Workshop Collaboration on e-Infrastructures for Nordic Biodiversity Informatics

From neicext
Jump to navigation Jump to search

Logistics

Dates & Location

Registration

Please register here before July 31rd 2015.

Organizers & Contact

  • Hanna Koivula
  • Frank Hanssen
  • Flemming Skov
  • Ulf Gärdenfors
  • Thomas Röblitz, NeIC Environmental Sciences area coordinator

In case of any questions, don't hesitate to contact Thomas Röblitz at thomas.roblitz@usit.uio.no


Workshop Introduction & Objectives

The workshop is co-hosted by NeIC and the Nordic LifeWatch Consortium. NeIC is an organization which facilitates the collaboration on the development and deployment of e-Infrastructure for topics of common Nordic interest.

LifeWatch is one of several ESFRI projects which aim to establish e-Infrastructures and databases in the field of biodiversity and ecosystem research. The Nordic LifeWatch initiative aims to facilitate increased data sharing and scientific collaboration in the field of biodiversity informatics through the development of common e-Infrastructures and analytical eTools. LifeWatch will be aligned with similar initiatives where the Nordic partners already are involved such as the Swedish Species Information Centre (SSIC), the Norwegian Biodiversity Information Centre (NBIC), the Global Biodiversity Information Facility (GBIF), the European Biodiversity Observation Network (EU BON), the Norwegian Marine Data Centre (NMDC) and the Long Term Ecological Research Network (LTER).

Objectives

The objectives of the meeting are:

  • to gather various stakeholders in biodiversity informatics (data providers, service developers, researchers, decision makers) to present the state-of-the-art in their field with an emphasis on e-Infrastructure,
  • to discuss plans and requirements on e-Infrastructure to support collaboration on the Nordic level (e.g., easily sharing data, combining data, making data openly accessible)
  • to define activities on the Nordic level to develop services enabling collaboration (e.g., coordination leading to a more cost-efficient development or deployment of services), these activities may receive co-funding from NeIC, national e-Infrastructure providers and the biodiversity community
  • to start planning an application to NordForsk for Nordic-Baltic LifeWatch collaboration

Presentations, key challenges and opportunities

As there are about 12 presentations, and we have two sessions scheduled, each talk including discussion shall not be longer than 15 minutes. From my point of view, all proposed presentations are very interesting. Of course, it is important to motivate collaboration on e-Infrastructure from scientific use cases, and also present the current state of using IT. However, each talk should highlight on what YOU want to collaborate on in the future. Neither NeIC nor I want to limit your creativity here. Everything that may improve your use of e-Infrastructure and thereby your research is within the scope of NeIC.

In the invitation, we asked you to bring 5 key challenges. I’d like to extend this to challenges and/or opportunities. I’d like to give a few examples, but do not feel limited by my likely incomplete understanding of your needs and plans:

  • improving the current way of using e-Infrastructure (make it easier to use, easier to maintain/operate, more efficient, ...) by training users, admins, by sharing knowledge, ...
  • developing/deploying new services to enable new science (this may not necessarily require collaborating in the research itself but sharing the cost)
  • scientific collaboration requiring joint work on e-Infrastructure

Schedule (tentative)

  • session chair in parentheses
  • all sessions except group work exclusively in meeting room at 7th floor
  • group work in meeting rooms at 7th and 8th floor

Day 1, Wednesday, August 26th 2015

11:30 - 12:30 Light lunch (served in the meeting room at the 7th floor)

12:30 - 13:00 Session 1 (Thomas Röblitz):

  • Thomas Röblitz // Introduction (Participants, Workshop goals, Agenda, NeIC) [1]
  • Frank Hanssen // Nordic LifeWatch [2]

13:00 - 14:30 Session 2 (Matthias Obst): Overview of scientific use cases, systems and services(about 15’ each)

