Periodic Reporting for period 2 - AGINFRA PLUS (Accelerating user-driven e-infrastructure innovation in Food Agriculture)
Berichtszeitraum: 2018-07-01 bis 2019-12-31
AGINFRA PLUS addressed the challenge of supporting user-driven design and prototyping of innovative e-infrastructure services and applications. It particularly tried to meet the needs of the scientific and technological communities that work on the multi-disciplinary and multi-domain problems related to agriculture and food. It used, adapted and evolved existing open e-infrastructure resources and services, in order to demonstrate how fast prototyping and development of innovative data and computing-intensive applications can take place.
• Identify the requirements of the specific scientific and technical communities working in three (3) targeted areas, abstracting new AGINFRA services that can serve all users
• Design and implement components that serve such requirements, by exploiting, adapting and extending existing open e-infrastructures
• Define or extend standards facilitating interoperability, reuse, and repurposing of components in the wider context of AGINFRA
• Establish mechanisms for documenting and sharing data, mathematical models, methods and components for the selected application areas, in ways that allow their discovery and reuse within and across AGINFRA and served software applications
• Increase the number of stakeholders, innovators and SMEs aware of AGINFRA services through domain-specific demonstration and dissemination activities
• Identify the requirements of the specific scientific and technical communities working in three (3) targeted areas, abstracting new AGINFRA services that can serve all users
• Design and implement components that serve such requirements, by exploiting, adapting and extending existing open e-infrastructures
• Define or extend standards facilitating interoperability, reuse, and repurposing of components in the wider context of AGINFRA
• Establish mechanisms for documenting and sharing data, mathematical models, methods and components for the selected application areas, in ways that allow their discovery and reuse within and across AGINFRA and served software applications
• Increase the number of stakeholders, innovators and SMEs aware of AGINFRA services through domain-specific demonstration and dissemination activities
During this second reporting period the following results have been achieved:
• Elaborated further on the project’s specific use cases in all three user-facing WPs, to provide requirements to the technology WPs and influence the development of both generic and customised tools & services.
• Selected and defined four (4) demonstration scenarios to be the ones to focus on, fine-tune, & showcase as the final AGINFRA+ Software Demonstrators.
• Shared methods, best practices and tools to support other EU projects that develop open science use cases.
• Design and implement components that serve such requirements, by exploiting, adapting and extending existing open e-infrastructures.
• Define or extend standards facilitating interoperability, reuse, and repurposing of components in the wider context of AGINFRA.
• The scientific environments and tools of D4Science VREs, Galaxy workflows, and Jupyter Notebooks have been reusing, extending and contributing back software implementations to the corresponding EOSC communities.
• The KNIME workflow integrations and customisations have been developed having in mind contributing back to the open innovation communities of KNIME.
• The integration, linking and extension of ontologies, taxonomies and terminologies of AGROVOC and GACS have been also made available through the semantic registries of AGINFRA PLUS and recognised community services such as the Agroportal.
• Establish mechanisms for documenting and sharing data, mathematical models, methods and components for the selected application areas, in ways that allow their discovery and reuse within and across AGINFRA and served software applications.
• Organised the 2nd and 3rd rounds of piloting activities within WP5, WP6 & WP6. A number of 7 pilot trials have been organised, with 132 participants in total.
• Organised a European contest for data science powered startups called the AGINFRA PLUS Data Science Challenge, attracting six (6) applications from Germany, the Netherlands, Serbia and Greece.
• Involved the data scientists working in BioCos (the bioinformatics SME that won the AGINFRA PLUS Data Science Challenge) into a hands-on experience of testing a VRE for their computationally intensive tasks.
The five (5) key technology offerings that have been decided to continue investing into are the following:
1. D4Science-powered VREs (CNR): existing or new Virtual Research Environments (VREs) that specific communities or organisations may continue using or creating, over the D4Science e-infrastructure.
2. EGI-powered Jupyter Notebooks (EGI): existing or new scientific applications that will be using Jupyter Notebooks for interactive data science and scientific computing, over the EGI e-infrastructure.
3. EGI-powered Galaxy Workflows (EGI): existing or new scientific workflows that will be executed over Galaxy, over the EGI e-infrastructure.
4. Data Harvesting & Data Linking Services (Agroknow): existing or new software applications that will be using the semantic indexing and data lookup services of Agroknow (or request a white label set up of their own similar service).
5. ARPHA-powered Data Journals (Pensoft): existing or new scientific data journals that will be powered by ARPHA.
• Elaborated further on the project’s specific use cases in all three user-facing WPs, to provide requirements to the technology WPs and influence the development of both generic and customised tools & services.
• Selected and defined four (4) demonstration scenarios to be the ones to focus on, fine-tune, & showcase as the final AGINFRA+ Software Demonstrators.
• Shared methods, best practices and tools to support other EU projects that develop open science use cases.
• Design and implement components that serve such requirements, by exploiting, adapting and extending existing open e-infrastructures.
• Define or extend standards facilitating interoperability, reuse, and repurposing of components in the wider context of AGINFRA.
