MS6 workshop

2nd BioVeL Workshop on taxonomic and phylogenetic workflows

Title

Developing interdisciplinary methods for conservation biology and ecosystem research –  taxonomic and phylogenetic workflows in biodiversity research

Venue
University of Gothenburg, Sweden at the Wallenberg conference center
10-11 May 2012 (MC and internal meeting on the 9th May)

Objectives and scope

• Foster the scientific cooperation in the biodiversity science community
• Identify important (web)services from the fields of taxonomy and phylogenetics for integration in workflows for biodiversity research
• Discuss use-cases that employ taxonomic and phylogenetic web-services
• Train the participants in workflow construction and management

Summary
The workshop has the objective to foster cooperation in the biodiversity science community and to identify workflows and use-cases that integrate analytical components from the field of taxonomy and phylogenetics. Such workflows should enable the analysis of complex patterns of biodiversity, i.e. be able to digest large and diverse biological data sets. The workshop is a part of the recently initiated European FP7 funded project ’Biodiversity Virtual e-Laboratory’, BioVeL (see above) as well as the LifeWatch infrastructure initiative. For two days we will have a scientific exchange about ways to explore patterns of biodiversity by compiling web-services from the fields of taxonomy and phylogenetics. The discussion will relate to representative applications, such as the spatio-temporal analysis of invasive or threatened species, the temporal analysis of biogeographic regimes, or the analysis of ecosystem services. Day one will consist of invited lectures and discussions of the scientific approach, as well as some breakout sessions. Day two will be devoted to technical discussions on how to integrate analytical  resources, as well as to present our showcases. Important services/workflows that are in the focus of the workshop will be: species distribution analysis - synonym resolution - historical biogeography - data cleaning issues - biodiversity richness analysis - phylogenetic diversity analysis - comparative phylogeography - vicariance analysis - molecular taxonomy.

Press Releases

Swedish LifeWatch
agINFRA
agroKNOW

Invited speakers

Neil Caithness, University of Oxford, UK
Topic: Beta diversity analytics and the Local Ecological Footprinting Tool (more information here)

Simon Creer, University of Bangor, UK
Topic: High-throughput approaches to describe community composition (more information here)

Alastair Culham, University of Reading, UK
Topic: Phylogeny, geography and climate, a taxonomists approach

Mike Hickerson, Queens College, City University of New York, USA
Topic: Comparative phylogeography and MTML-msBayes (more information, see here --pre-confirmed)

Peter Hovenkamp, National Herbarium Netherlands
Topic: Using phylogenetic information in biogeographical contexts

Niels Raes, Netherlands Centre for Biodiversity Naturalis (section NHN), Leiden University
Topic: The impact of glacial dynamics on the accuracy of species distribution models

Fredrik Ronquist, Swedish Museum of Natural History, Sweden
Topic: Bayesian biogeographic analytics

Rutger Vos, Netherlands Centre for Biodiversity, Netherlands
Topic: Geophylogenies in conservation research (more information here)

Campbell O. Webb, Harvard University, USA
Topic: Phylocom (more information here)


Programme

Wednesday, 9. May
13.30-13.30 Lunch at Wallenberg center
14.00 - 17.00 Internal affairs (internal project meeting)
18.00 - 22.00 Reception and dinner for everybody at the Natural History Museum

Thursday, 10. May
9.00 Workshop start

• 09.00-09.10 Welcome and practical details, Matthias Obst,
  presentation slides
• 09.10-09.40 Introduction to the BioVeL, LifeWatch, and the three thematic focus areas of BioVeL, Alex Hardisty, presentation slides
• 09.40-10.00 Workflows for data cleaning and refinement, Anton Guentsch, presentation slides
• 10.00-10.20 Workflows for geospatial visualization, Vera Hernandez, presentation slides
• 10.20-10.35 Showcase: Historical changes of marine biodiversity, Matthias Obst, presentation slides
• 10.35-11.00 Coffee break
• 11.00-11.30 Invited lecture: Geophylogenies in conservation research, Rutger Vos, presentation slides
• 11.30-12.00 Invited lecture: Comparative phylogeography and MTML-msBayes, Mike Hickerson, presentation slides
• 12.00-12.30 Invited lecture: Bayesian biogeographic analytics, Fredrik Ronquist, presentation slides

