Taverna can connect to a wide variety of bioinformatics resources and has been successfully applied to a number
of bioinformatics problems, listed below according to their sub-domains.
Bioinformatics systems/tools using Taverna:
- BioWEP - bioinformatics workflow enactment portal
- BioLinux - Ubuntu Linux distribution that includes Taverna and many other bioinformatics programs
Biodiversity¶
Gene and genome expression¶
- Next Generation Sequencing using Taverna 2 Server on Amazon cloud
- TavernaPBS - next generation sequencing analysis using a computational cluster that uses a PBS queuing system and Taverna 2 Workbench
- Coordination and Sustainability of International Mouse Informatics Resources (CASIMIR) - workflows to associate mouse genome and phenome
- Developmental Gene Expression Map (DGEMap)- analysis of human gene expression during development
- Graves disease - identification of genes responsible
- Examination of gene expression from MicroArray data using R - statistical analysis of gene expression
- SIGENAE - development of workflows to analyse breeding animal data
- Trypanosomiasis - identification of genes responsible for sleeping sickness
- Williams-Beuren syndrome - automation and confirmation of gene characterization
- PLANET - integration of plant genome resources
- Annotation of genomes
- Shared Genomics
- e-Fungi functional genomics in fungal species
Protein and proteomics¶
- Analysis of mass spectrometry data in proteomics
- Anthrax analysis - identification of proteins secreted by bacteria
- eFamily - integrating data from different databases
- European Model for Bioinformatics Research And Community Education (EMBRACE) - calling services on a grid; recovering a database
- iSpider - querying multiple data sources
- ProDom - running of Taverna workflows behind a portal to search a protein database
Biology and systems biology¶
- ENFIN – Enabling Systems Biology – calling of wrapped tools within workflows
- Manchester Centre for Integrative Systems Biology (MCISB) – modelling metabolomic pathways
- Systems Biology Operational Software (SB.OS) - a live DVD based on Ubuntu Linux that comes with a comprehensive list of Systems Biology Software (including Taverna)
- Tav4SB - Taverna workflows for systems biology, in particular for analysis of the kinetic models of biological systems
- Measuring of enzyme characteristics of yeast
- Automatic Functional Annotation in a distributed Web Service Environment (AFAWE) – protein prediction and annotation by a tool that calls workflows
- PLANET (A Network of European Plant Databases) – calling of workflows from a portal
Biomedicine and disease-related research¶
- Fighting dementia (VP-DARE@IT and VPH-SHARE)
- Analysis of the anthrax bacterium
- Study of resistance into trypanosomiasis (sleeping sickness)
- Identification of genes linked to Graves disease
- Characterisation of genes associated with Williams-Beuren syndrome
- caGrid - research into predicting limphoma cancer
- EU-ADR - detecting adverse drug reactions through the exploitation of clinical data from electronic healthcare records
BioWEP¶
Researchers at the Italian National Institute for Cancer Research Genoa (IST) have developed a Bioinformatics Workflow Enactment Portal called BioWEP.
The portal allows registered users to search for or select from a set of specified Taverna workflows. The workflow can be enacted by entering input values into a form. During enaction, the user can either wait for the result, or for longer running workflows, visit the portal later. The results of the enactment can be downloaded for external visualization.
Publications¶
The http://dx.doi.org/10.1186/1471-2105-8-S1-S19 Biowep: a workflow enactment portal for bioinformatics applications by Romano et al gives an overview of the intent and design of Biowep.
BioLinux¶
The UK’s Natural Environment Research Council (NERC) Environmental Bioinformatics Centre release BioLinux, an installation of Ubuntu Linux that includes many bioinformatics programs.
Among the programs included in the BioLinux distribution is Taverna.
The suite of programs are also available for installation on pre-existing Linux systems.
LUMC¶
People from the Leiden University Medical Center (LUMC in the Netherlands are using Taverna for analysis of mass spectrometry data in proteomics.
They presented a poster at the 2011 ASMS (the American Society for Mass Spectrometry) Conference on Mass Spectrometry and Allied Topics.
Please contact Dr. Magnus Palmblad for more details.
Measuring enzyme characteristics of yeast¶
The Manchester Centre for Integrative Systems Biology (MCISB) is in the process of measuring the kinetic and binding constants associated with enzyme reactions in metabolic pathways in the yeast, Saccharomyces cerevisiae. Quantitative models of these metabolic pathways are being integrated with transcriptomic, proteomic and metabolomic data by workflows that have been constructed and enacted using Taverna.
Publications¶
A poster by Peter Li describing the systems biology workflows was presented at the International Conference of Systems Biology 2006 and he has written several publications about the work.
Many of the workflows make use of Systems Biology Markup Language (SBML) as described in the paper Automated manipulation of systems biology models using libSBML within Taverna workflows by Li et al.
An example workflow using SBML is available on myExperiment.