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Swedish LifeWatch Annual Report 2014
Annual Report and Financial Report 2014Swedish LifeWatch 2015SLU.dha.2014.5.1-156Cover photos: Anna Maria Wremp, Johan Söderkrantz, Hans-Peter Fjeld (Wikimedia Commons), Johan Samuelsson and iStockphoto.
Swedish LifeWatch, ArtDatabanken SLU, Box 7007, SE-750 07 Uppsala, [email protected], +46 18-67 13 94
Swedish LifeWatch is a national consortium comprised of the following partners: The Swedish Univer sity of Agricultural Sci-
ences (SLU), The Swedish Meteorological and Hydrological Institute (SMHI), The Swedish Museum of Natural History in-
cluding GBIF, University of Gothenburg, Lund University and Umeå University. The project is hosted and coordinated by the
Swedish Species Information Centre (ArtDatabanken) at SLU, with financial support from the Swedish Research Council
(Vetenskapsrådet) and the Swedish Environmental Protection Agency.
With financial support from:
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ContentContent ................................................................................................................... 3The Director’s column ............................................................................................ 5Swedish LifeWatch in short .................................................................................... 6The infrastructure at a glance ................................................................................ 7Reports from the consortium partners .................................................................... 8
ArtDatabanken SLU .......................................................................................... 8Swedish Museum of Natural History ............................................................... 12Swedish Meteorological and Hydrological Institute (SMHI) ............................ 15 Department of Aquatic Resources SLU .......................................................... 16 University of Gothenburg ................................................................................. 17Lund University and CAnMove ........................................................................ 19Umeå University .............................................................................................. 19
International cooperation ...................................................................................... 20National cooperation ............................................................................................. 22Administration and organisation .......................................................................... 23 Communication ..................................................................................................... 24 Show cases and pilot studies ............................................................................... 25Key numbers ........................................................................................................ 32 Organisation ......................................................................................................... 34Financial report ..................................................................................................... 36 List of abbreviations .............................................................................................. 37
Appendix 1 – Deliverables and activities 2014 ..................................................... 39Appendix 2 – Detailed financial report .................................................................. 48
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Another successful year of the Swedish LifeWatch has elapsed. In 2014, SLW added much new data (now pro-viding more than 47 million species observations) and delivered new services and tools for exploration, analysis and visualization, contributing to a powerful e-infrastruc-ture including the Analysis portal. That is, the infrastruc-ture of SLW is now fully operational. Of course, there are – and will always be – requests for more data, func-tionalities, services and user support. Still, we can con-clude that overall, SLW has delivered what was promised in the original application, even if some deliverables were differently prioritized during the course, mainly due to views expressed in dialogue with users.
Several researchers have now started to use the Analysis portal and the first publications are seeing the light. Formas and VR have approved applications for projects explicitly utilizing the SLW infrastructure. This is very satisfying to see.
In the beginning of 2014, we planned for an application for a new period 2015–2019 for SLW. However in February, the Swedish Research Council (SRC) decided to postpone the announcement one year while investigating how their support to research infrastructures could be improved. Even though SRC supplied some further resources, it meant that the economy for 2014–2015 became somewhat constrained and the pace of development had to be retarded. To ensure that all nodes of the consortium would subsist through 2015, the Board re-allocated some resources after applications from all partners.
We are now working with the application to SRC for an extended consortium of e-infrastructures for biodiversity and ecology research for the period 2016–2023. Still focusing on species information, it will also include the genetic and ecosystem levels of biodiversity. Such a network has a great potential to become a powerful infrastructure providing free, high quality and easily accessible biodiversity big data to research and other parts of the society.
Ulf Gärdenfors, January 2015
The Director’s column
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In 2009, the Swedish Research Council launched a call for investment and operations of new in-frastructures. The Swedish LifeWatch application, with the goal to develop a research infrastructure for biodiversity data, was granted in 2010 and an agreement was signed between SRC and SLU, hosting the project.
Swedish LifeWatch is a joint effort between six national parties: the Swedish University of Agri-cultural Sciences (SLU), the Swedish Meteoro-logical and Hydrological Institute (SMHI), the Swedish Museum of Natural History (NRM) including the Swedish GBIF node, University of Gothenburg (UGOT), Lund University (LU) and Umeå University (UmU). The project is hosted by SLU and coordinated by the Swedish Species Information Centre (ArtDatabanken).
In addition to the main funding provided by SRC, the Swedish Environmental Protection Agency provides funding for the development of the Swedish Species Observation System (Artportalen), a core component of Swedish LifeWatch. All consortium partners also contrib-ute with co-funding.
In 2011, a consortium agreement was signed by the six parties and the construction phase was initiated. According to plan, we can now conclude that the Swedish LifeWatch was fully operational by the end of 2014.
Swedish LifeWatch follows the technical guidelines outlined by the European LifeWatch project, an initiative under the auspices of the European Strategy Forum on Research Infra-
structures (ESFRI). Sweden participated in the EU-funded preparatory phase for LifeWatch 2008-2011. LifeWatch is currently preparing an application to establish an ERIC (European Re-search Infrastructure Consortium) and Swedish LifeWatch maintains a close collaboration with the European LifeWatch project and other re-lated initiatives.
The objective of Swedish LifeWatch is to make all major biodiversity databases in Sweden interoperable and accessible through standard-ized web services, and to develop an analysis por-tal providing a single access point and a range of analytical services. The idea is not to collect new data or to construct new databases, but rather to make existing data available in a uniform way. Swedish LifeWatch shall strive to provide easily accessible resources to Swedish research groups, achieved by user support, strategic communi-cation, and education. The strategic goals also include cooperation with related national and international initiatives.
The undertaking is regulated by the contract between the Swedish Research Council (SRC) and SLU, and by the consortium agreement be-tween the six partners. The construction phase is outlined by the strategic plan which covers the construction phase from 2010 to 2014 (updated on a yearly basis). Annual plans further specify deliveries for each year.
This annual report summarizes the activities within Swedish LifeWatch during 2014.
Swedish LifeWatch in shortSwedish LifeWatch is a national collaboration between universities, public authorities and natural history museums in Sweden. The main goal is to construct a strong e-infrastructure for biodiversity research, where distributed databases holding data on biodiversity and environment are connected through web services, using agreed standards and a common taxonomy. A coherent Analysis portal provides a single access point and a range of analytical services.
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The infrastructure at a glance
NORS The National Register of Sur-vey test-fishing (Department of Aquatic Resources, SLU). Contains data from netfish-ing in Swedish lakes.
1 825 648 observations
SERSThe Database for electro-fishing in streams (Dept. of Aquatic Resources, SLU). Contains data from experi-mental fishing with electric-ity in Swedish rivers and streams.
247 988 observations
ArtportalenThe Species Observations System is an open access database for sightings of plants, fungi and animals in Sweden. Administered by The Swedish Species Infor-mation Centre at SLU.
44 230 444 observations.
ObsdatabasenA non public observation database of redlisted spe-cies. Access to data requires permission. Administered by The Swedish Species Infor-mation Centre at SLU.
1 014 184 observations
DINA & GBIFDINA is a national system for digitalization of natural history collections. Admin-istred by the Swedish Mu-seum of Natural History.
20 467 observations
WRAMWireless Remote Animal Monitoring (WRAM) is a na-tional system for automatic reception, long-time storage, sharing and analyzing of sensor data from animals. Adminstered by SLU.
0 observations
MVMMVM environmental data provides freshwater species observations. Administered by SLU.
475 798 observations
SMHIMarine observation data pro-vided by SMHI (SharkWeb). WebService delivered in 2014.
68 092 observations
Taxon Observation Service
GBIFService
SLW GeoServerWFS, WMS (DwC)
The Analysis Portal
Other users(authorities etc.)
New applications, portals, etc.
PrintObs (ArtDatabanken)
Artportalskopplingen (Länsstyrelseran)Blue boxes below shows the amount of observation data
connected to the infrastructure, in total 47,882,621 ob-servations (January 2015). The WRAM webservice is de-livered, but data is not yet harvested. The DINA & GBIF webservice is also up and running, though more datasets are waiting to be harvested.
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ArtDatabanken SLUThe rate of development was substantially lower in 2014 compared to previous years, due to restricted resources (even though, in hindsight, we can con-clude that we had not had to slow down as much as we did). A particular focus was given to user tests in order to evaluate usability of the Analysis portal1 and support to the users of different parts of the in-frastructure. Resources were also allocated to man-aging databases, web-services and development of more services (as described below) and adding data, including correcting errors in the dataflow from the data providers. After having connected the SHARK Marine monitoring data from SMHI to the LifeWatch infrastructure this year, the origi-nal plan of data provision was accomplished. In to-tal, more than 47 M species records were available at the Analysis portal by the end of the year.
The development of the Analysis portal was initiated in 2012. It was officially launched in De-cember 2013. In 2014, improvements were made of the various methods for downloading data, both in terms of file formats (CSV, XML, Excel, GeoJ-SON) and by providing a combination of spatially and taxonomically structured aggregations of sum-mary statistics particularly suitable for calculations of different biodiversity indexes.
Since the initiation of the Swedish LifeWatch project in 2010 a bunch of core services essential for the Swedish e-infrastructure for biodiversity analysis have been published (see Figure below). Two of them handle species observations provided from all connected data providers (DINA, The Species Observation System, Artportalen 1 (birds), SMHI, WRAM, MVM, NORS, SERS, and Red-listed species), i.e. the Swedish Species Observa-tion Service, and the Analysis Service. Both these services are connected to an intermediate database which is updated daily by the Harvest Service which looks for changes in the set of different data sources. In order to support taxonomic search mechanisms and listing tasks of taxa based on com-
1 www.analysisportal.se
Reports from the consortium partners
binations of taxonomic hierarchies or taxon attrib-utes, such as traits, conservation status or legislation, the Taxon Service and the Taxon Attribute Service were developed. Authentication and authorization management of all users handling data by any of the listed services is supported by the User Service. For those whom want to integrate any part of this infrastructure into other applications it is possible to download client code as NET-dll:s from the Swedish LifeWatch home page.
The functionality of the taxonomic backbone Dyntaxa, securing correct and consistent taxon concepts, was further improved in 2014, and the quality and quantity of its content (names) were substantially improved thanks to resources from the Swedish Taxonomy Initiative (Svenska artpro-jektet).
As the usage of the different core LifeWatch services increased the need of a tool for evaluating the current status of each of the services emerged. Therefore, a web application called Web Admin-istration ArtDatabanken SOA was developed in 2014. The system also provides a simple interface for managing the harvest service.
In 2014, the SLW Geoserver was made operable and now information about it is available at the Swedish LifeWatch home page. This service allows access through the WFS interface to all public spe-cies observation data in SLW infrastructure. This type of service enables direct integration of species observation data into GIS programs like ArcGIS and QGIS.
GeoServer is an open source software server written in Java that allows users to share and edit geospatial data. Designed for interoperability, it publishes data from any major spatial data source using open standards. GeoServer is the reference implementation of the Open Geospatial Con-sortium (OGC) Web Feature Service (WFS) and Web Map Service (WMS), recommended by the LifeWatch construction plan.
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SLW GeoServer (OGC: WFS, WMS)
PrintObs, ArtDatabanken
County administrations
Apps
Governmental agiencies
New portals
GBIF Sweden
Analysis Portal
Researchers
LW European network
GBIF Service
SLW is an infrastructure of web-services making data available
in different contexts
Collections DINA, NRM
Artportalen SLU
Fish, SLU
WRAM SLU CAnMove
Lund
Red-listed species,
SLU
Marine monitoring
SMHI
Freshwater monitoring
SLU
Taxon Observation Service
Illustration of main services provided by SLW. Data is harvested incrementally from the connected databases (light red) and is accessible through the Taxon Observation Service. The Analysis Portal provides an easy access point to the data, together with a range of analysis services (light blue). All these services are also available for other programmatic solu-tions. In addition, data can be accessed i GIS programmes through the SLW GeoService WFS.
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Data from Swedish Species Obser-vation Service shown in ArcMap.
Development of the new generation of Artpor-talen (Swedish Species Observation System) took place through the year (news and release history is available at the site of Artportalen1). In May 2014, all records of invertebrates in Artportalen 1 were migrated to Artportalen 2.
Artportalen is one of the largest data providers within the Swedish LifeWatch infrastructure. It is an internet-based, freely accessible reporting sys-tem and data repository for species observations, used by scientists, citizen scientists, governmental agencies, and country administrations. The system handles reports of geo-referenced species observa-tions of almost all major organism groups from all environments, including terrestrial, freshwater and marine habitats. In 2014, some 4.8 million new observations were submitted to Artportalen (1 & 2), now harbouring close to 45 million observa-tions of c. 29,000 different species.
The cconstruction of the new generation of Artportalen is a joint venture with the Norwegian Biodiversity Information Centre (NBIC), aiming
1 http://www.artportalen.se/Home/ReleaseHistory
Invertebrates were added to the new version of Artportalen (Swedish Species Observation System) in May 2014.
at a shared updated application for both countries. The development of the new version has mainly been financed by the Swedish Environmental Pro-tection Agency and the Norwegian Department of Environment.
During 2014, in total five ICT developers and two technicians were working to some extent within the Swedish LifeWatch project at ArtDa-tabanken. In addition, up to five developers were engaged with the new version of Artportalen (the Species Observation System). The SLW ICT de-velopment was led by ICT architect and coordina-tor Oskar Kindvall.
For communication, presentations, support, meetings and government of the consortium, see below.
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The analysis portalThe Analysis portal provides a single entry point to all data within the Swedish LifeWatch infrastructure. The portal enables free access to biodiversity and environ-mental data and a range of analytical and visualisation services. Here are three examples of its possibilities.