  • presenters shall be researchers with knowledge of e-Infrastructure needs
  • presenters shall be system designers, system architects (not hardcore developers ;)
  • 13:00 - 13:15 Patrik Strömberg // Swedish Lifewatch – activities at the Swedish Oceanographic Data Centre [3]
  • 13:15 - 13:30 Yuliya Fetyukova and Hannu Saarenmaa // Ecological Niche modelling of European butterflies on the BioVeL portal using GBIF data [4]
  • 13:30 - 13:45 Yuliya Fetyukova and Hannu Saarenmaa // Analysis of relative abundance trends of all European butterflies using GBIF data – building an infrastructure to obtain Essential Biodiversity Variables for species populations [5]
  • 13:45 - 14:00 Jesper Bladt // Development and maintenance of the Danish High Nature Value (HNV) farming indicator [6]
  • 14:00 - 14:15 Thorleifur Eiriksson // Inter institutional databases in Iceland in relation to NeIC-LifeWatch [7]
  • 14:15 - 14:30 Dag Endresen // Persistent identifiers for museum specimens [8]
  • 14:30 - 14:45 Finn Borchsenius // GBIF, DanBIF and the need for a national Danish biodiversity portal [9]

14:45 - 15:15 break

15:15 - 16:45 Session 3 (Dag Endresen): Overview of scientific use cases, systems and services (about 15’ each)

  • presenters shall be researchers with knowledge of e-Infrastructure needs
  • presenters shall be system designers, system architects (not hardcore developers ;)
  • 15:15 - 15:30 Matthias Obst // Current status, direction and requirements of European LifeWatch components - a Nordic perspective [10]
  • 15:30 - 15:45 Sonja Leidenberger // The Analysis Portal – an e-infrastructure for biodiversity data [11]
  • 15:45 - 16:00 Stefan Blumentrath and Anders Finstad // Infrastructure for data management and analysis in a small to medium research enterprise – an example from NINA [12]
  • 16:00 - 16:15 Tapani Lahti and Hanna Koivula // FinBIF infrastructure - status and plans [13]
  • 16:15 - 16:30 Anders Telenius // B2 Nordic NeIC NordTax Pilot Proposal [14]
  • 16:30 - 16:45 Andreas Jaunsen // National data and computing services in Norway [15]


19:00 - Social event, dinner (restaurant plah, www.plah.no)


Day 2, Thursday, August 27th 2015

09:00 - 09:30 Session 4 (Flemming Skov): Preparation for group work

09:30 - 11:30 Session 5: Group work, each group has its own chair/speaker

  • addressing specific topics in biodiversity informatics to breakdown scientific use cases into activities on e-Infrastructures

11:30 - 12:30 lunch (served in the cafeteria at entrance level or basement)

12:30 - 14:30 Session 6 (Ulf Gärdenfors & Dag Endresen): Results from group work

  • presentations, discussions, summary

14:30 - 15:00 break

15:00 - 16:30 Session 7 (Thomas Röblitz): Planning joint activities

  • for example, setting up teams / working groups to follow-up on prioritized activities
  • initiating preparation of more technical workshop (hackathon, plugfest, ...)

16:30 - 17:00 Session 8 (Thomas Röblitz): Wrap-up, next steps

Groups (tentative)

  • Group 1
    • Chair Hanna Koivula, University of Helsinki
    • Finn Borchsenius, Aarhus University / Science Museums
    • Siw Elisabeth Berge, NINA
    • Dag Endresen, UiO Natural History Museum / GBIF Norway
    • Matthias Obst, University of Gothenburg
  • Group 2
    • Chair Frank Hanssen, NINA
    • Jesper Bladt, Aarhus University
    • Ulf Gärdenfors, SLU / ArtDatabanken
    • Yuliya Fetyukova, University of Eastern Finland / Digitarium
    • Andreas Jaunsen, UNINETT Sigma2 / NorStore
  • Group 3
    • Chair Sonja Leidenberger, Swedish LifeWatch / ArtDatabanken / SLU
    • Wouter Koch, NBIC / Artsdatabanken
    • Patrik Strömberg, SMHI
    • Tapani Lahti, Finnish Museum of Natural History / Helsinki
    • Gudmund Høst, NeIC director
    • Thorleifur Eiriksson, The Icelandic Museum of Natural History
  • Group 4
    • Chair Flemming Skov, Aarhus University / Department of Bioscience
    • Thomas Röblitz, NeIC ENV area coordinator
    • Hannu Saarenmaa, University of Eastern Finland / Digitarium
    • Anders Telenius, Swedish Museum of Natural History
    • Sverker Holmgren, NeGI director

