Article

Symbiotic relationships between trees and microbes governed by climate

In and around the roots of the trees are fungi and bacteria living in symbiosis with the trees, exchanging nutrients for carbon. An effort to map the most common symbiosis types - based on data from more than 1.1 million specimens and 28,000 tree species - has revealed factors that determine where different types of mycorrhizae and nitrogen-fixing bacteria will thrive. The work can help researchers understand how symbiosis shapes the world's forests and how they can be affected by a warmer climate.

Researchers from Stanford University in collaboration with over 200 researchers from other universities, including SLU, generated these maps and published in Nature on May 16. The work reveals a new biological rule that the research team calls “Read’s Law”, after a pioneer in symbiosis research, Sir David Read.

For example, researchers used the survey to predict how symbiosis might change by 2070, if carbon dioxide emissions continue as they do today. This scenario led to a ten percent reduction in the biomass of tree species that have the type of soft-pink rhizomes found primarily in cooler areas. The researchers warn that such a loss of growth can increase the amount of carbon in the atmosphere.

“There’s only so many different symbiotic types and we’re showing that they obey clear rules,” said lead author Brian Steidinger, a postdoctoral fellow at Stanford. Our models predict major changes in the world’s forest symbiosis – changes that may affect the climate in which our grandchildren will live. – The result of the study is important in itself, but it also shows the strength and usefulness of the data collected in well-executed monitoring programs such as the National Forest Assessment, says Bertil Westerlund from SLU, who contributed Swedish data to the study.

The popular workshops series on computational skills and biodiversity informatics from the GGBC is back after the summer break with new and exciting topics for this autumn. See schedule below and make sure to spread this in your networks. For signing up, send 3 lines of motivation to join the course to Matthias Obst.


September 17th: SupersmartR. Develop pipelines in R for creating phylogenetic trees including mass sequence download, sequence identification, alignment, tree estimation, supermatrix and supertree construction. Sign up deadline 10/9

September 26th: Basic handling of spatial data in R. Spatial R course for beginners. Learn the essentials about polygons, spatial points, rasters etc. Sign up deadline 19/9

September 27th: Advanced handling of spatial data in R. Spatial R course, slightly advanced. Learn how to tackle common challenges that arrise when working with spatial data. Essential stuff for any publication/presentation quality display of spatial data. Sign up deadline 20/9

November 13th: Python for Biologists – basics. Ever found yourself wondering what all this Python talk is about? This is your chance to get started with this super handy and fun programming language and to learn how to apply it to biological data. Sign up deadline 6/11

December 4th: Python for Biologists – advanced. Slightly advanced Python course, with an emphasis on data processing and visualization. Sign up deadline 27/11

All workshops take place in the Botanical or Zoology building at University of Gothenburg. To enable participation from outside of Gothenburg the courses are designed as half-day modules starting at noon and including homework assignments. Lunch is provided at each occasion. The courses are financed by ForBio, Swedish LifeWatch, Biodiversity Atlas Sweden, and the Nordic e-Infrastructure Collaboration.


The courses are aimed at Swedish and Nordic students. If you need travel support to join a course, please add this request to your application. Please state in your application if you are a ForBio member.  For questions on the content of the courses please contact Tobias Andermann or Matthias Obst.

The technical coordinator, Vicente Ruiz Jurado of the Atlas of Living Spain, will be responsible for supporting developers, improving technical documentation and building a shared roadmap. The administrative coordinator, Marie Elise Lecoq of VertNet, will oversee communication, explore and document governance models and create training modules.

The LA community launched two video tutorials on 18 June 2019 with the aim of enabling end-users to take full advantage of the Atlases. The videos are one key output from a project to improve documentation for the Living Atlases funded through the 2018 Capacity Enhancement Support Programme (CESP). Both videos are available in English with subtitles in French, Spanish and Portuguese.

The first video demonstrates the structure of a Living Atlas including how to search, refine and download biodiversity data.
The second video focuses on the spatial components of the Atlas including the regions module, which allows the user to find species recorded within a defined region.
Article

The Swedish Biodiversity Data Infrastructure held its first National Coordination Group meeting in early June

The Swedish Biodiversity Data Infrastructure (SBDI) has had its first National Coordination Group meeting, during which several new opportunities for collaboration were identified.

The National Coordination Group consists of representatives from the partners in the SBDI consortium, i.e., Biodiversity Atlas Sweden and Svenska LifeWatch. Elected as Chairman and Vice Chairman of the National Coordination Group were, respectively, Matthias Obst, University of Gothenburg, and Maria Prager, Stockholm University/Karolinska Institutet.

Attendees of the first SBDI National Coordination Group, 11 June 2019

From left to right in the group photo are Maria Karlberg (SMHI), Fredrik Ronquist (NRM), Anna Rosling (UU), Anna-Lena Axelsson (video screen, big picture; SLU-SRH), Malin Werner (video screen, small picture; SLU- Aqua), Anders Telenius (NRM), Phil Buckland (UmU), Holger Dettki (SLU-ADb), Kevin Holston (NRM), Maria Prager (SU/KI), Matthias Obst (GU). Attendees not pictured are Anders Andersson and Johan Bäckman.