Species Richness Grid MapThe Analysis portal makes is possible to calculate different types of grid based spatial statistics. Here is an example of a species richness grid map where number of species per grid cell is shown in different shades of blue. In this case all public observations cur-rently available in the Swedish LifeWatch national web service for species observation are used. Same calculations can be done for any organism group or set of user defined set of taxa in order to explore patterns of biodiversity.
Time Series HistogramThe variation of species observations over time can be explored in the Analysis portal. This figure shows temporal variation of all species observations currently available in the Swedish LifeWatch infrastructure. When analysing observation data statistically, samp-ling efforts must be taken into consideration. A tool for analyzing time series based an abundance index which controls for sampling effort is now available in the portal.
Species Observation MapThe Analysis portal makes it possible to co-analyze species ob-servations and environmental data. This screen shot shows obser-vations of the bush cricket Pholidoptera brachyptera (yellow dots) and average time for first frost nights during autumn. In the red zone the frost comes later than in the bluish zones. In this case species observation data comes from the Swedish Species Observations System (Artportalen). The environmental data is provided by means of an OGC Map Service (WFS) at the Swedish Metrological and Hydrological Institute (SMHI).
www.analysisportal.se
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Swedish Museum of Natural History and GBIF
Media server NRM used a considerable portion of its SLW re-sources during 2014 for the development of an attachment (multimedia) server for the collection manager and other DINA Web clients. By year’s end, the attachment server was ready for initial testing and is now being tested and improved by our collaborators in Canada. It will be fully tested and released as a DINA Web component in the first quarter of 2015. The media server will han-dle images, 3D-images, videos, pdf´s etc. within the collection management system and its connected web clients. The bulk of current images in the DI-NA-system have already successfully been import-ed to the media server. The development of the API for the media server has also set the standard for the harmonization of data service APIs within the DINA system.
In September 2014 a DINA Technical Work-shop1 was arranged by NRM for programmers, developers and system engineers within the DINA International Consortium as well as for our EU-BON collaborators. The workshop included pres-entations from the different participants and demos of various systems, including existing and potential components of the DINA system. Harmonization of APIs, service oriented architecture, road map for
1 Read more about the workshop at http://www.dina-pro-ject.net/wiki/Workshop:_EU_BON_-_Stockholm,_16.-18._September_2014
distributed development, guidelines and principles on how to build a module and join the DINA-system development were also on the agenda. One of the outcomes was an agreement on a common repository for source code and standardization of the DINA web APIs.
The DINA-systemDINA is an international effort to develop an open-source, web-based collection management system. The effort builds on the Specify system, which is widely used at natural history museums around the world. The current production ver-sion of Specify is not web-based but consists of a “thick” Java client, installed on the local computer, communicating with a separate database manage-ment system. The emerging “DINA Web” system consists of a number of thin web clients, commu-nicating with core databases through web services in a service-oriented architecture. A hybrid system, referred to as “DINA Light”, is already in produc-tion at the Swedish Museum of Natural History and uses the current Specify Java client for core collection management, while other tasks are han-dled by web clients forming part of the emerging DINA Web. The first fully web-based version of DINA is slated for release in late 2015 or early 2016.
DINA has been adopted as the future collection management system by most large natural history collection institutions in Sweden, and forms the core of the future data flow between Swedish nat-ural history collections and the SLW infrastructure. DINA is currently used for daily management of the entomological collections at NRM, at Station Linné on Öland (the SMTP collection), and at the Gothenburg Natural History Museum. Migration or migration preparation efforts in 2014 focused on geology and zoology collections at NRM, on legacy specimen data from SMTP, and on the large botany databases at NRM and at the Museum of Evolution in Uppsala. By the end of 2014, the ge-ology collections at NRM had started using the DINA system for their daily collection manage-ment.
Members of the DINA Technical workshop 16-18 Sept at Swedish Museum of Natural History in Stockholm.
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New functionality of the web-based inventory client, designed for SMTP and similar large-scale inventory projects, was released in beta version in the fall as ”Naturfynd”2.The new functional-ity allows users to upload datasets in spreadsheets (Excel files) to the DINA database after validation and correction of errors. A public DNA barcode service (Swedish DNA key, “Svenska DNA-ny-ckeln”), exposing both Swedish and international DNA barcode reference libraries, was released in January 2014. In November 2014 a collaboration project with ArtDatabanken, Gothenburg Natural History Museum, Gothenburg University and NORBOL was initiated with the aim of making the DNA barcodes from the large Swedish Tax-onomy Initiative marine inventory project avail-able with images and voucher data through the public DNA barcode service. This also included a focus on migration of zoology data, primarily invertebrates, from the database system in use at the Gothenburg Natural History Museum to the DINA-system.
Currently, SLW harvesting of NRM web ser-vices is restricted to Swedish species-level records from the DINA database, about 20,000 records in total. The number of DINA records will grow rap-idly over the next few years as the major collection databases are migrated over to DINA. Eventually,
2 https://naturfynd.se.
we expect the DINA system to cover some 7-8 M records that are not currently available through the Swedish LifeWatch Analysis Portal.
DINA (Digital Information System for Natural History Col-lections) is an international effort to develop an open-sour-ce, web-based collection management system.
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Screenshot of the Inventory Client Naturfynd.
A public DNA barcode service (Swedish DNA key, “Svens-ka DNA-nyckeln”), exposing both Swedish and internatio-nal DNA barcode reference libraries, was released in Ja-nuary 2014.
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AquaMapsUsing resources from EU-BON, we have contin-ued the development of an AquaMaps modelling tool in R, which was initiated under the Swedish LifeWatch project. AquaMaps1 is a visual model-ling tool, combining niche modelling and expert knowledge. A concern with AquaMaps has been relatively slow computation time and limited com-patibility with open-source spatial software, both relating to the database format. Our solution is rAquaMaps, a standalone R application based on the published AquaMaps algorithm and associat-ed data sources. rAquaMaps reduces computation time significantly and is built in an open frame-work, promoting sustainability over the long term. The rAquaMaps package will permit advanced us-ers great flexibility in modeling, and will be made available to SLW (and EU-BON) users both as a web service and through an easy-to-use web inter-face. The first beta version will be publicly released in 2015.
1 www.aquamaps.org
Marine Biodiversity Map showing Marine mammals at the site AquaMaps.
CollaborationsDevelopment of the DINA system is a highly collaborative international effort backed by the DINA consortium, an international organization that was formalized in 2014 with the signing of a joint Memorandum of Cooperation among six institutions from six different countries: Sweden, Denmark, Estonia, Canada, Germany, and United Kingdom. Four members are core members and contribute resources to the development of the DINA system. During 2014, Sweden has chaired the DINA International Steering Committee and the DINA Technical Committee. Both groups met in connection with the TDWG meetings in Swe-den, and numerous times in Web meetings. For more information, see the consortium Web site2.
Fredrik Ronquist and Anders Telenius represent Sweden and SLW in GEO task BI-01-C1, Global Biodiversity Observation Network (GEO BON) Working Group 8, Data Integration and Interop-erability. Anders Telenius participated in the 2014 GEO Work Plan Symposium held in Geneva (2014-04-28 – 2014-04-30).
GBIFPresently the NRM web service provides access to over 7 M georeferenced records harvested and presented by GBIF-Sweden, including more than 1.1 M georeferenced musum specimen records delivered separately to GBIF-Sweden but later to be included in DINA. Already in 2013 The Swdish Research Council requested closer col-laboration between the board of GBIF-Sweden and the Steering Group of SLW, and a report was issued (but declined) suggesting combined gov-ernance. Then in early 2014 a proposal was made by NRM to create a joint project proposal for all major Swedish biodiversity informatics infrastruc-tures (GBIF-Sweden, SLW, WRAM CAnMove, SAMBA), eventually aligning activities within the forthcoming requirement of VR to merge and re-duce the number of national research infrastruc-tures quite drastically. The final proposal will be submitted in May 2015.
2 http://dina-project.net
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The Swedish Meteorological and Hydrological In-stitute (SMHI) contributes to Swedish LifeWatch mainly in three ways: an information system on aquatic microalgae, quantitative data from marine monitoring of other marine organisms, and ma-rine climate data. SMHI also takes part in marine show case studies.SMHI is the National Oceanographic Data Cen-tre (NODC) for Sweden and also the national data host for marine monitoring data. The data comes from national and regional monitoring programmes and is available at www.smhi.se. Part of the data was published using LifeWatch stand-ards in 2014 at http://sharkdata.se. The system is built for machine-machine communication. A web interface with information on the system is also available.
An information system for aquatic microalgae and heterotrophic flagellates has been developed in Sweden in co-operation with the other Nordic countries. Species lists of aquatic microalgae from Sweden, Norway, Denmark, Finland have been combined and quality controlled. This task is con-stantly ongoing because of changes in taxonomy, newly identified species etc. The system includes a web site1 and a database with quantitative informa-
1 http://nordicmicroalgae.org
tion on the distribution of microalgae and other protists. The web site also includes images, videos, information on size, toxicity etc. Images and videos are contributed by experts in the area. Information on biovolumes comes from the HELCOM-Phy-toplankton Expert Group. Information regarding harmfulness is obtained from the IOC-UNESCO Taxonomic Reference List of Harmful Micro Al-gae.
The web site became public in mid-2011. Sev-eral scientists in the Nordic countries contribute to the content. In 2014 the number of images con-tributed passed 1800. Approximately 150 unique visits were made every day during 2014.
Swedish Meteorological and Hydrological Institute (SMHI)
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Fig. 3. In 2014 marine biological data was published using a machine-machine interface at http://sharkdata.se. A screen shot of the web interface with information on the system is shown.
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Department of Aquatic Resources SLU
Preparing for fish data A pilot study on freshwater fish was intended to illustrate how species observations from differ-ent original databases could be harvested, filtered, aggregated and further explored in the Analysis portal and by using other online tools of Swed-ish LifeWatch. Exploration of temporal changes in regional fish species richness will be done after completed transfer of species observations from the PIKE database to the new Artportalen, ena-bling them to be harvested for use together with fish data from NORS or SERS.(Parts of the pilot study are presented in more details below.)
Several more or less uneducated visits to the Analysis portal during 2014 revealed interesting experiences on how species observations from dif-ferent data sources can be filtered and downloaded to excel-files for exploration in whatever external software. The uneducated visits also raised numer-ous questions on how to find and retrieve suitable environmental datasets from the Analysis portal, and how to actually combine species and envi-
ronmental datasets for e.g. environmental niche modeling (ENM).
A plan was made for a web service for the Data-base for Coastal Fish (KUL) to be developed in the spring 2015. The database contains fish data from coastal waters in Sweden.
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Electrofishing.
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Survey test fishing with Björn Ardestam.
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University of GothenburgTest of data flowsUGOT organized a SwedishLifeWatch-BioVeL hackathon in Gothenburg on 7-8 January 2014 with the goal to integrate BioVeL workflows into the SwedishLifeWatch portal. As a pilot case, the BioVeL workflow for ecological niche modelling1 was connected to the SLW portal. This workflow is particularly suitable for utilizing data aggregated by the Swedish systems (e.g. Artportalen). It uses occurrence and environmental data to model eco-logical niches with the openModeller web service, a library that provides a range of algorithms to model species distribution patterns. It also allows the spatial computation of changes in potential distribution maps by measuring the differences between raster layers calculated under different climatic scenarios using the R statistical environ-ment. The workflow can be executed on the SLW portal after filtering occurrence data2. (For more information, see parts of the pilot study that are presented below.)
Moreover, a series of individual test-runs during spring 2014 were performed. The objective was to establish use cases that rely on services from both systems (BioVeL and SLW), and specify how to integrate these services. The report identified some technical issues for improvement, and particularly highlights the importance of training, capacity building, and active user support in the coming years (see pilot study below).
Networking and coordinationBioVeL. The collaboration between SLW and BioVeL has progressed during 2014, with emphasis on coordination and co-development of a range of analytical services and workflows that are ac-cessible through the SLW infrastructure. BioVeL services can now be accessed through the SLW Analysis portal3, while workflows can be accessed and executed through the SLW web page4.
1 http://purl.ox.ac.uk/workflow/myexp-3355.202 https://www.analysisportal.se/Result/Download3 https://www.analysisportal.se/Data/MetadataSearch4 http://www.svenskalifewatch.se/en/tools/
The user statistics for services and workflows are as follows: • Biodiversity services. The BiodiveristyCata-
logue had >160,000 discovery queries across all BioVeL services during 2014.
• Biodiversity workflows. The portal executed and completed >6000 workflows during 2014. The overall number of the registered users on the portal was 204. In addition, 1231 work-flows were downloaded for external execu-tions outside the portal.
LifeWatch Europe. UGOT participated in coor-dination activities of the European LifeWatch ini-tiative. This included meetings in Granada (Janu-ary), Heraklion (June), and Amsterdam (October). Here European activities were planned and organ-
All BioVeL workflows are accessible on http://biovel.myexperiment.org/, documented on https://wiki.biovel.eu/display/doc/Start, and executed on http://portal.biovel.eu/.
The European Marine LifeWatch Portal .
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ized in relation to the establishment of the ERIC as well as a ‘LifeWatch lite’ program. The latter at-tempts to build an operational infrastructure from existing assets in Europe and has made particular progress in the marine sector. This activity is cur-rently sketching a European Marine LifeWatch Portal hosted by VLIZ1, which incorporates several assets developed by SLW.
VRE development. A new H2020 application (called LinkD) was prepared to answer the call ‘e-Infrastructures for Virtual Research Environments (VRE)’ (Topic EINFRA-9-2015). In this proposal SLW continues to integrate its assets with Euro-pean infrastructures for biodiversity and ecosystem research.