Participants

  • Denmark
    • Finn Borchsenius, head of collections, Aarhus University / Science Museums
    • Jesper Bladt, researcher, Aarhus University
    • Flemming Skov, deputy head of department, Aarhus University / Department of Bioscience
  • Finland
    • Yuliya Fetyukova, researcher, University of Eastern Finland / Digitarium
    • Hannu Saarenmaa, research director, University of Eastern Finland / Digitarium
    • Tapani Lahti, IT specialist, Finnish Museum of Natural History / Helsinki
    • Hanna Koivula, IT specialist, University of Helsinki
  • Iceland
    • Thorleifur Eiriksson, researcher, The Icelandic Museum of Natural History
  • Norway
    • Dag Endresen, project manager, UiO Natural History Museum / GBIF Norway
    • Frank Hanssen, GIS analyst & coordinator, NINA
    • Wouter Koch, adviser, NBIC / Artsdatabanken
    • Stefan Blumentrath, researcher, NINA
    • Andreas Jaunsen, UNINETT Sigma2 / NorStore
    • Siw Elisabeth Berge, developer, NINA
  • Sweden
    • Ulf Gärdenfors, director, SLU / ArtDatabanken
    • Matthias Obst, researcher/project manager, University of Gothenburg
    • Anders Telenius, GBIF node manager, Swedish Museum of Natural History
    • Sonja Leidenberger, researcher, Swedish LifeWatch / ArtDatabanken / SLU
    • Patrik Strömberg, head of environmental monitoring data group, SMHI
  • NordForsk
    • Gudmund Høst, NeIC director
    • Sverker Holmgren, NeGI director
    • Thomas Röblitz, NeIC ENV area coordinator

Practical Information

Travel to / in Oslo

  • via Oslo Airport Gardermoen:
    • by train: check timetables at www.ruter.no
      • local train about 20 min from Oslo Gardermoen to Oslo S @ 90 NOK at ticket vending machine; ticket valid for 2.5 hours including city center (meeting venue is approx 15 min from Oslo S by tram / subway and a bit of walking); about 3 departures every hour (check for early/late arrivals/departures); NOTE! ticket not valid for airport express!
      • flytoget / airport express about 20 min from Oslo Gardermoen to Oslo S @ 180 NOK at ticket vending machine; 6 departures to Oslo S every hour / 3 departures going on to Nationaltheatret (next stop, about 15 min walk to meeting venue); NOTE! ticket only valid for airport express and you have to catch the right one if you want to go on until Nationaltheatret!
    • by bus: check timetables at www.flybussen.no
      • SAS flybuss takes about 50 min to the city center; stops very close to meeting venue (5 min walk); 3 departures every hour @ 150 NOK
  • via other Airports (please ask)
  • via train: arriving at Oslo S (see www.ruter.no for public transport in Oslo)
  • in Oslo:
    • excellent bus, tram and subway
    • single ticket 30 NOK, 24 hour ticket 90 NOK
    • check www.ruter.no for timetables and links to smartphone apps

Accommodation

  • several hotels nearby the meeting venue such as
    • Thon Hotel Europe
    • Radisson Blu Scandinavia Hotel
    • Scandic Holberg
    • Thon Hotel Slottsparken
    • Scandic Edderkoppen
    • many more towards the central station
  • it's probably best to check prices with services such as tripadvisor.com; some prices differ significantly (for the same hotel)

