OpenBioMaps Data Management Service and Computational Tools
OpenBioMaps (OBM) is a free and open-source database platform for scientific and conservation purposes in the fields of biology, conservation biology, ecology, and biodiversity. It facilitates data management for nature conservation institutes, biodiversity research, and citizen science projects. Recent developments include the successful deployment of OpenBioMaps and the creation of computational services for project-specific computations. Use cases involve behavior ecology research groups and species distribution analysis in various regions.
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OpenBioMaps data management service for biological sciences and biodiversity conservation PI: Dr. Mikl s B n Shepherd: Miguel Caballer eosc-hub.eu @EOSC_eu EOSC-hub receives funding from the European Union s Horizon 2020 research and innovation programme under grant agreement No. 777536.
Overview The OpenBioMaps (OBM) is a free and open-source database platform for scientific and conservation purposes. Science areas: Biology, conservation biology, ecology, biodiversity - The OBM system is used for data management by nature conservation institutes, biodiversity research and citizen science projects. OBM provides a number of services that make day-to-day work with data easier, but it does not yet provide tools for analyzing the data. Particularly for high computing tasks. Current use cases: https://openbiomaps.org/projects/ -
Current status TOSCA template and Ansible recipes has been created (with Miguel) to launch OpenBioMaps portal from IM dashboard
Current status OpenBiomaps deployed successfully!
Computational node interface on an OpenBioMaps server
Computational service for OpenBioMaps Creating computational service for OpenBioMaps projects to help researcher using OBM databases to apply particular computations. This service accessible through OpenBioMaps servers for all users in the all projects The computation scripts can be R scripts. Computational servers are automatically chosen for computations (in this case it is our EOSC server)
Use cases Behavior Ecology Research Groups at University of Debrecen (Hungary): species distribution modelling B kk National Park (Hungary): species distribution analysis of fish species Milvus Group Association (Romania): species distribution analysis of birds
Missed things Deploying Satellite Image (geoss) interface B2Handle - Permanent Identifier Service - we have our own PID service, but we want to use B2Handle later when we will create common interfaces with external data repositories. B2Share - we also plan to deploy this service later using its REST API. So far, we have come up with an internal interface for storing data objects in external repositories that can communicate with Dataverse and B2Share interfaces. These services are likely to be used in several research projects soon. B2Drop, B2Find - We are not planning to integrate these services at the moment
Current status Status of access to the services and SLAs agreed with the providers (Created): SLA agreed with IFCA site (https://documents.egi.eu/public/ShowDocument?docid=3565) 1-8 VM, 48 CPUs, 130 GB RAM, 2.2 TB HD. Progress of the application: - OBM computation layer: done. It is available for all OpenBioMaps users. 2VM in production. - OBM as EOSC service: done. An OpenBioMaps server successfully deployed using Infrastructure Manager Dashboard. It is not publicly available. 1VM demo. - Initial version of TOSCA Recipes and Ansible roles created to deploy the application automatically using IM. Currently testing the automated deployment using Infrastructure Manager Dashboard: https://appsgrycap.i3m.upv.es:31443/im-dashboard/
Further plans B2Share, Dataverse data deposit interface B2Handle - PID interface Creating example computational packages Image processing interface Jupyter integration / using Jupyter API GIT integration Julia & Python support for computational packages Satellite image downloading interface ML support
Thank you for your attention! Contact banm@vocs.unideb.hu micafer1@upv.es Questions? @EOSC_eu eosc-hub.eu This material by Parties of the EOSC-hub Consortium is licensed under a Creative Commons Attribution 4.0 International License.