Support requests. UGOT established a number of external use cases with Swedish scientists who started using the infrastructure for their own re-search. Examples are below:
1. World soil data access. We received a request from the research group on Biogeography and Evolu-tion in the Neotropics at University of Gothen-burg. The researchers want to import data from the Harmonized World Soil Database into R- and workflow environments. The request has been an-swered with the provision of a generic protocol for layer transformation2, as well as delivery of the re-quested data package both within and outside the workflow environment.
2. Mosquito borne diseases. A group of scientists at the Swedish National Veterinary Institute 3 submit-ted a requested for data provision and processing (contact Gunnar Andersson). The group is work-ing on mosquitos borne diseases in Sweden, and asked for support in carrying out various modeling approaches. In particular, the group asked for en-vironmental data with land cover information at high resolutions (10-15 arc-sec) to be used for modeling mosquito distribution. The request was answered with the delivery of the requested data package that was obtained from the European En-vironmental Agency and thereafter transformed to
1 http://marinevre.lifewatch.be/2 documented under https://wiki.biovel.eu/x/BgHj3 http://www.sva.se/en/
include a smoothing radius (of 300 and 3000m) around the raster cells to simulate the access range of the organisms to vital environments such as farmland and forest.
3. Natural protection areas. A student at University of Gothenburg requested a compilation of natural protected areas in Southern Sweden (Skåne, Ble-kinge, Småland) into a spatial mask at resolutions of 1 arc-sec and 10 arc-sec (here picture screenshot soil). The request has been answered and the stu-dent used the masks in her BSc project to predict optimal sites for leaf frog protection under climatic changes (see below).
Supervision. One student was supervised with a bachelor project under the SLW program: Linn Nilsson (2015). The future of the leaf frog, based on environmental and climate changes. BSc thesis, University of Gothenburg, Sweden.
Marine GroupMarine VRE. No major national activities other than existing use cases (listed under publications) and dissemination activities (listed under attended meetings).
Genetic data integrationPhylogenetic services. During 2014 UGOT es-tablished SUPERSMART as a service (www.su-persmart-project.org). The software provides func-tionality to infer phylogenies from a given list of taxa by assembling a set of DNA sequences from the GenBank database, and thereafter infers phy-logenies in a multi-step procedure using the Max-imum-Likelihood estimator implemented in Ex-
Access to data from world soil database
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aML and the multi-species multi-locus coalescent approach implemented in *BEaST. Computations are performed in parallel on the BioVel server at Naturalis Biodiversity Center in Leiden, NL (biovel.naturalis.nl). The SUPERSAMRT service consists of 12 consecutive operations, which can be executed individually4. Additional phylogenetic services that define models, perform, test and use phylogenetic inference in downstream applications are now also operational5.
Genomic services. A microbial traits analysis service is now operational6. This service delivers a number of ecologically interesting traits of bacte-rial communities as observed by high-throughput metagenomic DNA sequencing. In addition, an amplicon processing service for prokaryotic, fun-gal, and eukaryotic samples has become opera-tional during 2014, called BioMaS7 (Bioinformatic analysis of Metagenomic AmpliconS). The services is a bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities, and includes all fundamental steps, from raw se-quence data arrangement to final taxonomic iden-tification, which are required in a Meta-barcoding high-throughput sequencing based experiments.
4 https://www.biodiversitycatalogue.org/services/78.5 https://www.biodiversitycatalogue.org/services/316 https://www.biodiversitycatalogue.org/services/647 https://www.biodiversitycatalogue.org/services/71
Umeå University
Umeå University delivered its case studies in 2011 and is awaiting the release of the new version of Artportalen, after which transfer of the PIKE data-base to Artportalen will be conducted. Umeå Uni-versity delivered the fish database and a user guide for the data set to Swedish LifeWatch during 2014. The next year, the data set will be implemented into Artportalen.
CAnMove members and developer have par-ticipated in LifeWatch meetings and coordinated the work with WRAM. CAnMove has further participated in the planning of the application of an extended e-infrastructure for biodiversity and ecosystem research in which CAnMove will be a member. Several internal meetings have been held within CAnMove to inform the users of the data-base development and to train members to upload data. Several datasets have been uploaded into the CAnMove database. The database development in CAnMove is supported by an external grant for large databases from VR to CAnMove.
The software that implements the data transfer from CAnMove to WRAM is ready. The solution is running on Linux and utilizes the Tomcat appli-cation server with the Axis2 Web Service interface module. The actual Web Service, as well as the Data Provider Sender, is coded in Java.
We are now waiting for WRAM to carry through tests to make sure that it all work when called from the WRAM system. Meanwhile we have tested to send Web Service requests on our own and even created a simple listener to make sure that the Data Provider Sender returns the cor-rect data in the right format over the net. So we are fairly confident that the WRAM tests will go well.
What then remains is to set up the interface in the production environment and of course load the CAnMove database with data that are eligible for exposure to the WRAM interface.
Lund University and CAnMove
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LifeWatch EuropeAn operational workshop was held in Granada, Spain, February 3-4, where Ulf Gärdenfors and Matthias Obst represented SLW. Here, it was dis-cussed how a fast implementation of the European LW could be commenced. Also, the participants discussed prerequisites of the formation of an ERIC with representatives from the EU Com-mission, and, in particular, the comments to the preliminary Statutes made by the Commission on January 28th. Over the year, Sweden has also sug-gested some improvements of the Statues in prepa-ration of the LW ERIC.
In June 3-5, LifeWatch Europe organized a ma-rine thematic technical workshop at the Hellenic Centre for Marine Research (HCMR), Heraklion, Crete. SLW was represented by Bengt Karlsson (SMHI), Oskar Kindvall (ArtDatabanken) and Matthias Obst (University of Gothenburg). The aim of this workshop was to develop a proposal of what should be delivered as the first steps towards a construction of a marine virtual laboratory for LifeWatch. As a direct result of the workshop the Belgium team was able to publish the first version of a web application for preview1.
The 11th LifeWatch Stakeholders Board Meet-ing took place in Crete, July 7-8, but Sweden was not able to participate.
SLW contributed with presentations describing the Swedish infrastructure with specific focus on systems for Citizen Science data on biodiversity at the annual Biodiversity Information Standards (TDWG) conference held in Jönköping October, 26-31.
SLW has also had cooperation on technical level with, in particular, LifeWatch Belgium, and on communication with the LifeWatch Service Centre in Italy.
At the end of the year, Belgium, Greece, Italy, the Netherlands, Portugal, Romania, and Spain had declared their intention to become members of the planned LifeWatch ERIC, while France, Hungary, Norway, Slovakia, Slovenia, and Sweden planned to start as observer states.
1 http://marinevre.lifewatch.be/
International cooperation
Nordic LifeWatch initiativeThe final project report from the meeting in Akureyri on northern Iceland 6-8 May 2013, formulating a joint Nordic LifeWatch vision and work, was presented to NordForsk in March 2014. In May, the Nordic LifeWatch “consortium” sub-mitted a Letter of Interest to the Nordic e-Infra-structure Collaboration (NEIC). It pointed to the scientific needs, challenges, priorities, and recom-mended actions related to the realization of a com-mon Nordic research infrastructure in the field of biodiversity informatics, maybe contributing to NeIC establishing a new area for environmental sciences (ENV) from January 1st, 2015. In October, NINA and ten Norwegian co-partners submitted an application to the Norwegian Research Coun-cil for funding of a 5 year project with the aim of developing a Norwegian Terrestrial and Lim-nic Data Centre (NTLDC). If approved, NTLDC will serve as a coordinating unit for ecological data from terrestrial and limnic ecosystems and substan-tially enhance the Nordic LifeWatch cooperation.
BioVeLBioVeL (Biodiversity Virtual e-Laboratory, biovel.eu), is a European project financed with EUR 5 million from EU’s 7th Framework Programme. BioVeL integrated web services for analytical workflows to analyse biodiversity patterns, so-called “virtual e-Laboratories” that are of direct utility for LifeWatch and SLW.
The collaboration between SLW and BioVeL has progressed during 2014 (see above UGOT).
Nordic MicroalgaeThe Nordic cooperation related to the informa-tion system on microalgae and aquatic protozoa continues. During 2014 nordicmicroalgae site2 was developed further. The start page is now available in twelve languages. The number of scientists that contributes material has increased and the number of images is approaching 2000. There are approxi-mately 150 unique visitors every day from all parts
2 http://nordicmicroalgae.org
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of the world. The Nordic Microalgae committee, which contribute to the quality control of Nor-dic Microalgae and the Nordic Microalgae check list, met in Lund, Sweden, 13-14 March 2014. Participants include scientists from the University of Oslo, Norway and the University of Copenha-gen, Denmark. The cooperation with AlgaeBase and the HELCOM Phytoplankon Expert Group (HELCOM-PEG) and HELCOM-ZEN Zoo-plankton Ecology Network continues.
Screen shot of the Nordic Microalgae site.
Number of sessions per day at Nordic Microalgae, http://nordicmicroalgae.org
May and a version 1.0.1 in November 20143. The software was presented during the International Conference on Harmful Algae in Wellington, NZ, 27-31 October. In November scientists from the University of Tasmania started to evaluate the soft-ware for use with Southern Ocean plankton data.
GEO BON and EU BONGEO BON is a global partnership where over 100 governmental, inter-governmental and non-gov-ernmental organizations are collaborating to report on the status and trends of the world’s biodiversity. The group seeks to ensure that adequate biodiver-sity data and information will be generated, ana-lyzed and included in the ongoing effort to estab-lish a Global Earth Observation System of Systems (GEOSS). GEO BON has been recognized by the Parties to the Convention on Biological Diversity (CBD) and provides expert support to CBD.
EU-BON, a large European network support-ing the GEO BON objectives, was funded in 2012 and started its activities in early 2013.
In 2014, the Swedish Museum of Natural Museum has participated in the Working Group 8, Data Integration and Interoperability (GEO BON) and in a workshop (EU BON) (see above SMNH).
3 The software is available from http://nordicmicroalgae.org/tools
Screen shot of Plankton Toolbox.
Some of the participants in the Plankton Toolbox workshop arranged in Gothenburg 26-27 May 2014. And a plankton cake.
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A workshop on plankton data analysis was ar-ranged in Gothenburg 26-27 May 2014. The analysis tool Plankton Toolbox, a product of Swed-ish Lifewatch, was used during the workshop. This stand-alone open source software includes specialized functions for working with phyto- and zooplankton data. Version 1.0.0 was released in
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WRAM WRAM (Wireless Remote Animal Monitor-ing), hosted by SLU, represents the national e-infrastructure for biotelemetry sensor data from fish and wildlife. WRAM started at a small scale in 2003 as an initiative to handle data originat-ing from animal deployed GPS-tags. Since then the extent of the collected data has expanded enor-
who are linked to the WRAM data broker, to ag-gregate their data. This web service is operational, but not fully implemented as neither WRAM nor CAnMove database systems became fully opera-tional during 2014.
Additionally, WRAM has developed and set up a specific web service to consume data from CAnMove as detailed above and has provided CAnMove with the appropriate documentation. CAnMove has set up a web service on their side to deliver both raw and aggregated data to the WRAM Data Broker (WDB) and through the WDB to the SLW Analysis Portal. WRAM has tested the communication between WBD and the CAnMove web service using a test user and test data. Upon completion of the CAnMove database all appropriate data will be available in aggregated form in the SLW Analysis Portal.
The WRAM database infrastructure is men-tioned together with LifeWatch and GBIF in the Swedish Research Councils current 2014 hand-book ‘Guide to research infrastructures’ as one of the database infrastructures of national importance. Further, during 2014 the process was initiated to merge WRAM, LifeWatch and GBIF, together with CAnMove and other smaller research infra-structures into a new, common national e-Infra-structure for biodiversity and ecosystem research and apply for operational funds from the SRC in 2015.
ECDSCollaboration with ECDS on metadata handling has not yet been formalised, but SLW and ECDS maintain a dialogue and plan for future coop-eration and joint solutions. The Director of SLW (UG) is also a member of the ECDS Board. In addition, ECDS and SLW collaborate on commu-nication activities. Ulf participated in two meetings in 2014.
SITESThe Director of SLW (UG) is member of the SITES Board in which information about the two infrastructures is exchanged. Ulf participated in four meetings in 2014.
National cooperation
mously due to technical development of sensors and improved possibilities for real-time data trans-fer. Currently (January 2015) WRAM stores loca-tion, acceleration, proximity, and temperature data for 2325 animals from 20 species in 8 countries in Europe and Africa, resulting in more than 99.7 million database records. The system handles at the moment automatically 14 data formats from 10 different sensor providers. Since 2011 the Swed-ish Research Council has provided funding for a three-year project ending in 2014 to upgrade the current database system (WRAM 1) into a national e-infrastructure and database network (WRAM 2).
Funded by a grant from SLW, during 2014 WRAM developed integration tools to make suit-able spatial biotelemetry data in the WRAM Data Warehouse and the new CAnMove database avail-able in the SLW Analysis Portal. For this a specific web service was developed to regularly collect and aggregate data from the WRAM Data Warehouse.
Administrators can easily add and configure various aggregated transformations that are calcu-lated on their sensor data held within the WRAM data warehouse. In addition, the same component is used by external data providers as CAnMove
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The SLW Board had four regular meetings in 2014, in February, June, October and November. In addition, in November the committee agreed per capsulam on the allocation of two of the nodes’ funding for 2015. Compare minutes.
The National Coordination Group consists of representatives for all consortium partners. The group had two meetings during 2014, one meeting in May at NRM and one in October at SMHI in Gothenburg. The Coordination Group meetings have mainly focused on reports of project progress and coordinating planning and resources, budget and operational plan.
To this come meetings with representatives from current and planned consortium partners to discuss and coordinate an application to Swed-ish Research Council/Council for Research Infrastructures for the next period. A meeting at ArtDatabanken in February 12th was planned to prepare for the new application in 2014, but – after a decision by Council for Research Infrastructures to postpone the call one year – the meeting had to discuss how the partners could allocate the limited
Administration and organisation
resources and survive until 2016. In the autumn, three meetings were conducted planning for the next consortium application in spring 2015.