Meeting venue

  • NordForsk, Stensberggata 25
  • 7th floor
  • excellent public transport by tram (lines 17 & 18 about 5 minutes from stops Dalsbergstien or Frydenlund; latter stop is only serviced in direction from city center to Rikshospitalet)
  • subway any line (in fact all) that stops at Nationaltheatret or Stortinget (about 15 min walk from either stop)

Social event / dinner, Wednesday August 26th

  • www.plah.no, 7pm, to be confirmed

Weather forecast

Presentations

  • Matthias Obst, University of Gothenburg
    • Title: Current status, direction and requirements of European LifeWatch components - a Nordic perspective
    • Abstract: The Swedish LifeWatch infrastructure as well as other European LifeWatch components are currently moving from construction into operational phase. This implies a shift from a few and often internal scientific showcases cases to the support and coordination of an increasing number of external research activities. It also implies a shift from primarily developmental work to issues dealing with system maintainance and performance as well as user education. The presentation will introduce a number of current scientific support cases from Denmark, Sweden, and Finland in order to explain important infrastructure functions that need to be provided to build up a broad user-base in Scandinavia and ensure user-driven development of the infrastructure in the future. The presentation will also give examples of increasing interactions between LifeWatch components on a European level and explain the benefit for Nordic researchers.
  • Stefan Blumentrath and Anders Finstad, NINA
    • Title: Infrastructure for data management and analysis in a small to medium research enterprise – an example from NINA
    • Abstract: The idea is to show NINAs infrastructure for gathering, maintaining, analysing and presenting relevant data in a shared, mulit-user environment. The focus will be on showing how (spatial) data from both internal and external sources is handled in these directions, covering e.g. general GIS data, Remote sensing, telemetry / GPS tracking, wildlife camera traps, temperature loggers, monitoring data. The technical infrastructure (in terms of hard- and software setup) is currently undergoing major changes due to increased usage. A crucial aspect of this infrastructure is the combination of data gathering and processing “at one place” (in other words, the “work where your data is” strategy of RStudio Server). We will show selected examples from the ECCO/BiWa projects, a collaboration of UiO, NTNU, NINA. From these experiences we will phrase key needs for e-infrastructure with respect to a researchers everyday work-life.
  • Sonja Leidenberger, Swedish LifeWatch / ArtDatabanken / SLU
    • Title: The Analysis Portal – an e-infrastructure for biodiversity data
    • Abstract: The Analysis Portal is a web portal where Swedish species observations can be analysed and compared with different kinds of environmental or climatic data. The portal will support data retrieval from all available data providers of species observations that are connected to the Swedish LifeWatch infrastructure. The e-infrastructure for biodiversity data that will be presented here is for researchers, conservation biologist and policy makers, for frontline research and a better understanding and suitable management of biodiversity and ecosystem services. The Analysis Portal integrates biodiversity data and explanatory variables from a broad network of distributed national databases, like the Species Observation System (Artportalen), Global Biodiversity Information Facility (GBIF) Sweden, different fish databases (PIKE, NORS, SERS), Miljödata MVM, marine monitoring data from the SMHI (SHARK), natural history museum collections (DINA) and wireless remote animal monitoring data (WRAM). As a single entry point to all data, the Analysis Portal enables free access to biodiversity and environmental data and a range of analytical and visualisation services, like species richness grid map, time series histogram, species observation map and ecological niche modelling tools.
  • Yuliya Fetyukova and Hannu Saarenmaa, University of Eastern Finland (Talk 1)
    • Title: Ecological Niche modelling of European butterflies on the BioVeL portal using GBIF data
