Building Biodiversity Workflows with Taverna
5-6 December 2013, School of Computer Science, Kilburn Building, The University of Manchester, UK. M13 9PL.
Room 2.19 (2nd Floor) School of Computer Science at The University of Manchester
Thu 5th Dec, 2013, 10:00 – 17:00
Fri 6th Dec, 2013, 09:30 – 16:00
The course is a two-day hands-on training event. The course will accommodate 10-15 researchers. The program consists of introductory lectures, practical computer work, and discussions. Researchers will be contacted upon admission in order to consider their own research objectives for the course.
Target community & qualifications
The target community is developers and data scientists working in all areas of biodiversity research, for example taxonomy, ecology, environmental sciences, genetics, population genetics, species distribution and population modelling, bioinformatics, phylogenetics, or the like.
A pre-requisite for the course will be some level of exposure to computer programming, for example developing in R.
The training event will introduce participants to the BioVeL project, and teach the attendees how to:
- run workflows via the BioVeL portal
- develop workflows using the Taverna workbench,
- register and discover services in the biodiversity catalogue and
- share workflows via myExperiment.
In the last two decades the relationship between biodiversity and ecosystem function has become a central issue in ecology, while biodiversity loss has been identified as a major driver of ecosystem change. As a result, ecological research transforms into a species-rich scientific discipline with increased focus on the ability to document, study, and predict the biodiversity composition in ecosystems. However, the analysis of patterns of biodiversity over large temporal and spatial scales is still very difficult to achieve as it requires biologists and environmental scientists to integrate their expertise, data, and methodologies across the traditional biological disciplines.
The Biodiversity Virtual e-Laboratory, BioVeL, addresses this challenge. In the BioVeL, scientists and computer engineers are working together to develop tools for pipelining data and analysis into efficient analytical pipelines, called workflows. Workflows are complex digital data manipulations and modelling tasks that execute sequences of web services. BioVeL designs and deploys such workflows for a selected number of important areas in systematic, ecological, and conservation research, e.g. for the analysis of data sets with ecological, taxonomic, phylogenetic, and environmental information.
The workflows allow the researcher to
(i) explore, access, refine, and format large data sets from major data providers,
(ii) combine disparate data sets with the researchers' individual data, and
(iii) run complex and computationally intense analytical cycles.
Introduction to the BioVeL technical infrastructure, practical workflow building using worked examples, utilising workflow components, discovering and registering services, sharing workflows.
After completion of course the participants are expected to be able to
- Have an understating of the BioVeL infrastructure (Taverna workbench, portal, workflows, services)
- Construct simple workflows in order to support their own biodiversity research
- Discover and share workflows and webservices
- Participants need to bring their own laptops.
- Installation of the Taverna Workbench is required prior to the workshop. Simple online instructions will be provided.
- Short CV/biography (½ page).
- 15 line research objectives, incl. any data you want to analyse and the scientific question you wish to address.
- Session 1. will set the stage with a presentation of a scientific showcase based on a BioVeL Workflow, including a live demonstration of the workflow in action. We will continue with an overview of the BioVeL (www.biovel.eu) project, including a brief introduction to newly released workflows, including taxonomic data refinement, ecological niche modeling, metagenomic traits based analysis.
- Session 2. will introduce the BioVeL technical infrastructure, including the Taverna Workbench, BioVeL Portal, myExperiment and Biodiversity Catalogue.
- Session 3. will include a practical example of building a biodiversity workflow using the Taverna workbench. Including the discovery of services via biodiversity catalogue and sharing workflows via myExperiment.
- Session 3 continued.
- Session 4. will include an introduction to building modular workflows using workflow components and a hands- on session where attendees will be able to address their own scientific questions by chaining together services discovered via biodiversity catalogue.
Training workshop for Ecosystem Modelling studies
May 29-30, Budapest, Hungary
Introduction to using BioVeL workflows and Biome-BGC Project database for terrestrial ecosystem modelling, carbon sequestration and ecosystem service quantification studies
Joint GBIF-France/BioVeL training workshop
March 24-25, Paris, France
Formation sur la qualité, l’utilisation et la publication de données sur la biodiversité
Biodiversity data quality, use, and publication
BioVeL at Upcoming Conferences
- Forest Change 2014, April 2-4, Freising, Germany
- GBIF 6th European nodes meeting, April 8-11, Brussels, Belgium
- European Geoscience Union General Assembly 2014, April 27-May 02, Vienna, Austria
- EGI Community Forum 2014, May 19-23, Helsinki, Finland
- Pro-iBiosphere Final Event, June 10-12, Brussels, Belgium