The Scientific Advisory Group’s task is to monitor the project and give advice with respect to scientific and international development in the field. The group is internationally composed of sci-entists with extensive knowledge and experience of biodiversity analysis. No physical meeting took place in 2014, but the group was informed by the Secretariat about ongoing activities.
The Secretariat, administrated by ArtDatabanken SLU, coordinates SLW national and international activities including communication and support. In 2014, activities embraced arranging of meetings, workshops, annual work plan, annual report, budg-et, yearly updating of strategic plan and decommis-sioning plan, contracts and agreements with nodes and other partners, support and education of us-ers, documentation, web-pages, newsletter, posters, participation in conferences, and meetings, discus-sions and coordination of international activities.
www.analysisportal.se
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Communication
Communication strategyThe communication strategy for SLW is updated on a yearly basis and supplemented by an activity plan which is updated on a more regular basis. Main communication tools/channels include:- Website- Presentations (e.g. at meetings, workshops and
conferences)- Posters and exhibitions- Publications- PR material, e.g. flyers, brochures, etc.- Social media
The SLW website contains information on the project and links to various tools and resources that are available. It is also the place for SLW news and information about events.
The SLW electronic newsletter contains news about SLW and news from related initiatives or projects that may be of relevance for the SLW stakeholders. Three issues of the electronic news-letter have been distributed in 2014, plus a special invitation to a WRAM workshop in April. The number of subscribers now adds up to 539 ad-dresses. In addition, three newsletters in English have been produced and sent out to a list of ca. 50 international subscribers.
Several posters have been produced to a num-ber of different meetings and conferences. Folders about the project have been handed out at vari-ous meetings. Also, small cards with QR code and URL to the Analysis portal have been printed to be distributed at various occasions. A four-page folder directed at conservationists was produced and distributed at the conference Flora & Fau-navård and Miljöövervakningsdagarna.
Meetings and participation in conferences are another important part of the communication. Many of the collaborators from the different con-sortium partners have presented SLW at confer-ences and meetings, regionally as well as nationally and internationally. At couple of conferences like OIKOS and the international IENE, SLW was presented with an exhibition and demonstration of the Analysis portal.
The number of Twitter followers has expanded from 85 followers (January 2014) to 184 (January 2015).
To this comes the direct support of the infra-structure, of IT aspects, usage of the Analysis portal and other components of the SLW network, an activity that has grown substantially over the year.
SLW exhibition stand at IENE (Infra Eco Network Europe) international conference in Malmö 16-19 Sep.
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One pilot study of data quality in Artportalen, in-cluding how to measure and declare it, and two scrutinizing functionality and usability of Analys-portalen, were conducted. A forth marine pilot study was commenced but is not yet finalized.
Simple algorithms to display ignorance maps on species ob-servation databasesAlejandro Ruete, postdoctorand at the Swedish Species Information Centre, SLU, has analysed the assessment of the bias inherent to bird data pro-vided by the Swedish LifeWatch infrastructure. Open-access biodiversity data often have limita-tions through sampling bias (recording favoured distribution, lack of survey assessment, lack of cov-erage), why an evaluation of uncertainties should be included in technical assessments, monitoring programs and scientific research.
The focus in this pilot study was to develop and test simple algorithms allowing the user to evalu-ate optically and numerically the spatial bias which is presented by so called “ignorance maps”. The potential of the developed tools lies in the simplic-ity of the algorithms (normalized, log-normalized, inversed ignorance) and that no assumption about the bias distribution has to be made. The present ignorance is expressed by a scale of 0 to 1 (1: abso-lute ignorance and 0: absolute certainty/credibility on the data). To visualize the ignorance only based on raw data relied on the least amount of possible assumptions is also feasible. To use observation re-ports summarized per grind cell only, allows the user to modify the evaluation analysis to its specific needs.
As a result of the pilot study, the Swedish Life-Watch analysis portal will implement algorithms to display and download ignorance maps as a tool, which allow reporting the relative spatial distribu-tion of sampling effort or lack on it. It will take more time to make these implementations acces-sible on the portal, but they are already available on the project website1.
1 http://alejandroruete.github.io/IgnoranceMaps
A scientific article presenting the method has been submitted to a peer-reviewed journal. (For more information see abstract of the paper under pub-lications.)
BioVeL–SLW integrationSonja Leidenberger, postdoctorand at the Depart-ment of Biology and Environmental Sciences, University of Gothenburg, made a series of test runs during the beginning of 2014 (see pilot study Leidenberger & Obst 2014). The objective was to establish use cases that rely on services from both systems, specify how to integrate these services, and identify integration issues.
Below is a list of problems and issues that can be addressed to help integrating both systems. When working with the SLW Analysis portal, we encoun-tered a number of issues when trying to explore, assemble, and download species occurrence data. The following summary lists suggestions for im-provements, based on several individual test runs:
* It must be easier to get started. It is very time consuming to read how to start. Already on the start page/homepage, there must be the possi-bility to enter the species name. It is not clear for new users where to find this tool. Perhaps the design could be more ‘intuitive’, similar to
Show cases and pilot studies
Information on Ignorance maps on the project site.
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many software products, where users learn a lot by simply clicking buttons. Or the ‘taxa’ button can be changed to ‘search taxa’ button, and situ-ated in the first line of buttons (between the in-formation and overview button).
* The manual is nice, but time consuming. Moreo-ver, all the explained functions have a further link with much more information to read (the original link to www.svenskalifewatch.se). A short demonstration movie would help as a quick start. In addition, a more extended pdf-file with a step-by-step guide would be help-ful, demonstrating a use case and showing the user which buttons execute the most important functions. The movie and/or pdf-file should be available under the information button.
* In general, there is the impression that some but-tons could be bigger. Why not using the whole visible page? Especially, third line buttons are difficult to read.
* If workflows are executed from within the portal, information about what they do (e.g. bioinfor-matics functions) and how they work (tutorial) needs to be provided by linking to the appropri-ate documentation from the BioVeL sites. Also, a SLW specific description needs to be provided on how to generate the workflow input files on the SLW portal.
* Workflows should perhaps be placed under ‘Cal-culations’, rather than under ‘Download’
* If the user logs in and out of the SLW portal, previous queries are no longer available. A list of queries sorted by dates could be nice. Here is an example: A user may want to repeat a query after 6 months for two reasons, (i) to compare how the data results have changed, or (ii) because he/she has forgotten how the data were generated in the first place and want to reproduce them. For that it would be nice if the users ‘current settings’ can be logged for each run under the users personal account, or alternatively that the user can download his/her ‘current settings’ for a given run.
* When exploring species occurrences in com-bination with environmental data, there are a number of obstacles. The environmental data can be retrieved from the GeoPortal, but it is not clear how to find them. There has to be a man-ual explaining how to explore the GeoPortal for mapping services and how to load a data layer into the SLW portal (e.g. URL for the data layer needs to be copied from the metadata directory of the respective service in the GeoPortal). Also, the manual should explain what is the difference between ‘Environmental data’ and ‘Map layers’ window of the SLW portal. A tutorial would be very helpful.
BioVel integration in the Analysis portal. Picture showing the integrated functionality of SLW and BioVeL platforms. Spatial and taxonomic queries can be made in the Analysis portal, and thereafter further processed though BioVeL work-flows.
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* When uploading WMS layers from the GeoPor-tal it is not clear how to visualize these as over-lays with the species data. Intuitively, you would expect the environmental data to be shown under ‘Results > Maps > GridMapsOfEnviron-mentalData. But when you go there, you can never select the layer you imported. The layers are visualized using the blue pop-out window, but you have to find out this. Also, sometimes the services are not up and the layers are dis-played as a red screen. This may be due to mal-function of the Geo service.
* Unless it already exists, a group of scientific test-ers should be established whom have short but regular online meetings devoted to testing and development of documentation. These meetings should be used to (i) identify and document sci-entific use cases, (ii) report bugs, improvement suggestions, and performance, and (iii) generate training/documentation material.
Kattegat case studyIn 2013 a survey of available data available for the Kattegat case study was started. After discussions with scientists specialised on marine fish and on benthic fauna from the Institution for aquatic re-sources, SLU in Lysekil, a more elaborate study was carried out in 2014. The focus of the study is the environmental effects on growth of cod (Gadus morhua), e.g. effects related to food availability, cli-mate/weather, hydrography, nutrients, phytoplank-ton, zooplankton. The work on the case study is in progress.
Pilot study on freshwater fishKerstin Holmgren, researcher at the Department of Aquatic Resources, SLU, made a set of visits to the Analysis portal during 2014 from a beginners or non-specialist perspective. Some guiding docu-ments were used:- Svenska LifeWatch. 2014. Analysportalen för
biodiversitetsdata. Användarguide (in Swedish)- BioVeL. 2014. Directory of BioVel tools for
biodiversity and ecosystems research. - BioVeL. 2014. Training Manual. Ecological
niche modeling and related workflows. Version 1.1. April 2014.
From the Analysis portal, it was more straightfor-ward to make filtered searches for species observa-tions, and to view hits on a map, or to download results to excel-files. When looking at typical la-custrine species (e.g. roach, Rutilus rutilus) expected observations from NORS were received, but com-parably few of expected historical observations (e.g. by using a temporal filter from years 1850 to 1930). A latter example consisted of roach observations from many lakes in the county of Värmland, origi-nating from observations by Cederström. This is just one of the historical datasets previously evalu-ated by e.g. Schreiber et al. (2003), before it was in-cluded in the database PIKE. As the DatasetName of these observations was “Nya Artportalen”, it was assumed that this might actually be one of all sub-sets of data stored within PIKE, and perhaps one of a few that had so far been transferred from PIKE to “Nya Artportalen”.
In contrast, there was limited success in retriev-ing additional data through the buttons “Environ-mental data” and “Map layers”, i.e. to get indica-tion of selected data in the box “Current settings”. A problem was to understand how to get any results of combined selection of “species observa-tions” and “Environmental data” and/or “Map lay-ers”. For example, it was not possible to retrieve any excel-lists with aggregated (by grid distances or categorized regions) environmental data from digital maps connected to the Analysis portal.
Sometimes the selection of environmental data or map layer was skipped, and instead went di-rectly to download of filtered species observation data (one fish species at a time) to “Workflows” and “Ecological Niche Modeling (ENM)”. It was possible to view my Swedish fish observations on a map within “BioSTIF”, but to manage a run through a whole workflow to get other than error messages as results. My overall impression was that there are many steps that can failure if you are not completely sure about the consequences of choos-ing different options.
During my visits to the ENM workflow it was nice to see that most of the types of models used for fish habitat modeling in coastal areas (e.g. Sund-blad et al. 2014) or inland waters (e.g. Markovic et al. 2012) were optionally available through the workflow. The range of environmental data layers available for creating niche models was impressive.
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It was, however, not easy to trace environmental data layers back to the original sources, or to judge whether, e.g. the climate layers were suitable for modeling fish species observations from our Swed-ish lakes. It furthermore seemed like ENM could handle only environmental data layers already con-nected in the workflow.
Research based on the SLW e-infrastructureAs the infrastructure now is up and running re-searchers have started to use it, although we do not have full overview yet. Examples from SLU are Åke Berg, Ulf Grandin, Lena Gustafsson, Phil Harrison, Kirsi Jokinen, Nic Kruys, Mari Jönsson, Louise Mair, Tomas Pärt, Cristina Trigal, Alejan-dro Ruete, and Tord Snäll. Moreover, the research council Formas granted a large study of long-term effects of wetland restoration, based on SLW data. Furthermore, some county boards, government agencies, communes and consultants have started to use the infrastructure for resolving various bio-diversity issues.
A description of the infrastructure was published in the journal Human Computation (Gärdenfors et al. 2014). Also, a number of papers utilizing the infrastructure were published or produced in 2014 – see publications.
PublicationsGonzález-Talaván A, Mathew C, Obst M, Paymal E (2014). Data Refinement Using the BioVeL Portal. 67 pp. Copen-hagen: Global Biodiversity Information Facility1.
This document is a practical guide on how to as-sess the quality of biodiversity datasets, like those accessible through the GBIF Network using the online workflows portal produced for the Euro-pean project BioVeL. The manual takes a practical tutorial-based approach that the reader can repeat using the sample datasets provided. A complement of practical exercises based on real-case scenarios should help users attain the skills demonstrated in the tutorials. The manual also provides a generic introduction about data quality and the use of workflows for those who wish to familiarize them-selves with the basic theory behind these practices.
1 Available at http://www.gbif.org/orc/?doc_id=5983
Gärdenfors, U., Jönsson, M., Obst, M., Wremp, A. M., Kindvall, O. & Nilsson, J. (2014). Swedish LifeWatch – a biodiversity infrastructure integrating and reusing data from citizen science, monitoring and research. Human Computation 1(2): 147-161.