    • Abstract: Ecological niche modelling (ENM) for a comparative analysis of European butterfly species for change of their distribution is presented. All records of butterflies within the geographic Europe available through the GBIF Data Portal were downloaded and cleaned. 368 data sets on species occurrences in the years 1960 – 1990 were obtained for the modelling of the distribution of butterfly biodiversity. For each species, biodiversity centre of mass for historical and future projections of species distribution were identified as well as their shifts over time were computed. The results of modelling Hesperiidae show on average a 471 km shift towards north between the years 1960 – 1990 and the projection to 2050. There was no difference in the overall extent of distributions, indicating that distributions had just shifted, but not changed in extent. The BioVeL data refinement workflow and ENM related services via the BioVeL portal (portal.biovel.eu) were used. In order to automate modelling and analysis of large amount of species, the BioVeL portal sweep function for batch processing was used.
  • Yuliya Fetyukova and Hannu Saarenmaa, University of Eastern Finland (Talk 2)
    • Title: Analysis of relative abundance trends of all European butterflies using GBIF data – building an infrastructure to obtain Essential Biodiversity Variables for species populations
    • Abstract: All records of butterflies within the geographic Europe in the years 1960 – 2014 available through the GBIF Data Portal were downloaded and processed. Data of 562 European butterfly species were acquired. After cleaning, the data sets included 3,037,038 occurrences with known parameters of year, latitude, longitude, country and basis of record. “Scaling” is a major research topic which deals with the question on how to conclude abundance measures from heterogeneous occurrence records and big data. This is needed for producing Essential Biodiversity Variables which underlie biodiversity indicators. Trends of abundance for each European butterfly family were computed. Here, relative abundance means the percentage of records of each taxon out of all records. Relative abundance trends were also assessed for each species within families for different countries. All calculations were performed in R. The next step is to build a public web service and infrastructure for the FinBIF portal to enable processing of relative abundance trends of any organism groups with sufficient data.
  • Patrik Strömberg, SMHI
    • Title: Swedish Lifewatch – activities at the Swedish Oceanographic Data Centre
    • Abstract: The Swedish Oceanographic Data Centre at the Swedish Meteorological and Hydrological Institute (SMHI) holds marine biological and physical/chemical data from the Baltic Sea and the Kattegat-Skagerrak. Essentially all data is freely available at http://www.smhi.se. There is currently approximately 6 500 000 values for physics/chemistry and 2 800 000 biological data. As part of the Swedish Lifewatch effort data is being made available through a computer-computer interface at http://sharkdata.se. SMHI has also developed tools for working with plankton data. The web site http://www.nordicmicroalgae.org holds information such as traits and images for Nordic microalgae and aquatic protozoa with a focus on phytoplankton and micro zooplankton. Plankton specialists in the Nordic countries, Estonia, Lithuania, Latvia, Poland, and Germany contribute to the content. The Nordic Microalgae Committee update taxonomic information and do quality checks regularly working together with the Swedish Species Centre (Artdatabanken, Dyntaxa, Sweden), the Norwegian Species Centre (Artsdatabanken, Norway), the World Register of Marine Species (WoRMS) and AlgaeBase. Plankton Toolbox, a tool for working with large data sets of plankton data has been developed and is freely available as a stand-alone application for Windows and MacOS. A Linux version can be made available upon request. SMHI uses open source software, mainly Python and PostgreSQL for the Lifewatch-work. A brief look into future possibilities with new data from automated imaging systems, oceanographic buoys and FerryBox-systems etc. will also be presented.
  • Dag Endresen, UiO Natural History Museum / GBIF Norway
    • Title: Persistent identifiers for museum specimens
    • Abstract: The Global Biodiversity Information Facility (GBIF) provides an open and global e-infrastructure for publishing species occurrence information. When integrating specimen collection data from Natural History History museums, the catalog numbers used as locally unique specimen identifiers are no longer sufficiently unique on this global platform. A system of institute prefixes (institute code + collection code + catalog number) has been tested with various success. The Norwegian participant node of GBIF hosted by the Natural History Museum at the University of Oslo have developed a set of new, globally unique and machine readable (resolvable) identifiers. Standard tools are used for generation of Universally Unique Identifiers (UUIDs). The UUIDs are prefixed by a PURL to provide a persistent redirection (HTTP 303 "see other") to a resolver established at http://purl.org/nhmuio/[UUID]. Using content negotiation the user or machine can access descriptive information as html, comma-separated-values (csv), tab-delimited text-files, n3/turtle RDF data, and json. These formats can also be accessed directly (without calling content negotiation) using the file extension http://purl.org/nhmuio/[UUID].[html|csv|txt|n3|json]. See also: doi.org/10.13140/2.1.4516.9606