12.30-13.30 Lunch

• 13.30-14.00 Invited lecture: Using phylogenetic information in biogeographical contexts, Peter Hovenkamp, presentation slides
• 14.00-14.30 Invited lecture: Campbell O. Webb, Phylocom, presentation slides
• 14.30-15.00 Invited lecture: Beta diversity analytics and the Local Ecological Footprinting Tool, Neil Caithness, presentation slides
• 15.00-15.30 Coffee break
• 15.30-16.00 Invited lecture: High-throughput approaches to describe community composition, Simon Creer, presentation slides
• 16.00-16.20 Workflows for phylogenetic analysis of alpha diversity, Saverio Vicario, presentation slides
• 16.20-17.20 Breakout session I: Discussion of important services and the three thematic areas
• 17.20-17.50 Wrap-up

19.00 - 22.00 Dinner at S/S Marieholm (dinner starts at 20-20.30)

Friday, 11. May
9.00 Workshop start

• 09.00-09.30 Invited lecture: Phylogeny, geography and climate, a taxonomists approach, Alastair Culham, presentation slides
• 09.30-10.00 Invited lecture: The impact of glacial dynamics on the accuracy of species distribution models, Niels Raes, presentation slides
• 10.00-10.20 Workflows for Ecological Niche Modeling, Renato De Giovanni, presentation slides
• 10.20-10.35 Showcase: Ecological niche modeling of forest pests in Europe, Paivi Lyytikainen-Saarenmaa, presentation slides
• 10.35-11.00 Coffee break
• 11.00-11.15 Showcase: Ecological niche modeling of invasives in the Baltic, Sarah Bourlat, presentation slides
• 11.15-12.30 Breakout session II: Play with the workflow

12.30 - 13.30 Lunch

• 13.30-14.00 Breakout session II: Play with the workflow (continued)
• 14.00-14.20 Best practices for workflows, Kristina Hettne/Marco Roos, presentation slides
• 14.20-14.40 Scratchpad - BioVeL service integration, Neil Caithness, presentation slides
• 14.40-15.00 SwedishLifeWatch - BioVeL service integration, Oskar Kindvall, presentation slides
• 15.00-15.30 Coffee break and early departure by coach to the airport
• 15.30-16.10 Breakout session III: Discussion of Taverna based workflows
• 16.10-16.50 Panel discussion
• 17.00 Workshop ends

17.15 Departure to the airport

Photos from the workshop

Background

The aim of the Biodiversity Virtual e-Laboratory (BioVeL) project is to provide a seamlessly connected environment that makes it easier for biodiversity scientists to carry out in-silico analysis of relevant biodiversity data and to pursue in-silico experimentation based on composing and executing sequences of complex digital data manipulations and modelling tasks. In BioVeL scientists and technologists work together to enable pipelining of large and complex data into efficient analytical tasks, so-called workflows. This will be accomplished by integrating existing web-services from various biological disciplines into the myGRID platform. The methods include the development of people-oriented process models and computational workflows that can be used in the Taverna workflow system. Workflows in Biodiversity science will compose data and analytical components from all classical biological disciplines, such as Taxonomy, Phylogenetics, Ecological niche modeling, Population modeling, Genomics, and Ecosystem modeling. The project started in September 2011 and will run until August 2014. This is the first workshop in which the BioVeL consortium will make contact with external scientists and projects.


Local organizers and contact

The workshop is organized in collaboration with Swedish LifeWatch and ViBRANT

This workshop is hosted by the Swedish BioVeL partner, the Department of Biological and Environmental Sciences, Göteborg University, Sweden.