With continued pressure on biodiversity and ever-growing conflicts with human development, quali-fied systems for scenario modelling, impact assess-ment and decision support are urgently needed. Such systems must be able to integrate complex models and information from many sources and do so in a flexible and transparent way. To that end, as well as for other complicated and data-intensive biodiversity research purposes, the concept of Life-Watch has emerged. The idea of LifeWatch is to construct e-infrastructure and virtual laboratories by integrating large data sources, computational capacities, and tools for analysis and modelling in an open, serviceoriented architecture. To be ef-ficient and accurate, a continuous inflow of large quantities of data is essential. However, even with new techniques, government-funded monitoring data and research data will not feed the system with up-to-date species information of sufficient scale and resolution. To fill this void, skilled amateur ob-servers (citizen scientists) can contribute to a very valuable extent. After a preparatory phase, a Swed-ish LifeWatch (SLW) consortium was initiated in 2011. Swedish LifeWatch developed an infrastruc-ture where all components are accessible through open web services. At the SLW Analysis portal, dif-ferent formats of species and environmental data can be accessed instantly, and integrated, analysed, visualized and downloaded at selected temporal, spatial or taxonomic scales. Swedish LifeWatch currently provides 46 million species observations from eight different databases, all harmonized ac-cording to standardized formats and the Dyntaxa taxonomic backbone database. Almost 40 million of these observations were provided by citizens through the online reporting system named the Species Observation System (SOS) or Artportalen. This paper describes this system, as well as the in-centives that make it so successful. The citizen sci-ence data in the SOS are accessible, together with data from research and monitoring, in the SLW infrastructure, making the latter a powerful instru-ment for large-scale data extraction, visualization and analysis.
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Hanssen, F. (ed), Heggberget, T. (ed), Bladt, J., Endre-sen, D., Forsius, M., Gudmundsson, G., Gärdenfors, U., Heiðmarsson, S., Kindvall, O, Koch, W., Koviula, K., Laiho, E.L., Laine, K., Obst, M., Skov, F., Telenius, A., Valland, N., Wasowicz, P. and Wremp, A.M. 2014. Nordic LifeWatch Cooperation. Final report. 68 pp (to be printed in 2015).
The main goal of the report is to outline the pos-sibilities for an enhanced cooperation between the Nordic countries within eScience and biodiversity. LifeWatch is one of several ESFRI projects which aim to establish eInfrastructures and databases in the field of biodiversity and ecosystem research. Similarities between Nordic countries are exten-sive in relation to a number of biodiversity related issues. Most species in Nordic countries are com-mon, and frequently the same challenges concern-ing biodiversity and ecosystem services are ad-dressed.
The report has been developed by establishing a Nordic LifeWatch network with delegates from each of the Nordic countries. It has been written jointly by the delegates, and the work was organ-ized by establishing working groups with the fol-lowing themes: strategic issues, technical develop-ment, legal framework and communication. The following main issues are discussed: - Scientific needs for improved access to biodiver-
sity data and advanced eScience research infra-structure in the Nordic countries.
- Future challenges and priorities facing the inter-national biodiversity research community.
- Scientific potential of openly accessible biodi-versity and environmental data for individual re-searchers and institutions.
- Spin-off effects of open access for the general public.
- Internationally standardized Nordic metadata in-ventory.
- Legal framework and challenges associated with environmental-, climate-, and biodiversity data sharing, communication, training and scientific needs.
- Finally, some strategic steps towards realizing a Nordic LifeWatch construction and operational phase are discussed.
Easy access to open data on biodiversity and the environment is crucial for many researchers and re-search institutions, as well as environmental admin-istration. Easy access to data from different fields
of science creates an environment for new scien-tific ideas to emerge. This potential of generating new, interdisciplinary approaches to pre-existing problems is one of the key features of open-access data platforms that unify diverse data sources. In-terdisciplinary elements, access to data over larger gradients, compatible eSystems and eTools to han-dle large amounts of data are extremely important and, if further developed, represent significant steps towards analysis of biological effects of climate change, human impact and development of opera-tional ecosystem service assessment techniques.
Several steps concerning organizing and fund-ing of a future Nordic LifeWatch are discussed, and an action plan towards 2020 is suggested. One main conclusion is to arrange a Nordic LifeWatch conference as soon as possible. This conference should involve Nordic research councils, scientists and relevant stakeholders. The national delegates from the participating countries in the Nordic LifeWatch project are prepared to present details from the report and developments so far as a basis for further development of Nordic LifeWatch. The work is financed by NordForsk and in-kind contributions from participating institutions.
Holl S, Garijo D, Belhajjam K, Zimmermann O, Giovanni RD, Obst M, Goble C (2013). On specifying and sharing scientific workflow optimization results using research objects. WORKS13. DOI 10.1145/2534248.2534251.
Reusing and repurposing scientific workflows for novel scientific experiments is nowadays facilitated by workflow repositories. Such repositories allow scientists to find existing workflows and re-exe-cute them. However, workflow input parameters often need to be adjusted to the research problem at hand. Adapting these parameters may become a daunting task due to the infinite combinations of their values in a wide range of applications. Thus, a scientist may preferably use an automated opti-mization mechanism to adjust the work- flow set-up and improve the result. Currently, automated optimizations must be started from scratch as op-timization meta-data are not stored together with workflow provenance data. This important meta-data is lost and can neither be reused nor assessed by other researchers. In this paper we present a novel approach to capture optimization meta-data by extending the Research Object model and re-
30
using the W3C standards. We validate our proposal through a real- world use case taken from the bio-divertsity domain, and discuss the exploitation of our solution in the context of existing e-Science infrastructures.
Laugen AT, Hollander J, Obst M, Strand A (in press) The Pacific Oyster (Crassostrea gigas) invasion in Scandina-vian coastal waters in a changing climate: impact on local ecosystem services. In Biological Invasions in Aqua-tic and Terrestrial Systems: Biogeography, Ecolo-gical Impacts, Predictions, and Management. De Gruyter, Warsaw.
Shellfish has always played an important role as subsistence and source of income for coastal com-munities. Shallow-water bivalve beds are easily accessible and have been exploited and overex-ploited for centuries. Depletion of stocks have lead to farming and aquaculture of many species. Few species, if any, have been as popular and success-ful as the the Pacific oyster (C. gigas). Its highly efficient filter feeding, high growth rates, massive repoductive output, and tolerance to a large range of abiotic conditions, has not only made it one of the world’s 20 most cultured species, but also one of the most invasive. This chapter tracks the Pacific oyster on its way towards the North-Eastern cor-ner of its European distribution, predicts its future distribution, and discusses the implications for local ecosystems.
Leidenberger S, Obst M, Kulawik R, Stelzer K, Heyer K, Hardisty A, Bourlat SJ (under review) Evaluating the po-tential of ecological niche modelling as a component in invasive species risk assessments. Marine Pollution Bulletin.
Marine biological invasions have dramatically in-creased with the development of global trading, causing the homogenization of communities and the decline of biodiversity. A main vector is ballast water exchange from shipping.
This study evaluates the use of ecological niche modelling to predict the spread of 18 invasive species along a shipping route and their potential habitat suitability (hot/cold spots) in the Baltic Sea and Northeast Atlantic, using >22, 000 occurrence records and workflow based tools.
Results show that, contrary to current risk as-sessment methods, temperature and sea ice con-centration determine habitat suitability for 61%
of species, rather than salinity (11%). We show high habitat suitability for invasive species in the Skagerrak and Kattegat, a transitional area for in-vasive species entering or leaving the Baltic Sea. The e-science approach developed here offers user-friendly tools for integration of biodiver-sity data providing valuable up-to-date predictive modelling for invasive species and ballast water management.
Mathew C, Guentsch A, Obst M, Vicario S, Haines R, Wil-liams AR, de Jong Y, Goble C (2014). A semi-automated workflow for biodiversity data retrieval, cleaning, and qua-lity control Biodiversity Data Journal 2: e4221. DOI: 10.3897/BDJ.2.e4221.
The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid under-standing of data formats and service APIs provided by biodiversity informatics infrastructures. We de-signed and implemented a Taverna-based Data Re-finement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infra-structures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.
Ruete, A. (under review). Simple algorithms to display ig-norance maps for raw distributional data accessed from species observation databases: SLW implementation. Methods in Ecology and Evolution.
Open-access biodiversity databases have limita-tions which include: sampling bias in favour of recorder distribution, lack of survey effort assess-ment, and lack of coverage of the distribution of all organisms. Any technical assessment or scientific research should thus include an evaluation of the uncertainty of its results. Therefore, open-access databases are ethically obliged to inform about the data quality, as researchers are obliged to acknowl-edge this information in their analysis.
I present simple algorithms to display ignorance maps as a tool to report the relative spatial distribu-
31
tion of sampling effort (or lack of it). Ignorance scores are expressed solely based on raw data in order to rely on the fewest assumptions possible. The rationale is based on the assumption that it is appropriate to use species’ groups as a surrogate for sampling effort because it is likely that an entire group of species observed by similar methods will share similar bias. Simple algorithms are then used to transform raw data into ignorance scores scaled 0-1 that are easily comparable and scalable. Sim-plicity is crucial for web-based calculations over big datasets.
Potential users of the ignorance maps are: 1) consultants performing environmental impact as-sessments; 2) observers planning future observa-tion campaigns; and 3) researchers that want to acknowledge the bias present in the data.
Any infrastructure for biodiversity information could use these algorithms to offer a quality report of the observations stored in different databases. The potential of this tool lies in the simplicity of its algorithms and the lack of assumptions made about the bias distribution, giving the user the freedom to tailor analysis to their specific needs.
Snäll, T., Forslund, P., Jeppsson, T., Lindhe, A., O’Hara, R.B. (2014). Evaluating temporal variation in Citizen Sci-ence Data against temporal variation in the environment. Ecography 37: 293-300.
Citizen Science Data (CSD) is increasingly con-tributing to the assessment of biodiversity and ecosystems. However, there is a need to evaluate the usefulness of CSD for different purposes. Ide-ally, CSD from populations should be evaluated against independent population data collected us-ing a proper sampling design, but such data are lacking for almost all species. We propose an ap-proach for evaluating CSD against environmental data. First, an evaluation model is formulated based on knowledge of how environmental variables af-fect population dynamics. Second, the hypotheses of the evaluation model are tested statistically. Sup-port for the evaluation model is interpreted as sup-port for the CSD. We applied the approach to six longhorn beetle species using Swedish data from 1930–2000. The evaluation model assumed that early summer temperature affects larval develop-ment time. We found support for the evaluation model in two species, and some evidence in its fa-
vour in one species. This suggests that the CSD from these species reflect true inter-annual varia-tion. We also found statistical evidence for popula-tion trends in three to four species. In two of these, the evaluation model was supported thus provid-ing particular support for the trend estimates. Lack of support for the evaluation model may be due to biological inaccuracy, the general characteristics of CSD, or low resolution of the environmental evaluation data. We also discuss alternative envi-ronmental data for evaluating CSD.
Strand M, Panova M (2015). Size of genera – biology or taxonomy? Zoologica Scripta, 44:106-116.
The topic is the highly skewed size distribution of genera in parallel with the current willingness and rapid development of analytical tools for us-ing taxonomic ranks as measures for biodiver-sity (e.g. taxonomic sufficiency). Firstly, we test whether the hollow curve distribution of the size of genera still holds in the era of molecular sys-tematics (since most of the earlier examples were obtained long before 2000s). We use eight differ-ent taxonomic groups, including a total of 5869 genera/32173 species, and a complete national subsample of 14336 genera/57095 species from Sweden (Dyntaxa). Secondly, we summarize the existing attempts to explain the biological nature of this phenomenon and the concerns of the bias in genus sizes introduced by the taxonomic prac-tice. We arrive at the conclusion that we are still surprisingly far from a consensus view on to what extent the genus size is biological reality and to what extent – a manmade product. We also touch upon the possible implications of our uncertainty about the nature of monotypic genera in a broad context when estimating biodiversity.
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Statistics 2014 for UserService of the SLW Analysis portal.
The total number of users has increased over the years. In 2014 the number of re-cords (users, roles and authorities) was nearly 7,000 (see picture below). The Swed-ish LifeWatch infrastructure has different entry points. The Analysis Portal is only one of those and has had 2,025 user and 52,050 web page views (PV) during 2014. Compared to the last year, the PV increased with 7,77% and the user number with 10,33%. Another entry is Dyntaxa, with 27,678 users and a PV of 58,846 during 2014. The increase was lower for Dyntaxa (increase PV:0,37% and user: 1,66%).The majority of the users came from Sweden (Analysis Portal: 84,50% and Dyntaxa: 80,45%) and is going back to the chosen web page (Analysis Portal: 59,70% and Dyntaxa: 55,60%).
Key numbers
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Service Data types Status Number of records
User Service Users, Roles and Authorities Delivered 2011 6 800 users in total (26% increase)800 users with extended authorisation
Taxon Service Taxa, Taxon names, Taxon hierarchies
Delivered 2012 92 000 taxa (2% in-crease)
Taxon Attribute Service Taxon specific attributes, traits, habitat preferences legislation, Redlist informa-tion
Delivered 2014 2.3 million taxon specific attribute values on >85 000 taxa.
Swedish Species Observation Service /Analysis Service
Species Observations Delivered 2011 47.6 million observations* (25% increase)
SLW Geoserver (OGC: WMS, WFS): Swedish Species Observa-tions DwC 1.5
Species observations Delivered 2012 43.3 million observations*
SHARK Swedish Ocean Archive Marine Species Observa-tions
Delivered 2014 68 000 observations
DINA Species Observation Service Species observations Delivered 2013 20 000 observations
Information system aquatic microal-gae www.nordicmicroalgae.org
Taxon hierarchies images, videos, information on size, biovolume, toxicity etc.
Version 1.0 delive-red 2011
Species: 4486Taxa: 6600Images: 855
The Database for electrofishing in streams (SERS)
Species observations Delivered 2013 248 000 observations
The National Register of Survey test-fishing (NORS)
Species observations Delivered 2013 1.83 million observations
MVM Species Observation Service Species observations Delivered 2013 476 000 observations
CAnMove Observation Service Species observations Uncertain
WRAM Species Observation Service
Species observations Delivered 2013 20 000 records
Swedish GBIF Occurrence Service Species Observations Existing 46,6 milj observations*
*) These observations are to a large extent the same, but made available through different services
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Coordination and contactSwedish LifeWatch is led and coordinated by:ArtDatabanken SLU (the Swedish Species Infor-mation Centre at the Swedish University of Ag-ricultural Sciences), Box 7007, 750 07 Uppsala, Sweden, tel 018-67 10 00 Managing Director: Ulf Gärdenfors, ArtDatabank-en, +46 18-67 26 23, [email protected] secretary and communicator: Anna Maria Wremp (on parental leave 2015)
Organisationwww.svenskalifewatch.sewww.swedishlifewatch.se
Organisational chart for Swedish LifeWatch
Communicator: Johan Samuelson, ArtDatabanken, +46 18-67 34 09, [email protected] secretary and support: Sonja Leidenberger, ArtDatabanken, +46 18-67 13 94, [email protected] support: Oskar Kindvall, ArtDatabanken, +46 18-67 22 61, [email protected].
