Pre-Meeting Workshop

Workshop 1: GFÖ Pre-Conference Data Management Workshop (GFBio) cancelled!
This Workshop has been calncelled!

GFÖ Pre-Conference Data Management Workshop (GFBio)


Introduction:

Ecology is an inherently cross disciplinary science that has grown into a highly collaborative and data intensive science over the last decade. New data is created across all ecological relevant disciplines at an increasing rate driven by the development of new techniques e.g. with remote sensing using extensive sensor and satellite networks or in high throughput techniques for screening and gene sequencing. This opens many new ways for researchers to gain insights into the functioning of our ecosystems on a more fine granular temporal scale than ever before. While many of the data is very uniform in structure we also face highly heterogeneous data in ecology. This data is gathered in manual fashion by small projects with a specific focus and project design to allow answering very specific ecological research questions. Both of these types of data are valuable in the long term perspective and thus need to be preserved for future research. However, they have different requirements in terms of maintenance and preservation. Thus many data related tools and services arose over the last years to assist researchers throughout the whole life cycle of data from the data acquisition over the refinement and description of the data up to the publication of the data itself.



Figure 1 The data life cycle is a conceptual tool which helps to understand the different steps that data follow from data collection up to the publication and the creation of knowledge. Source: http://www.gfbio.org/


Furthermore the DFG recently funded the project called “The German Federation for Biological Data” (GFBio). The project plans to go in its second phase and works on tying together and complementing existing infrastructure, tools and services of national key players (e.g. Max-Plank Institutes, Museum of Natural Sciences) to provide access to environmentally related data and services under a consistent framework. The overall goal is to provide a sustainable, service oriented, national data infrastructure to facilitate the management and the sharing of data as well as to stimulate data intensive sciences answering environmentally relevant questions over large temporal and spatial scales.

Goals:

The workshop will introduce the participants to the life cycle of data and give an overview about available tools and services that assist in each step along the cycle. The workshop includes practical and theoretical parts. We get in touch with tools and services which are adopted by the GFBio project are as well as with already existing international tools and services of interest in terms of data management. The list below is exemplary and might change slightly towards finalizing the workshop:

  • Diversity Workbench Mobile (Data gathering)
  • Right field, Open-Refine (Data gathering, Refinement)
  • EML, DWC, Morpho, EML for R, DataUp (Metadata)
  • GFBio (Data preservation)
  • GFBio, KNB (Data discovery)
  • ROpenScience (Data access and Anaysis)
  • GFBio (Data Integration)
  • Kepler, Pegasus (Workflows)
  • GFbio (Data publishing)

Organisatory:

The workshop takes place the weekend before the GFOE 2016 from 03th to the 04th of September. Each course day starts at 9am and ends at 4pm.
(An exact time schedule with topics will be sent to the participants after registration, and when we have the room number the course takes place in).

The workshop is limited to 12 participants and will cost 40 Euros per person. Programming Skills are not needed for the course but some skills in R will be helpful in understanding the R Tools we present. What you should bring is some interest in the topic and your own laptop!

The workshop is given by the two GFBio members
  • Claas-Thido Pfaff (University of Leipzig, )
  • Tanja Weibulat (IT Center, Staatliche Naturwissenschaftliche Sammlungen Bayerns, )
  • Johannes Drönner (Uni Marburg, )
  • Marco Schmitt (Senckenberg Biodiversity and Climate Research Centre (BiK-F), )


Workshop 2: Introduction to working with spatial data in R

Introduction to working with spatial data in R


Introduction:

Space plays an important role in many ecological research questions. The location of measurements can be used to answer question directly (e.g., What is density of plants in a given area? How does the location of animals change over time?) or to account for spatial autocorrelation. To handle the spatial component of ecological data, Geographic Information System (GIS) are usually used.

The statistical program R has become very popular and widely used in ecology. However, it is less well known that R offers a wide range of spatial functionality that is comparable to standard GIS packages. Handling and managing spatial data in R has the advantage that all analytical steps can be conducted within one software package. This workshop will give a practical introduction on how to manage, visualize and work with spatial data in R.

Goals:

After the workshops participants will have gained an overview of functionalities that are available in R to handle spatial data, how to read and write spatial data (e.g., ESRI shapefiles or GeoTiffs), and basic vector and raster operations. The workshop will consist of a mix of short lectures and hands-on sessions in R.

Organisatory:

The workshop takes place the weekend before the GfÖ 2016 from 3rd to the 4th of August in the Carolinenhaus, Deutschhausstr. 12, room 00 A19. Saturday starts at 10:45 and ends at 16:30, Sunday starts at 09:00 and ends at 16:30. Places are limited to 20 participants and will cost 40 Euros per person.

Time Slot
Day 1
Day 2
9:00 – 10:30
 
Raster data in R
10:45 - 12:15
Introduction
Raster operation
13:15 – 14:45
Vector data
Interpolations
15:00 - 16:30
 
Vector operations
Outlook

Participants should bring their own laptops with a recent version of R and spatial packages (detailed instructions will be circulated among the participants prior to the workshop). Participants should possess some familiarity with programming in R (if in doubt, please feel free to contact me in advance). The workshop will be given by Johannes Signer (jsigner@gwdg.de) and Jan Engler.
Workshop 3: Putting biotic interactions into correlative species distribution analyses: is it possible, and if so, how?

Putting biotic interactions into correlative species distribution analyses: is it possible, and if so, how?


Introduction:

This pre-symposium workshop essentially aims at writing a paper reviewing the ecological and statistical approaches to the detection and correlative modelling of biotic interactions at macroecological scales. There are now a good dozen or so publications that in one way or another put biotic interactions into species distribution models (reader will be provided two weeks in advance). Some seem to be more wishful thinking, others make very clever arguments. So can we, or can we not, put biotic interactions into SDM? And if so, do these publications tell us how?

Ideally participants will have some first-hand experience with collecting data on species distributions or population size; basic knowledge of population ecology (e.g. Lotka-Volterra-like models to represent biotic interactions); and superficial familiarity with SDMs (i.e. spatial analysis of species occurrence/abundance data). Anti-authoritarian tendencies must be considered an advantage (and are required if some well-known scientist has ventilated a questionable idea).

Format:

The workshop will fill two intense working days, largely in subgroups, interspersed with plenary feedback sessions. There will be no talks (other than a brief overview of papers and practices), and the aim is to have a review structured and ready for delegation to subgroups to finalise the details, to be submitted within a few months after the workshop.

Organisation:

The workshop takes place in Marburg the weekend before the GFOE 2016 from 3 - 5 Sept., specifically: 3.9. 12:00-18:00, 4.9. 9:00-18:00, and 5.9.2016 9:00-12:00. (room 01 A03, Carolinenhaus, Deutschhausstr. 12). The workshop is limited to 25 participants and will cost 40 Euros per person (lunch and drinks).

Please do bring your laptop/tablet for internet activities and writing.

The workshop will be orchestrated by
  • Carsten Dormann (University of Freiburg, )
  • Casper Kraan (University of Freiburg & Alfred Wegener Institute, Bremerhaven, )