For more information contact Matthias Obst, Göteborg University, Box 463, SE-405 30 Göteborg, Sweden, Tel: +46(0)317863662, Fax: +46(0)31416729, matthias.obst@bioenv.gu.se


List of participants

BioVeL Consortium Partners

Alex Hardisty, project coordinator, Cardiff University, United Kingdom
Matthias Obst, workshop organiser, University of Gothenburg, Sweden

Sarah Bourlat, University of Gothenburg, Sweden
Renato De Giovanni, Centro de Referência em Informação Ambiental, Brazil
Yde de Jong, Netherlands Centre for Biodiversity, The Netherlands
Giacinto Donvito, National Institute for Nuclear Physics, Italy
Jonathan Giddy, Cardiff University, United Kingdom
Carole Goble, University of Manchester, United Kingdom
Anton Guentsch, Free University of Berlin, Botanical Gardens and Museum, Germany

Rob Haines, University of Manchester, United Kingdom
Vera Hernandez, Fraunhofer-Gesellschaft, Institute IAIS, Germany
Ferenc Horváth, Hungarian Academy of Sciences Institute of Ecology and Botany, Hungary
Andrew Jones, Cardiff University, United Kingdom
Abraham Nieva de la Hidalga, Cardiff University, United Kingdom
Norman Morrison, University of Manchester, United Kingdom
Elisabeth Paymal, Fondation pour la Recherche sur la Biodiversité-FRB, France

Hannu Saarenmaa, University of Eastern Finland, Finland
Päivi Saarenmaa, University of Eastern Finland, Finland
Saverio Vicario, National Research Council institutes, Italy
Alan R Williams, University of Manchester, United Kingdom

Invited Participants


Alexandre Antonelli, University of Gothenburg, Sweden
Bank Beszteri, Alfred Wegener Institute for Polar and Marine Research, Georgia
Rasa Bukontaite, Swedish Museum of Natural History, Sweden
Neil Caithness, University of Oxford, United Kingdom
Guy Cochrane, EBI, Hinxton, United Kingdom
Chuck Cook, EBI, Hinxton, (EMBRC), United Kingdom
Simon Creer, University of Bangor, United Kingdom
Alastair Culham, University of Reading, United Kingdom
Klaas Deneudt, VLIZ, (PESI), Belgium
Markus Döring, GBIF Secretariat, (GBIF)
, Denmark
Ulf Gärdenfors, SLU, (Swedish LifeWatch)
, Sweden
Kristina Hettne, University Medical Center Amsterdam, (Wf4ever), The Netherlands
Mike Hickerson, Queens College, City University of New York, USA
Peter Hovenkamp, National Herbarium Netherlands, The Netherlands
Oskar Kindvall, Swedish University of Agricultural Sciences, (Swedish LifeWatch)
, Sweden
David King, Open University, (VIBRANT/agINFRA), United Kingdom
Ellen Larsson, University of Gothenburg, Sweden
Kenneth Lundin, Natural History Museum Gothenburg, Sweden
Svante Martinsson, University of Gothenburg, Sweden
Johan Nylander, Swedish Museum of Natural History, (BILS/ELIXIR), Sweden
Urban Olsson, University of Gothenburg, Sweden
William Piel, Yale Peabody Museum, (TREEBASE)
, USA
Vassilis Protonotarios, Agro-Know Technologies, (agINFRA)
, Greece
Niels Raes, Netherlands Centre for Biodiversity, The Netherlands
Stéphane Rivière, EBI, Hinxton, United Kingdom
Fredrik Ronquist, Swedish Museum of Natural History, Sweden
Marco Roos, University of Amsterdam, (Wf4ever)
, The Netherlands
Monica Santamaria, Italian National Research Council, Italy
Ann Strömberg, Director of Natural History Museum, Gothenburg, Sweden
Per Sundberg, University of Gothenburg, Sweden
Bart Vanhoorne, VLIZ, (PESI)
, Belgium
Rutger Vos, Netherlands Centre for Biodiversity, The Netherlands
Camilla Wandin, University of Gothenburg, Sweden
Campbell O. Webb, Harvard University, USA
Anna Maria Wremp, SLU, (Swedish LifeWatch), Sweden

photos: Matthias Obst and Elisabeth Paymal