Consortium Contract
Organisational chart for Swedish LifeWatch
Swedish Species Information Centre, SLU (Swedish University of Agricultural Sciences)
SMHI
GBIF
Coordination group Director/Secreteriat
Steering committee
Swedish Research Council (SRC)
SLU Vice-Chancellor
Scientific Advisory Group
Swedish Museum of Natural History
CanMove, Department of Biology, Lund University
Deparment of Zoology, University of Gothenburg
Department of Ecology and Environmental Science, Umeå University
Contract SRC-SLU
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SLW BoardThe mandate of the Board was extended by the SLU vice chancellor until 2014-12-31, awaiting a new organisation. The Committee had four regu-lar meetings in 2014. In addition, the board agreed per capsulam on one occasion (on additional de-tails of the budget for 2015). The board members are:Ulla Mörtberg, Royal Institute of Technology
(KTH), chairAnna-Lena Axelsson, SLU Stefan Claesson, Swedish Museum of Natural His-
toryHenrik Svedäng, SLULars Westerberg, Linköping UniversityHannah Östergård, Swedish Environmental Protec-
tion Agency
The managing director, the project secretary and the chair of the Coordination group have also par-ticipated in the SLW Board meetings.
Coordination GroupThe Coordination Group consists of 1-3 repre-sentatives from each consortium part. The group had two regular meetings in 2014: 22 May (Stock-holm) and 13 October (Göteborg). In addition, an extra meeting was held in Uppsala 12 February to plan for the meant 2014 application to SRC (which was postponed to 2015).The Coordination Group had the following repre-
sentatives during 2014:
University of Gothenburg: Matthias Obst (chair)Lund University: Susanne Åkesson, Mats SvenssonSMHI: Bengt Karlson, Lars Johan Hansson, Patrik
Strömberg, Arnold AndreassonArtDatabanken: Ulf Gärdenfors, Oskar Kindvall,
Anna Maria WrempUmeå University: Göran Englund
Swedish Museum of Natural History and GBIF: Fredrik Ronquist, Anders Telenius, Karin Karls-son
SLU Aquatic Resources: Kerstin Holmgren och Anders Kinnerbäck
WRAM: Holger Dettki Stockholm University1: Peter Hambäck
Scientific Advisory GroupThe scientific advisory group last met in Uppsala on October 25, 2013. No physical meeting was conducted in 2014, but the group receives updates from the project on a regular basis. The committee consists of:Walter BerendsohnDepartment of Biodiversity Informatics and Labo-ratories, Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, GermanyLena GustafssonUniversity of Agricultural Sciences, Department of Ecology, UppsalaAnna GårdmarkInstitute of Coastal Research, Department of Aquatic Resources, Swedish University of Agri-cultural SciencesNiclas JonzénDepartment of Biology, Theoretical Population Ecology and Evolution Group, Lund UniversityJannicke MoeNorwegian Institute for Water Research (NIVA), NorwayCynthia ParrEncyclopedia of Life, National Museum of Natural History, Washington D.C.Hannu SaarenmaaDigitarium – Digitisation Centre of the Finnish Museum of Natural History and the University of Eastern Finland
1 Stockholm University has accepted to be a future con-sortium partner and was therefore invited to join the group already in 2014.
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Financial reportTable 1. Summary of the financial report for all consoritum partners. All figures SEK.
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 8 766 623 10 536 571 10 577 864 6 641 215
Allocated funds 9 000 000 9 000 000 9 000 000 4 524 085 4 475 915 36 000 000
Co-financing 2 550 000 2 420 263 2 818 119 3 399 793 1 945 921 13 134 096
Other revenue 28 652 5 348 0 297 776 -242 454* 89 322
Total revenues 11 578 652 11 425 611 11 818 119 8 221 654 6 179 382 49 223 418
Staff costs 1 645 296 4 919 800 5 877 726 5 890 842 3 875 080 22 208 744
Consultant costs 0 1 297 888 1 995 773 2 813 178 1 763 007 7 869 846
Other costs 279 153 401 545 304 430 393 656 823 604 2 202 388
Depriciation 0 140 993 241 702 241 702 117 482 741 879
Premises 110 859 273 185 332 541 304 622 148 104 1 169 311
Overhead costs 776 721 2 622 252 3 024 654 2 514 303 1 467 970 10 405 900
Total costs 2 812 029 9 655 663 11 776 826 12 158 303 8 195 247 44 598 068
Result 8 766 623 10 536 571 10 577 864 6 641 215 4 625 350 4 625 350
Total Table 8. Total financial report. All figures SEK. *Including adjustment 2013.
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List of abbreviationsADb ArtDatabankenALTER-net Long-Term Biodiversity, Ecosystem and Awareness Research NetworkAPI Application programming interfaceBioMaS Bioinformatic analysis of Metagenomic ampliconSBioVeL Biodiversity Virtual e-LaboratoryBITS Baltic International Trawl SurveyBOLD Barcode of Life Datasystems CAnMove Centre for Animal Movement ResearchDINA Digital information system for natural history collectionsECDC Environment Climate Data SwedenEMBOS Development and Implementation of a pan-European Marine Biodiversity Observatory SystemEMBRC European Marine Biological Resource CentreERIC European Research Infrastructure ConsortiumEU BON European Biodiversity Observation NetworkFOMA Fortlöpande miljöanalys vid SLU (environmental monitoring and assessment at SLU)GBIF Global Biodiversity Information FacilityGEO BON Group on Earth Observations Biodiversity Observation NetworkGEOSS Global Earth Observation System of SystemsGU Göteborgs universitet (University of Gothenburg)HELCOM Helsinki Commission (Baltic Marine Environment Protection Commission)IBTS International Bottom Trawl SurveyICT Information and communications technologyITIS Integrated Taxonomic Information SystemKUL Kustfiskedatabasen (Database for Coastal Fish)LTER Long-Term Ecosystem ResearchLU Lund UniversityLW LifeWatchNIVA Norsk Institutt for VannforskningNODC National Oceanographic Data CentreNORS Database with data from netfishing in lakesNBIC Norwegian Biodiversity Information CentreNRM Naturhistoriska riksmuseet (Swedish Museum of Natural History)OBIS Ocean Biogeographic information SystemOGC Open Geospatial Consortium PIKE A database covering the distribution of freshwater fish in FennoscandiaRFI Rådet för forskningens infrastrukturer (Council for Research Infrastructures)SITES Swedish Infrastructure for Ecosystem ServiceSLW Swedish LifeWatch (Svenska LifeWatch)SLU Sveriges lantbruksuniversitet (Swedish University of Agricultural Sciences)SLU Aqua SLU Department of Aquatic ResourcesSMHI Sveriges meteorologiska och hydrologiska institut SMTP Swedish Malaise Trap ProjectSRC Swedish Research Council (Vetenskapsrådet)SERS Swedish Electrofishing Register TDWG Biodiversity Information Standards (formerly the Taxonomic Databases Working Group)UmU Umeå University UGOT University of GothenburgVR Vetenskapsrådet (Swedish Research Council)VRE Virtual Research EnvironmentWFS Web Feature Service Interface Standard WMS Web Map Service WRAM Wireless Remote Animal Monitoring
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39
Appendix 1
ICT-deliverablesDeliverable Details Status Responsible
Web sites / databases
Information system for aqua-tic micro algae
Nordic Microalgae http://nordicmicroalgae.org Operational since 30 June 2011, updated several times
Bengt Karlson (SMHI)
Further development of http://nordicmicroalgae.org
Multi language support on starting page Operational 24 April 2014 Bengt Karlson (SMHI)
Development of analysis tools for plankton data: Plankton Toolbox
Counting module, additional statistical tests, etc. Plankton toolbox 1.01 available 25 Nov. 2014. Some planned new fun-ctionality is still in development.
Bengt Karlson (SMHI)
CAnMove Database General Features Working, 50% done Mats Svens-son
CAnMove Database Tracking Radar Module Working, 80% done Mats Svens-son
CAnMove Database Generic Module Working, 90% done Mats Svens-son
CAnMove Database Nano Lab Module Working, 10% done Mats Svens-son
http://marinevre.lifewatch.be/
European Marine LifeWatch Portal draft version Matthias Obst, UGOT and Bengt Karls-son (SMHI)
http://www.svenskalife-watch.se/en/tools/
Implementation of BioVel workflows to the SLW infrastructure
available beginning of 2014 Matthias Obst, UGOT, Oskar Kindvall (Art-Databanken)
DNA-key: www.dnakey.se A public DNA barcode service Released in January 2014 NRM / DINA team
Naturfynd: http://naturfynd.se
Inventory client New features in December 2014 NRM / DINA team
http://alejandroruete.github.io/IgnoranceMaps/
Ignorance maps tool up to now not implemented, but on-going to do so
Alejandro Ruete (ArtDa-tabanken)
Web application for ArtData-banken SOA Administration
Implementing functionality to handle Harvest Service
Oskar Kindvall (ArtDataban-ken)
Analysis portal Adding a mulit check button on the Data provi-der page
O. Kindvall
Analysis portal Adding unique identifiers for gridcells in all export files handling grid data
O. Kindvall
Analysis portal Including new functions for export of grind data showing all species specific results
O. Kindvall
Analysis portal A new and more simple background map respe-senting Sweden among default layers
O. Kindvall
Analysis portal Adding possiblity for users to define species observation search from an uploades GeoJSON file
O. Kindvall
Appendix 1 – Deliverables and activities 2014
40
Analysis portal Improving grind presentation in maps when using white background
O. Kindvall
Analysis portal Adding csv format for all download functions O. Kindvall
Analysis portal Performing user tests with unexperiences users O. Kindvall
Analysis portal Implementing setting fuctionality for changing current coordinae system for map views and exports
O. Kindvall
Analysis portal Adding functionality for species richness heat map as downloadable png files
O. Kindvall
Analysis portal Adding download function for species observa-tion counts per listed taxon
O. Kindvall
Analysis portal Adding format setting page spedifically for csv fiels
O. Kindvall
Analysis portal Improvements on the filter setting mechanism related to enviornemtal data based on user test performed in 2013
O. Kindvall
Analysis portal New download function for Polygon specific occruences for all listed taxa
O. Kindvall
Analysis portal Adding new filter mechanisms for species observation search based on field content inclu-ding fre text search
O. Kindvall
Analysis portal Adding harvest meachanism for sea depth infor-mation from the species observation system
O. Kindvall
Analysis portal Adding coordinate accurance filter O. Kindvall
Data flow management and bug fixes
O. Kindvall
Tools and services
SHARKdata machine-mach-ine interface for distribution of marine biological data and marine climate data
http://sharkdata.se In test operation since mid 2014. The system is fully functional but not yet filled with a large amount of data
Bengt Karlson (SMHI)
Lightship marine climate data: Historical data from lightships
Data available in SLW Data has been quality controlled. System for making the data available through http://sharkweb.smhi.se is up and running in test mode.
Bengt Karlson (SMHI)
Plankton Toolbox SMHI
biodiversity services all services accessible through https://www.analysisportal.se/Data/MetadataSearch
operational Matthias Obst, UGOT
workflows all workflows accessible http://www.svenskalife-watch.se/en/tools/ or http://portal.biovel.eu/
operational Matthias Obst, UGOT
Media server code on Git-hub for external testing
Available in November 2014 NRM / DINA team
GeoServer improved function and bug fix for Wfs tool Oskar Kindvall (ArtDataban-ken)
Migration of SLW GeoSer-ver and PostGIS
to a more powerful server environment O. Kindvall
SLW geo tool Running in the new improved environment O. Kindvall
Species Observation Reharvesting them from various data providers after bug fixes at the provider side
O. Kindvall
WRAM Web Service Data transfer from CAnMove to WRAM Ready for testing Mats Svens-son
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Appendix 1Documentation
Documentation of SHARK-data
http://sharkdata.se Bengt Karlson (SMHI)
Manual for Plankton Toolbox Description of functionality and how to use Plankton Toolbox
First version available at http://nordic-microalgae.org/tools
Bengt Karlson (SMHI)
Aquamaps extension to nonmarine organisms
Development and documentation Paper to be submitted in 2015 NRM / Bio-Fresh
Documentation of the SLW GeoServer
Oskar Kindvall (ArtDataban-ken)
Documentation of all code Oskar Kindvall (ArtDataban-ken)
Case studies
Regional diversity of fish in Sweden
Planned K Holmgren and A Kinner-bäck, SLU
Kattegat cod case study
Case study on effects of environmental factors on the growth of cod in Kattegat -
A multidisciplinary description of long term trends in the Kattegat region
Work in progress SMHI and SLU
Ecological niche modelling as a component in marine invasive species risk as-sessments
see publications In review Sonja Leiden-berger and Matthias Obst, UGOT
Case study on leaf frogs see publications In press Lena Nilsson and Matthias Obst, UGOT
External support request on world soil data access
see report closed Matthias Obst, UGOT
External support request on mosquito borne diseases
see report closed Matthias Obst, UGOT
External support request on natural protect areas
see report open Matthias Obst, UGOT
Other
Plankton Toolbox Workshop Demonstration and training of how to use Plankton Toolbox using marine monitoring data on phyto- and zooplankton
Workshop arranged 19-20 May with ~15 participants
Bengt Karlson, SMHI
AlgaeBase Collaboration regarding aquatic microalgae taxonomy etc.
