- NeISS – runnig social simulations workflows deployed on a Taverna 2 Server in a social simulations platform with a portal front-end
Bundled with products¶
Several packages include Taverna as part of their distribution:
- BioLinux - a version of Ubuntu Linux that includes distributions of many bioinformatics programs and Taverna
- OMII-UK - included with the OMII-UK's open-source software developed to enable a sustained future for the UK e-Research community
- Systems Biology Operational Software (SB.OS) - Systems Biology Software based on Ubuntu Linux containing the distribution of Taverna
- CalcTav (bundled with OpenCalc) - a plugin to OpenOffice Calc with the aim of allowing calling bioinformatics services as spreadsheet functions
Taverna by domain¶
Various domains where scientists have used Taverna so far include:
- Annotation
- Arts
- Astronomy
- Biodiversity
- Bioinformatics
- Biology
- Chemistry
- Data and text mining
- Databases
- Document and image analysis (digital preservation)
- Education
- Engineering
- Geoinformatics
- Information quality
- Medicine
- Multimedia
- Natural language processing
- Protein and proteomics(/introduction/taverna-in-use/protein-and-proteomics)
- Service provision
- Service testing
- Social sciences
Taverna-in-use chronology¶
More than 350 organizations around the world, both academic and commercial, are known to use Taverna. It is employed in a significant number of differing domains to facilitate novel research or to accelerate, formalise or share existing research.
2013¶
VP-DATE@IT and VPH-SHARE - active
2012¶
PML Plymouth Marine Laboratory (Institute)
2011¶
TSB Completed Dec-2012
BioVeL - Active
Mass spectrometry data analysis in proteomics - Active
SCAPE - Active
Tav4SB - Software
BioWEP- Software
Open software development wfs - Active
Trypanosomiasis - Active
CalcTav - Active
2010¶
PANACEA - Completed Dec-2012
DAE - Active
TavernaPBS - Active
Next generation sequencing - Active
SB.OS - Software
JPL - Active
MCISB - Completed May-2012
ChemTaverna - Active
2009¶
NeISS - Completed Mar-2012
e-LICO - Completed 2012
HELIO - Completed Dec-2012
2008¶
IMPACT - Completed Jan-2012
MetWare - Software
EU-ADR - Completed Jan-2012
BioLinux - Software
AFAWE - Institute
caGrid - Completed Nov-2009
ENGAGE - Active
ONDEX Completed Mar-2011
2007¶
Shared Genomics - Completed Feb-2010
AID - Active
Graves disease - Active
Course generator - Active
TaWeka - Active
Composing music - Active
MicroArray analysis
REFINE - Completed Jun-2010
2006¶
CCPN - Active
PLANET - Active
Anthrax analysis - Active
KnowARC - Completed 2009
MIASGrid - Completed 2006
eCHASE - Completed2006
MOTEUR - Active
PLANET - Active
2005¶
ENFIN - Completed Nov-2010
CICC - Completed 2008
EMBRACE - Completed May-2006
DGEMap - Completed 2009
SIGENAE - Active
Measuring yeast characteristics - Completed Apr-2010
2004¶
eFamily - Active
Williams-Beuren syndrome - Active
Qurator - Completed Jul-2007
ProDom - Database
e-Fungi - Completed Jun-2008
iSpider - Completed Jun-2007
2002¶
CASIMIR - Completed May-2006
2001¶
SIMDAT - Active
Moby consortium - Active
AstroGrid - Completed 2009