• The scientific environments and tools of D4Science VREs, Galaxy workflows, and Jupyter Notebooks have been reusing, extending and contributing back software implementations to the corresponding EOSC communities.
• The KNIME workflow integrations and customisations have been developed having in mind contributing back to the open innovation communities of KNIME.
• The integration, linking and extension of ontologies, taxonomies and terminologies of AGROVOC and GACS have been also made available through the semantic registries of AGINFRA PLUS and recognised community services such as the Agroportal.
• Establish mechanisms for documenting and sharing data, mathematical models, methods and components for the selected application areas, in ways that allow their discovery and reuse within and across AGINFRA and served software applications.
• Organised the 2nd and 3rd rounds of piloting activities within WP5, WP6 & WP6. A number of 7 pilot trials have been organised, with 132 participants in total.
• Organised a European contest for data science powered startups called the AGINFRA PLUS Data Science Challenge, attracting six (6) applications from Germany, the Netherlands, Serbia and Greece.
• Involved the data scientists working in BioCos (the bioinformatics SME that won the AGINFRA PLUS Data Science Challenge) into a hands-on experience of testing a VRE for their computationally intensive tasks.
The five (5) key technology offerings that have been decided to continue investing into are the following:
1. D4Science-powered VREs (CNR): existing or new Virtual Research Environments (VREs) that specific communities or organisations may continue using or creating, over the D4Science e-infrastructure.
2. EGI-powered Jupyter Notebooks (EGI): existing or new scientific applications that will be using Jupyter Notebooks for interactive data science and scientific computing, over the EGI e-infrastructure.
3. EGI-powered Galaxy Workflows (EGI): existing or new scientific workflows that will be executed over Galaxy, over the EGI e-infrastructure.
4. Data Harvesting & Data Linking Services (Agroknow): existing or new software applications that will be using the semantic indexing and data lookup services of Agroknow (or request a white label set up of their own similar service).
5. ARPHA-powered Data Journals (Pensoft): existing or new scientific data journals that will be powered by ARPHA.
AGINFRA PLUS addressed the challenge of supporting user-driven design and prototyping of innovative e-infrastructure services and applications.
The Agro-climatic and Economic Modelling Community managed to showcase the application of the AGINFRA PLUS infrastructure to use cases pertaining to its needs via three use cases: Regional, large scale crop agro-climatic model simulations, Crop phenology estimation, AgroDataCube (later integrated in the two former use cases), and a generic Software Demonstrator titled “Distributed simulation of arable crops at farm field scale”.
The Food Safety Risk Assessment Community managed to showcase the application of the AGINFRA PLUS infrastructure to use cases pertaining to its needs via the establishment of two independent use cases for different communities inside this domain: the “Risk Assessment Knowledge Integration Platform” (RAKIP) community and the Determination and Metrics of Emerging Risk (DEMETER) community, and the introduction of a generic Software Demonstrator titled “Sharing and running simulations of harmonized food risk assessment models”.
The Food Security Community managed managed to showcase the application of the AGINFRA PLUS infrastructure to the use case of high-throughput phenotyping which should enable to select the plant varieties which are the most adapted to specific environments and to global changes. This was achieved with the following tasks: the Identification of general requirements of researchers in the phenotyping community, Specification of analytics, semantics and visualization needs, Carrying out the required development activities for the Food Security VRE, and the introduction of a generic Software Demonstrator titled “Management, access & visualisation of heterogeneous plant phenotyping resources”
Project activities also concluded with the introduction of a novel Software Demonstrator titled “The executable paper for agriculture & food scientists”
The Agro-climatic and Economic Modelling Community managed to showcase the application of the AGINFRA PLUS infrastructure to use cases pertaining to its needs via three use cases: Regional, large scale crop agro-climatic model simulations, Crop phenology estimation, AgroDataCube (later integrated in the two former use cases), and a generic Software Demonstrator titled “Distributed simulation of arable crops at farm field scale”.
The Food Safety Risk Assessment Community managed to showcase the application of the AGINFRA PLUS infrastructure to use cases pertaining to its needs via the establishment of two independent use cases for different communities inside this domain: the “Risk Assessment Knowledge Integration Platform” (RAKIP) community and the Determination and Metrics of Emerging Risk (DEMETER) community, and the introduction of a generic Software Demonstrator titled “Sharing and running simulations of harmonized food risk assessment models”.
The Food Security Community managed managed to showcase the application of the AGINFRA PLUS infrastructure to the use case of high-throughput phenotyping which should enable to select the plant varieties which are the most adapted to specific environments and to global changes. This was achieved with the following tasks: the Identification of general requirements of researchers in the phenotyping community, Specification of analytics, semantics and visualization needs, Carrying out the required development activities for the Food Security VRE, and the introduction of a generic Software Demonstrator titled “Management, access & visualisation of heterogeneous plant phenotyping resources”
Project activities also concluded with the introduction of a novel Software Demonstrator titled “The executable paper for agriculture & food scientists”