Updating of Nordic Microalgae Com-mittee check list and http://nordicmi-croalgae.org in progress
Bengt Karlson, SMHI
Intergovernmental Oceano-graphic Commission (IOC)
Collaboration regarding IOC-UNESCO Taxono-mic Reference List of Harmful Micro Algae
Updated species lists of harmful algae http://nordicmicroalgae.org
Bengt Karlson, SMHI
Intergovernmental Council for the Exploration of the Sea (ICES) and HELCOM
Updating of lists on bio volumes and species of phytoplankton
Updated information in nordicmicro-algae.org
Bengt Karlson, SMHI
Supervision Linn Nilsson open Matthias Obst, UGOT
Test of data flow Ecological niche modelling workflow v.20 inte-grated in SLW
closed Sonja Leiden-berger, UGOT
Writing a newsletter to alla county administrations with information on new tools and functionality in the infrastructure.
to all country administrions with information on new tools and cuntionality in the infrastructure
closed Oskar Kindvall (ArtDataban-ken)
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Implementation of data from the PIKE fish database from Umeå
need to be imported to the Species Observation System weh the required funtionality is ready
on-going Oskar Kindvall (ArtDataban-ken)
Support to Scientist using Analysis portal on-going Oskar Kindvall
Support to external develpers utelizing the web services of the SLW infrastructure
on-going Oskar Kindvall
Underlag till Hack of Swe-den
Oskar Kindvall
MeetingsMeeting Date Details Participants
Steering committee
Steering commitee meeting 2014:1
12 February 2014
ArtDatabanken, Uppsala. Ulla Mörtberg, Anna-Lena Axelsson, Stefan Claesson, Henrik Svedäng, Ulf Gärdenfors, Matthias Obst (online), Anna Maria Wremp
Steering commitee meeting 2014:2
04 June 2014 Naturvårdsverket, Stock-holm.
Ulla Mörtberg, Anna-Lena Axelsson, Stefan Claesson, Hannah Östergård, Lars Westerberg, Ulf Gärdenfors, Anna Maria Wremp
Steering commitee meeting 2014:3
17 October 2014
Naturvårdsverket, Stock-holm.
Anna-Lena Axelsson, Stefan Claesson, Henrik Svedäng, Hannah Östergård, Lars Westerberg, Ulf Gärdenfors, Anna Maria Wremp
Steering commitee meeting 2014:4
10 November 2014
Ulla Mörtberg, Anna-Lena Axelsson, Stefan Claesson, Hannah Östergård, Lars Westerberg, Henrik Svedäng, Anna Maria Wremp
Steering commitee meeting 2014:5
21 November 2014
Naturvårdsverket, Stock-holm.
Ulla Mörtberg, Anna-Lena Axelsson, Stefan Claesson, Henrik Svedäng, Hannah Östergård, Lars Westerberg, Ulf Gärdenfors, Matthias Obst (online), Anna Maria Wremp
Coordination group
Coordination group 13 February ArtDatabanken, Uppsala. Matthias Obst, Fredrik Ronquist, Ulf Gärdenfors, Anna Maria Wremp, Bengt Karlson, Holger Dettki, Anders Kinnerbäck,Peter Hambäck
Coordination group 22 May Naturhistorska riksmuseet, Stockholm.
Matthias Obst, Anders Telenius, Fredrik Ronquist, Ulf Gärdenfors, Anna Maria Wremp, Oskar Kindvall, Kerstin Konitzer, Bengt Karlson, Patrik Strömberg,Holger Dettki, Anders Kinnerbäck, Kerstin Holmgren, Peter Hambäck
Coordination group 13 October SMHI, Göteborg. Matthias Obst, Anders Telenius, Fredrik Ronquist, Ulf Gär-denfors, Anna Maria Wremp, Oskar Kindvall, Bengt Karl-son, Patrik Strömberg, Arnold Andreasson, Holger Dettki, Anders Kinnerbäck, Kerstin Holmgren, Peter Hambäck
SeIBER constortium meetin
SeIBER consortium meeting 26 September 2014
Vetenskapsrådet, Stock-holm.
Ulf Gärdenfors, Matthias Obst, Bengt Persson, Fredrik Ronquist, Anders Telenius, Anna Maria Wremp, Mats Andersson, Maria Thuveson
SeIBER consortium meeting 20 October 2014
Webex-möte Holger Dettki, Göran Eriksson, Ulf Gärdenfors, Matthias Obst, Fredrik Ronquist, Anders Telenius, Anna Maria Wremp, Susanne Åkesson
SeIBER consortium meeting 10 November 2014
SciLifeLab, Stockholm. Anna-Lena Axelsson, Holger Dettki, Göran Ericsson, Ulf Gärdenfors, Peter Hambäck, Matthias Obst, Bengt Pers-son, Fredrik Ronquist, Anders Telenius, Anna Maria Wremp
SeIBER consortium meeting 17 December 2014
Naturvårdsverket, Stock-holm.
Anders Andersson, Holger Dettki, Ulf Gärdenfors, Bengt Karlson, Matthias Obst, Fredrik Ronquist, Anders Telenius, Anna Maria Wremp, Hannah Östergård
43
Appendix 1National
CAnMove - WRAM Meeting Umeå
January 2014 planning and interantions with WRAM
Johan Bäckman, Mats Svensson
NILS SLU 24 January 2014
Ulf Gärdenfors, Oskar Kindvall, Anna Maria Wremp, Johan Svensson, Pernilla Christensen
Naturvårdsverket 28 January 2014
Ulf Gärdenfors, Anna Maria Wremp
WRAM 10 February 2014
Umeå Ulf Gärdenfors
SVA 17 February 2014
SITES 13 March Stockholm Ulf Gärdenfors
WRAM Phone Conference 01 March 2014
planning and interantions with WRAM
Johan Bäckman, Mats Svensson
ECDS 12 May Stockholm Ulf Gärdenfors
SITES 21 May Erken laboratory Ulf Gärdenfors
Jordbruksverket 04 April 2014 Oskar Kindvall, Anna Maria Wremp
ECDS 5 May At ArtDatabanken Anna Maria Wremp, Oskar Kindvall, Ulf Gärdenfors
National coordination of infrastructures
26 September 2014
Vetenskapsrådet, Stock-holm
Anna Maria Wremp, Ulf Gärdenfors, Fredrik Ronquist, Anders Telenius, Matthias Obst
ECDS 18 September 2014
Video meeting Ulf Gärdenfors
SITES 7 October Skogaryd Ulf Gärdenfors
SAMSA meeting, Lund 11 November 2014
Karin Karlsson, Per Ericson, Jan-Olov Westerberg
SITES 24 November 2014
Arlanda Ulf Gärdenfors
SITES workshop on bio-diversity and ecosystem research
12 December 2014
Stockholm Ulf Gärdenfors
International
LifeWatch ERIC construc-tion meeting
2 – 5 January 2014
Granada, Spain. Matthias Obst
LW operational meeting, Granada
3-4 January 2014
Ulf Gärdenfors
Nordic OIKOS meeting 3-7 February 2014
Stockholm, Sweden. Anders Telenius, Fredrik Ronquist, Stefan Daume
Nordic Microalgae Commit-tee meeting
13-14 March Lund, Sweden. Bengt Karlson
EUBON General Meeting, Crete
31 Mars-6 April 2014
Karin Karlsson, Fredrik Ronquist, Onésime P'rudhomme
BENELUX conference on invasive species
02 April 2014 Ghent University, Belgium. Sonja Leidenberger
ICES Working Group on Phytoplankton and Microbial Ecology
Spring 2014 Plymouth, United Kingdom. Malin Mohlin
GEO Work Plan Symposium 28 April-30 April 2014
Anders Telenius
ICES-IOC Working Group on Harmful Algal Bloom Dynamics
29 Apr. - 2 May 2014
Haarlem, the Netherlands. Bengt Karlson
HELCOM Phytoplankton Expert Group
12-16 May Helsinki, Finland. Plankton Toolbox was presented.
Marie Johansen, Malin Mohlin
44
LifeWatch Marine Technical Meeting
2-5 June Heraklion, Crete, Greece. Bengt Karlson, Matthias Obst
SPNCH-Cardiff 23-29 June 2014
Karin Karlsson, Kevin Holston
IENE International Confe-rence - Life for a Greener Transport Infrastructure
16-19 Sep-tember
Malmö, Sweden. Anna Maria Wremp
H2020 preparatory (LinkD) 18 September 2014
Natural History Museum in London, UK
Matthias Obst
CETAF, Earth Science Work-shop, Vienna
13 October 2014
Kevin Holston
LifeWatch ’light’ construction meeting
15-17 Oc-tober
Amsterdam, Netherlands Matthias Obst
International Conference on Harmful Algal Blooms
27-31 Oc-tober
Wellington, New Zealand. Poster presentation on Plankton Toolbox
Bengt Karlson
TDWG 2014, Jönköping 27-31 Octo-ber 2014
Markus Skyttner, Ingimar Erlingsson, Ida Li, Karin Karlsson, Kevin Holston, Stefan Daume, Fredrik Ronquist
Global Genome Biodiversity Network-meeting, Vienna
25-26 No-vember 2014
Karin Karlsson, Kevin Holston
Workmeetings
SLW-BioVeL hackathon 7-8 January hackathon, Gothenburg, Sweden.
Matthias Obst, Oskar Kindvall,
Work meeting for the Life-Watch Kattegat case study
Lysekil, Sweden. four participants
Work meeting for the Life-Watch Kattegat case study
Gothenburg, Sweden. six participants
iSPOT 23 April 2014 Meeting with Jonathan Silvertown, in Lund
Ulf Gärdenfors
Trondheim, Artsdatabanken/Artdatabanken
24-25 April 2014
Karin Karlsson, Ingimar Erlingsson
DINA Technical Workshop 16-18 Sep-tember 2014
Markus Skyttner, Ingimar Erlingsson, Ida Li, Karin Karlsson, Kevin Holston, Stefan Daume, Fredrik Ronquist
CAnMove database seminar 01 November 2014
Information on database use
Mats Svensson and CAnMove members
Internal meetings CAnMove several Planning Mats Svensson, Johan Bäckman, Susanne Åkesson
Public meetings
Digitization Symposia 9 January 2014
Stefan Daume, Anders Telenius
Launch of DNA-nyckeln 21 January 2014
Johan Nylander
Information at VR/RFI 12 December 2014
Stockholm Ulf Gärdenfors
Other
WRAM user workshop May 2014 information share to users Johan Bäckman, Mats Svensson, Susanne Åkesson
Video meeting 15 December 2015
Webservice LifeWatch-KUL (coastal fish)
A Kinnerbäck, O Kindvall, G Sandberg (KUL), C Carlsson (SLU-IT)
45
Appendix 1
AdministrationActivity Date Details Responsible
Main strategic documents
Annual Report 2013 Anna Maria Wremp
Avvecklingsplan version 2014-12-01 Anna Maria Wremp
Operational plan 2015 Anna Maria Wremp
Applications
ENVRI+ 02 September 2014
submitted Matthias Obst, UGOT
IPBISCO 02 September 2014
submitted Matthias Obst, UGOT
LinkD 14 December 2014
finalized (submission date 14 Jan 2015)
Matthias Obst, UGOT
Employment and recruiting
New person in charge of marine biological data at SMHI January 2014 Patrik Strömberg has replaced Lars Johan Hansson as the person in charge of the marine biological database at SMHI. Lars Johan now works at the Swedish Agency for Marine and Water Management.
SMHI
Sonja Leidenberger February - April 3 months employment to carry out tests on the SLW system and finalize use cases
Matthias Obst, UGOT
Recruting Project Secretary Oct-Dec 2014 Ulf Gärdenfors, Anna Maria Wremp, Oskar Kindvall
Presentations, publications and educationActivity Date Details Presenter / producer
/ author
Presentations at conferences/meetings
Nordic Digitization Symposium, Stockholm, Sweden 09 January 2014
presentation of showcase Matthias Obst
Ten years of GBIF: Are we collecting the right data? 3 February 2014 Nordic OIKOS meeting Fredrik Ronquist
Citizen Cyberscience Summit 20-22 Feb 2014
London. Presentation of Artpor-talen and SLW
Anna Maria Wremp
CAnMove Database presentation 28 February 2014
Status and plans for the data-base
Mats Svensson
ECDS 5 May 2014 Meeting with ECDS at ArtData-banken
Anna Maria Wremp, Oskar Kindvall, Ulf Gär-denfors
HELCOM Phytoplankton Expert Group workshop 12-16 May 2014
Helsinki, Finland, Plankton Tool-box was presented
Malin Mohlin
BENELUX conference in Ghent, Belgium 02 April 2014 presentation of showcase Sonja Leidenberger
46
The DINA system 02 April 2014 EUBON General Meeting, Crete Karin Karlsson, Fredrik Ronquist
CeMEB 11th Assembly (Centre for Marine Evolutio-nary Biology), Strömstad, Sweden
9-11 April 2014 presentation of showcase Sonja Leidenberger
Citizen Science Workshop 24 April 2014 International workshop, Lund Ulf Gärdenfors
Developing and Testing Tools and Processes for Creating a Swedish Digital Natural History Collection, e-BioColl.se
26 June 2014 SPNCH-Cardiff Karin Karlsson
Architectural road map 16 September 2014
DINA Technical Workshop Stefan Daume
Vision on "Module of Modules" 17 September 2014
DINA Technical Workshop Markus Skyttner
Demo Media Server 17 September 2014
DINA Technical Workshop Ingimar Erlingsson
Creating DINA-modules - how can we do this? 17 September 2014
DINA Technical Workshop Markus Skyttner
Digitization in DINA Geoscience Collections 13 October 2014
CETAF, Earth Science Work-shop, Vienna
Kevin Holston
TDWG 27-30 Oct 2014
Several presentations from SLW. International conference, Jönköping
Oskar Kindvall, Ulf Gärdenfors, Anna Maria Wremp, Anders Tel-lenius, Fredrik Ronquist, Mattias Obst - fler?