Article

Second Nordic course on “FAIR data stewardship”

NeIC and DM-Forum in Denmark are jointly hosting the second Nordic course "FAIR Data Stewardship” on 18-22 November 2019, this time in Copenhagen.

This is a five-day training event which will provide much needed foundational skills for competent data stewards and data managers in the Nordic countries with knowledge of the FAIR principles and their application.

Trainers from GO-FAIR will provide a broad introduction to data stewardship. Registration will be limited to max 35 persons and the course is subsidised by NeIC and DM-Forum.

To register follow this link: https://bit.ly/FAIRds-Nordic.

Overview
FAIR Data Stewardship, as a new profession, is rapidly gaining momentum. New requirements from national and international funders are driving the need for training of competent, professional data stewards and data managers with knowledge of the FAIR principles and their application. This course introduces the required knowledge and skills in a broader data stewardship context, including topics like semantic data modeling, metadata modeling, the FAIRification process, publishing FAIR Data Points, and other topics related to managing research project’s data requirements. After completion of the course participants will be able to work with domain specialists in making their data FAIR and preserving them for re-use.

Who should attend
This course is aimed at librarians or data experts at universities, research institutions and research support centres who are dealing with the ever growing complexity of data integration. Currently data technicians/ICTers spend between 70 and 80 percent of their time on data wrangling such as dealing with data selection & retrieval, format issues, identifiers, ontologies, massaging the data so that it is ready for big data analysis. For large organisations choosing to GO FAIR, integration and re-use of data sets becomes less labor intensive, leaving more time to dive into more complex data analysis answering research questions.

”Most early career scientists are today confronted with big data in their research projects and we feel that we need to provide some guidance about theory, methods and tools when dealing with such large data volumes”, says the workshop organizer Jesper Bladt.

Participants in the course ‘Machine Learning for Biologists’, Photo: Jesper Bladt

To this end the course leaders brought together a team of experts in data science and biodiversity research from Scandinavia and Estonia. They designed computer exercises and build up a course program where students apply deep learning methods to newly emerging analytical problems in ecology, such as image processing and species distribution analyses. After three days, a new course had been established on an emerging hot topic, and it is likely to attract many students in the future. The workshop was financed by the Nordic e-Infrastructure Collaboration (NeIC) and featured invited teachers from Aarhus University, the Gothenburg Global Biodiversity Center (GGBC), and the Swedish Biodiversity Data Infrastructure (SBDI).

Lecture in progress, Photo: Jesper Bladt

Data for estimation and modelling of forest resources

Date: November 4 – November 22, 2019

Place: SLU Umeå

Description:

The aim of the course is to provide PhD students with knowledge of different types of available environmental monitoring data and how these could be used in research and for environmental monitoring.

Recommended background: To be eligible, students need to be a registered PhD student in the field of forest management, technology, ecology or related field.

Course level: PhD level

Contact: Torgny Lind

 

We hereby invite you to a 2-day seminar (June 11th – 12th 2019) focusing on fair data management and open science in ecology, wildlife management and conservation. The seminar is organised by the Living Norway Ecological Data Network (www.livingnorway.no) and the Nordic eInfrastructure Collaboration DeepDive project (https://neic.no/deepdive/). Read more about the event here.

Dates: June 11. – 12. 2019

Venue: The seminar and workshops will be located at NINA (June 11th) and NTNU (June 12th) in Trondheim.

Registration: You can register to the seminar, the lunches and the conference dinner here. Registration deadline May 25th 2019.

 

We are recruiting a Systems architect within BAS/SBDI. The position will be placed at the Swedish Museum of Natural History.

The technical platform for SBDI is based on open source code that is developed in international collaboration; the original code base comes from Australia. The technical work in Sweden involves system developers and programmers at several of the universities and authorities involved in SBDI. As a System architect for SBDI you will lead the Swedish development work within the infrastructure as well as the coordination between the Swedish developers and the international teams.

Follow this link for more information.

Essential tools to remove biases in spatial data using R

Date: May 21th 2019, 12.00-17.00

Place: Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg, Room 10 (Sal 10)

Description:

In this workshop we will cover common challenges that arise with any kind of spatial coordinate data in biology. Knowledge of the tools introduced in this workshop is essential when presenting spatial biological data (e.g. a map of sampling sites) in presentations or publications.

More specifically we will discuss strategies to deal with the non-independence of spatial data points also known as spatial autocorrelation. Further we will address challenges arising in global analyses from the simple fact that the earth is round. We will also touch upon some of the globally available environmental predictors often applied in spatial analyses and their potential challenges.

Participants are required to have basic knowledge of the R programming language and we assume that the participants are familiar with basic spatial operation in R. In case of doubt, we encourage participants to review the tutorial of our previous workshop ”Handling spatial data in R” here.

Course teachers: Søren Faurby, Tobias Andermann, Matthias Obst

Recommended background: Basic R knowledge required

Course level: PhD level (motivated Master’s students welcome)

Food: Lunch will be provided for all course participants

Application: Send a short motivation (5 lines stating goals and expectations) to matthias.obst@marine.gu.se latest by 14th May 2019.

Contact: Søren Faurby (soren.faurby@bioenv.gu.se), Tobias Andermann (tobias.andermann@bioenv.gu.se), Matthias Obst (matthias.obst@marine.gu.se)