  • Andreas Jaunsen, UNINETT Sigma2
    • Title: National data and computing services in Norway
    • Abstract: We present the current provisioning of national services in the context of the Norwegian e-infrastructure for sciences and highlight some of the expected aspects and benefits of the next generation facilities in the period 2017-2021. The presentation will emphasis the data-related challenges and services.
  • Finn Borchsenius, Aarhus University / Science Museums
    • Title: GBIF, DanBIF and the need for a national Danish biodiversity portal
    • Abstract: Good data is a prerequisite for efficient management of biodiversity. Biodiversity data result from many sources, including public monitoring programs, museum specimens and citizen science observations. GBIF serves more than 500 mio dataposts, including 8,7 million dataposts from Denmark, representing ca. 20,000 species. However, the total potential pool of data posts concerning Danish species is substantially larger. To fully realise the value of Danish biodiversity data a coordinated effort is needed to bring together all data and stakeholders in a single organisation. An overview of the status, challenges and potential rewards related to the establishment a full-fledged national Danish biodiversity portal is given.
  • Jesper Bladt, Aarhus University
    • Title: Development and maintenance of the Danish High Nature Value (HNV) farming indicator
    • Abstract: All EU membership countries are obliged to develop a High Nature Value (HNV) farming indicator as a basis for informed decisions in prioritizing agricultural subsidies. From 2015 and onwards the Danish HNV farming indicator will be implemented for allocating around 33 million € subsidies under the Rural Development Program. The Danish HNV indicator was developed as a map in 10m resolution covering all agricultural areas as well as Natura 2000 areas and nationally protected sites in Denmark. It is based on data from multiple sources of landscape structural parameters, known occurrences of natural and semi-natural habitats, current land use and the distributions of rare and threatened species. The indicator will be updated annually to represent new available data. Currently these updates are done in a manual or semiautomatic process of data extraction and extensive data processing. E-infrastructures could potentially make it feasible to implement automatic updates of the indicator thereby reducing the annual costs.
  • Tapani Lahti, Finnish Museum of Natural History / Helsinki & Hanna Koivula, University of Helsinki
    • Title: FinBIF infrastructure - status and plans
    • Abstract:
  • Anders Telenius, Swedish Museum of Natural History
    • Title: B2 Nordic NeIC NordTax Pilot Proposal
    • Abstract: The B2 Nordic project proposal aims to foster the uptake of EUDAT B2 services (http://eudat.eu/) within the Nordics. Favouring OpenScience workflows and approaches, by harmonizing the former Baltic Diversity project delta protocol for data exchange and the taxonomy module from the University of Tartu with the appropriate existing EUDAT services (B2DROP, B2SHARE, B2SAFE, B2STAGE, B2FIND) NordTax represents an effort to synchronize available checklists of known multi-cellular species occurring in the Nordic countries and Estonia.
  • Thorleifur Eiriksson, The Icelandic Museum of Natural History
    • Title: Inter institutional databases in Iceland in relation to NeIC-LifeWatch
    • Abstract: Icelandic institutions, as The Icelandic Institute of Natural History, The Icelandic Museum of Natural History, The Marine Research Institute and the University of Iceland, working on biodiversity sensu latu are doing so on local databases according to their different needs. Data sharing is minimal and there is no concordant e-infrastructure present. Public access to biodiversity data and information is in general very limited. There is, however, awareness and understanding at government level on the importance of strategic planning for research- and e-infrastructure. Guidelines from a workgroup on these subjects are to be released this autumn.

Materials

  • Talk by Frank Hanssen at NeIC 2015 conference [16]
  • Report Nordic LifeWatch project [17]


Attachments

Retrieved from "https://wiki.neic.no/w/ext/index.php?title=Workshop_Collaboration_on_e-Infrastructures_for_Nordic_Biodiversity_Informatics&oldid=3827"