Distributed open-source development in the DINA consortium
28 October 2014
TDWG 2014, Jönköping Fredrik Ronquist
The DINA Web API 28 October 2014
TDWG 2014, Jönköping Markus Skyttner
Demonstration of a DINA compliant MediaServer 28 October 2014
TDWG 2014, Jönköping Ingimar Erlingsson
TDWG conference, Lidköping, Sweden, 27-30 October 2014
2 presentations Matthias Obst
DINA overview 11 November 2014
SAMSA meeting, Lund Karin Karlsson
CAnMove Database demo 20 November 2014
Demo of the generic database module
Mats Svensson
European Topic Centre on Biodiversity 28 Nov One day meeting discussing content and experiences from SLW
Anna Maria Wremp, Mora Aronsson
Lectures/Education and training
Demonstration of Analysis Portal 19 March Sjöfartsmuseet, Göteborg. Ar-ranged by Lst Västra Götaland
Malin Strand
Presentation for Rotary Uppsala June 5 About Artportalen and SLW Anna Maria Wremp
Poster presentations
Poster presentations
OIKOS conference, Stockholm 3-4 Feb Roll-ups and exhibition
Flora- och faunavårdskonferensen, Uppsala 29 April Poster
IENE international conference, Malmö 16-19 Sep Roll-ups and exhibition
SLU Faculty Day, Uppsala 24 Sep Poster
Miljöövervakningsdagarna, Visby 10-11 Oct Poster
47
Appendix 1The DINA Consortium 27-31 Oct TDWG 2014, Jönköping Markus Skyttner, Kevin
Holston, Ida Li, Ingimar Erlingsson, Stefan Daume, Karin Karlsson, Fredrik Ronquist
International Conference on Harmful Algal Blooms 27-31 October ”Poster presentation: Plankton Toolbox – open source software making it easier to work with planktondata”
Bengt Karlson, SMHI
Graphic productions
Advert in Forskning & Framsteg #2 2014 Advertisment for the Analysis Portal
Roll-up Analysis Portal January
Roll-up SLW January
4 pages A4 information folder April + Oct
Publications
Information on www.smhi.se 13 November Article on: Plankton Toolbox – a new tool for working with plank-ton data
SMHI
Leidenberger S, Obst M, Kulawik R, Stelzer K, Heyer K, Hardisty A, Bourlat SJ (In Review) Evaluating the potential of ecological niche modelling as a component in invasive species risk assessments. Marine Pollution Bulletin.
Laugen AT, Hollander J, Obst M, Strand A (In Press) The Pacific Oyster (Crassostrea gigas) invasion in Scandinavian coastal waters in a chan-ging climate: impact on local ecosystem services. In Biological Invasions in Aquatic and Terrestrial Systems: Biogeography, Ecological Impacts, Predictions, and Management. De Gruyter, Warsaw.
Mathew C, Guentsch A, Obst M, Vicario S, Haines R, Williams AR, de Jong Y, Goble C (2014) A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control Biodiversity Data Journal 2: e4221. DOI: 10.3897/BDJ.2.e4221.
Gärdenfors U, Jönsson M, Obst M, Wremp AM, Kindvall O, Nilsson J (2014) Swedish LifeWatch ─ a biodiversity infrastructure integrating and reusing data from citizen science, monitoring and research. Human Computation 1(2): 147-161.
González-Talaván A, Mathew C, Obst M, Paymal E (2014). Data Refinement Using the BioVeL Portal. 67 pp. Copenhagen: Global Biodiversity Information Facility. Available online at http://www.gbif.org/orc/?doc_id=5983.
Davies N, Field D, Amaral-Zettler L, Clark M, Deck J, Drummond A, Faith D, Geller J, Gilbert J, Gloeckner FO, Hirsch P, Leong JA, Meyer C, Obst M, et al. (2014) The Founding Charter of the Genomic Observatories Network. Giga Science 3: 2.
Holl S, Garijo D, Belhajjam K, Zimmermann O, Giovanni RD, Obst M, Goble C (2013) On specifying and sharing scientific workflow optimization results using research objects. WORKS13. DOI 10.1145/2534248.2534251.
Written and reported about SLW (not including own website and publications)
Journal / webpage Header Link Date
www.slu.se SLU är med och ordnar täv-lingen Hack for Sweden
http://www.slu.se/sv/om-slu/fristaende-sidor/ak-tuellt/alla-nyheter/2014/2/slu-ar-med-och-ordnar-tavlingen-hack-for-sweden/
2014-02-12
Ann-Ka-trin Hallin
48 49
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 8 616 743 9 510 229 9 051 020 5 341 787
Allocated funds 8 583 600 6 696 400 6 820 000 2 970 000 3 238 636 28 308 636
Co-financing 2 550 000 1 650 000 2 150 000 2 480 000 940 000 9 770 000
Other revenue 28 652 5 348 31 237 89 322
Total revenues 11 162 252 8 351 748 8 970 000 5 474 085 4 209 873 33 958 085
Staff costs 1 583 698 4 137 714 4 838 133 4 169 925 2 294 217 17 023 687
Consultant costs 653 808 1 618 033 2 321 022 1 386 551 5 979 414
Other costs 105 030 320 536 194 856 243 324 638 192 1 501 938
Depriciation 140 993 241 702 241 702 117 482 741 879
Premises 110 859 242 248 306 107 264 160 103 928 1 027 302
Overhead costs 745 922 1 962 963 2 230 378 1 943 185 1 092 047 7 974 495
Total costs 2 545 509 7 458 262 9 429 209 9 183 318 5 632 417 34 248 715
Result 8 616 743 9 510 229 9 051 020 5 341 787 3 919 243 3 919 243
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 149 880 -18 187 -297 775 0
Allocated funds 416 400 718 600 820 000 755 000 1 061 364 3 771 364
Co-financing 485 263 290 000 935 756 370 598 2 081 617
Other revenue 0
Total revenues 416 400 1 203 863 1 110 000 1 690 756 1 431 962 5 852 981
Staff costs 61 598 484 005 630 571 618 082 542 762 2 337 018
Consultant costs 619 380 394 207 432 315 376 456 1 822 358
Other costs 174 123 26 543 49 525 33 543 63 525 347 259
Depriciation 0
Premises 0
Overhead costs 30 799 242 002 315 285 309 041 271 381 1 168 508
Total costs 266 520 1 371 930 1 389 588 1 392 981 1 254 124 5 675 143
Result 149 880 -18 187 -297 775 0 177 838 177 838
ArtDatabanken
SMHI
Table 1. Financial report for ArtDatabanken’s commitments within Swedish LifeWatch. All figures SEK.
Table 2. Financial report for SMHI’s commitments within Swedish LifeWatch. All figures SEK.
Appendix 2 – Detailed financial report
Bilaga 2 – Detaljerad ekonomisk redovisning
49
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 8 616 743 9 510 229 9 051 020 5 341 787
Allocated funds 8 583 600 6 696 400 6 820 000 2 970 000 3 238 636 28 308 636
Co-financing 2 550 000 1 650 000 2 150 000 2 480 000 940 000 9 770 000
Other revenue 28 652 5 348 31 237 89 322
Total revenues 11 162 252 8 351 748 8 970 000 5 474 085 4 209 873 33 958 085
Staff costs 1 583 698 4 137 714 4 838 133 4 169 925 2 294 217 17 023 687
Consultant costs 653 808 1 618 033 2 321 022 1 386 551 5 979 414
Other costs 105 030 320 536 194 856 243 324 638 192 1 501 938
Depriciation 140 993 241 702 241 702 117 482 741 879
Premises 110 859 242 248 306 107 264 160 103 928 1 027 302
Overhead costs 745 922 1 962 963 2 230 378 1 943 185 1 092 047 7 974 495
Total costs 2 545 509 7 458 262 9 429 209 9 183 318 5 632 417 34 248 715
Result 8 616 743 9 510 229 9 051 020 5 341 787 3 919 243 3 919 243
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 0 241 692 199 236 165 786
Allocated funds 280 000 255 000 245 000 200 000 980 000
Co-financing 85 000 85 000 170 000 340 000
Other revenue 0
Total revenues 0 280 000 340 000 330 000 370 000 1 320 000
Staff costs 17 347 280 702 146 513 404 421 848 983
Consultant costs 0 0
Other costs 8 754 25 023 37 207 34 010 104 994
Depriciation 0 0
Premises 6 529 18 434 25 520 31 667 82 150
Overhead costs 5 678 58 297 69 210 66 619 199 804
Total costs 0 38 308 382 456 278 450 451 717 1 235 931
Result 0 241 692 199 236 250 786 84 069 84 069
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 0 620 452 1 374 694 853 454
Allocated funds 780 000 895 000 400 000 2 075 000
Co-financing 188 500 251 369 155 063 128 468 723 400
Other revenue 0
Total revenues 0 968 500 1 146 369 555 063 128 468 2 798 400
Staff costs 44 858 785 919 609 525 1 440 302
Consultant costs 24 700 -16 467* 59 841 43 374
Other costs 4 848 -1 723* 67 209 75 981 141 467
Depriciation 0
Premises 0
Overhead costs 318 500 365 459 163 334 0 528 793
Total costs 0 348 048 392 127 1 076 303 685 506 2 1539 36
Result 0 620 452 1 374 694 853 454 296 416 296 416
University of Gothenburg
Swedish Museum of Natural History
Table 4. Financial report for UGOT’s commitments within Swedish LifeWatch. All figures SEK. In the financial report for 2014 corrections have been made regarding 2011 and 2013. A total of SEK 100 000 has been added to co-financing and SEK 185 000 to staff costs.
Table 3. Financial report for NRM’s commitments within Swedish LifeWatch. All figures SEK.
*) Redovisar ett plus på posterna konsultkostnader och övriga kostnader för att vissa kostnader från 2011 lyfts bort under 2012 då det beslutats att de ska ligga på enhetens driftkonto eller andra projekt
50 51
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 0 106 223 96 611 124 227
Allocated funds 140 000 110 000 105 000 355 000
Co-financing 39 079 39 079
Other revenue 0
Total revenues 0 140 000 110 000 105 000 39 079 394 079
Staff costs 39 046 39 649 43 249 121 944
Consultant costs 0
Other costs 20 902 36 749 10 041 11 896 58 686
Depriciation 0
Premises 12 442 12 509 24 951
Overhead costs 12 875 43 817 15 252 17 713 76 782
Total costs 0 33 777 119 612 77 384 85 367 282 363
Result 0 106 223 96 611 124 227 77 939 77 939
Lund University
Table 5. Financial report for Lund University’s commitments within Swedish LifeWatch. All figures SEK.
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 0 58 770 136 686 138 569
Allocated funds 350 000 100 000 25 000 475 000
Co-financing 83 500 41 750 41 750 167 000
Other revenue 0
Total revenues 0 433 500 141 750 66 750 0 642 000
Staff costs 265 564 44 416 45 754 65 906 421 640
Consultant costs 0
Other costs 16 374 2 332 18 706
Depriciation 0
Premises 24 000 8 000 2 500 34 500
Overhead costs 68 792 11 418 14 281 20 210 114 701
Total costs 0 374 730 63 834 64 867 86 116 589 547
Result 0 58 770 136 686 138 569 52 453 52 453
Umeå UniversityTable 6. Financial report for Umeå University’s commitments within Swedish LifeWatch. All figures SEK.
Bilaga 2 – Detaljerad ekonomisk redovisning
51
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 8 766 623 10 536 571 10 577 864 6 641 215
Allocated funds 9 000 000 9 000 000 9 000 000 4 524 085 4 475 915 36 000 000
Co-financing 2 550 000 2 420 263 2 818 119 3 399 793 1 945 921 13 134 096
Other revenue 28 652 5 348 0 297 776 -242 454* 89 322
Total revenues 11 578 652 11 425 611 11 818 119 8 221 654 6 179 382 49 223 418
Staff costs 1 645 296 4 919 800 5 877 726 5 890 842 3 875 080 22 208 744
Consultant costs 0 1 297 888 1 995 773 2 813 178 1 763 007 7 869 846
Other costs 279 153 401 545 304 430 393 656 823 604 2 202 388
Depriciation 0 140 993 241 702 241 702 117 482 741 879
Premises 110 859 273 185 332 541 304 622 148 104 1 169 311
Overhead costs 776 721 2 622 252 3 024 654 2 514 303 1 467 970 10 405 900
Total costs 2 812 029 9 655 663 11 776 826 12 158 303 8 195 247 44 598 068
Result 8 766 623 10 536 571 10 577 864 6 641 215 4 625 350 4 625 350
Total Table 8. Total financial report. All figures SEK. *Including adjustment 2013.
2010 2011 2012 2013 2014 Total
Last year surplus/deficit 0 17 462 0 0
Allocated funds 35 000 35 000
Co-financing 13 070 13 070
Other revenue 0
Total revenues 0 48 070 0 0 0 48 070
Staff costs 15 170 10 072 25 242
Consultant costs 0
Other costs 3 588 1 045 4 633
Depriciation 0
Premises 408 906 1 314
Overhead costs 11 442 5 439 16 881
Total costs 0 30 608 17 462 0 0 48 070
Result 0 17 462 0 0 0 0
SLU Aquatic ResourcesTable 7. Financial report for SLU Aqua’s (former Fiskeriverket) commitments within Swedish LifeWatch. All figures SEK.
