DMMCore: Data and Model Management Core for ERASysAPP & Europe
Lead Research Organisation:
University of Manchester
Department Name: Computer Science
Abstract
This project, in partnership with colleagues in HITS, Heidelberg and Sybit, Switzerland, aims at establishing an internationally sustained Data and Model Management service to the European Systems Biology community.
Many projects in Systems Biology have been funded worldwide. However, it is often not clear how the results are made available to further research. Some result data sets or models are stored in public resources, but not all. Other repositories are ripe for a greater exploitation world-wide. Funding agencies now expect new projects to publish their results using open access and to provide a data management and data sustainability plan to assure that their investment has the desired impact. However, the researchers often have neither the means nor the knowledge necessary to publish and maintain their results according to the necessary standards so that they remain available beyond the end of their project. The results as requested by the publishers are often insufficient to be able to reliably reproduce results. Models and standard operating procedures are often not available or are not sufficiently described to be reproducible. This introduces inefficiencies, as the limited reusability and impact of project results on future projects leads to reinventions of methods and tools and slows the pace of scientific progress.
Systems Biology projects often have large and heterogeneous data sets, always have mathematical models based on experimental data. Such projects usually have researchers from various disciplines at many locations collaborating, where direct communication is often difficult not just because of the locality but also due to different semantics among disciplines. A shared software interface with transparent data and links to models is essential to allow for interdisciplinary research and to interact among research groups in Systems Biology. The iterative cycle between experiment and models that is typical in System Biology projects, mandates a good versioning system for experiment and model versions as well as investigation-study organisational structures such that the project workflow is clear and reproducible. Furthermore, a strict adherence to community standards and standard operating procedures is important for linking data and models created by different project members. A management platform needs to support experimental workflows and model and data linkages, with good tools for data and model annotation and adherence to standard formats of representation. In order to have all the information for a reproducible scientific process, data for model construction and model validation need to be clearly separated and all data, models and Standard Operating Procedures must be made available for download. Dedicated software platforms and tools are necessary to lift scientific research in Systems Biology up to industrial standards of reproducibility and quality control.
In this project we will establish a sustainable European data and model e-infrastructure for the European systems biology community with a long-term business model. We will found a European wide Data & Model Management Network to support and promote data and model management and capacity building, using the EraSysAPP ERANet as a seed. We will disseminate knowledge and standards, coordinating with related e-infrastructures such as ELIXIR and ISBE, and interacting with community related policy and standards settings. We will develop the necessary toolset and set up a data and model management platform for Systems Biology projects by combining and further developing/improving the well-proven software platforms SEEK and openBIS with a pool of public tools and resources, working closely with both the user and the developer communities. Finally, we will establish a sustainable training programming on the use and development of the platform and on data/model management practices for Systems Biology.
Many projects in Systems Biology have been funded worldwide. However, it is often not clear how the results are made available to further research. Some result data sets or models are stored in public resources, but not all. Other repositories are ripe for a greater exploitation world-wide. Funding agencies now expect new projects to publish their results using open access and to provide a data management and data sustainability plan to assure that their investment has the desired impact. However, the researchers often have neither the means nor the knowledge necessary to publish and maintain their results according to the necessary standards so that they remain available beyond the end of their project. The results as requested by the publishers are often insufficient to be able to reliably reproduce results. Models and standard operating procedures are often not available or are not sufficiently described to be reproducible. This introduces inefficiencies, as the limited reusability and impact of project results on future projects leads to reinventions of methods and tools and slows the pace of scientific progress.
Systems Biology projects often have large and heterogeneous data sets, always have mathematical models based on experimental data. Such projects usually have researchers from various disciplines at many locations collaborating, where direct communication is often difficult not just because of the locality but also due to different semantics among disciplines. A shared software interface with transparent data and links to models is essential to allow for interdisciplinary research and to interact among research groups in Systems Biology. The iterative cycle between experiment and models that is typical in System Biology projects, mandates a good versioning system for experiment and model versions as well as investigation-study organisational structures such that the project workflow is clear and reproducible. Furthermore, a strict adherence to community standards and standard operating procedures is important for linking data and models created by different project members. A management platform needs to support experimental workflows and model and data linkages, with good tools for data and model annotation and adherence to standard formats of representation. In order to have all the information for a reproducible scientific process, data for model construction and model validation need to be clearly separated and all data, models and Standard Operating Procedures must be made available for download. Dedicated software platforms and tools are necessary to lift scientific research in Systems Biology up to industrial standards of reproducibility and quality control.
In this project we will establish a sustainable European data and model e-infrastructure for the European systems biology community with a long-term business model. We will found a European wide Data & Model Management Network to support and promote data and model management and capacity building, using the EraSysAPP ERANet as a seed. We will disseminate knowledge and standards, coordinating with related e-infrastructures such as ELIXIR and ISBE, and interacting with community related policy and standards settings. We will develop the necessary toolset and set up a data and model management platform for Systems Biology projects by combining and further developing/improving the well-proven software platforms SEEK and openBIS with a pool of public tools and resources, working closely with both the user and the developer communities. Finally, we will establish a sustainable training programming on the use and development of the platform and on data/model management practices for Systems Biology.
Technical Summary
In the course of the ERA-Net EraSysAPP and European research infrastructure project ISBE, three national funding agencies have agreed to support a Data and Model Management Core Project - DMMCore - for the European life science research community. This joint action aims at establishing an internationally sustained Data and Model Management service to the European systems biology community seeded by research projects funded by ERASysAPP. Previous funding programs (SysMO and SystemsX.ch) dedicated support projects (SysMO-DB and SyBIT) have been set up to create the necessary tools and resources, and to interact with the research projects to assure proper data and model management. We are building on the experience and expertise of those projects to:
1) Develop a standards-based Data and Model Management Platform by combining the openBIS and SEEK platforms (openSEEK) with a Core Tool Pool of community software and archives.
2) Establish a sustainable European infrastructure using the platform, including a community Facility called EuroSEEK to host projects that do not want to operate their own local openSEEK platform. We will establish a Data & Model Management Network of community actions of experts, users and developers, sustainability mechanisms for the EuroSEEK Facility that federates national activities in countries in addition to the DMMCore countries; and a SysBioDMM Foundation to manage future membership funding of the resources and the community networks. We will actively engage in standards and work with standards and policy setting organisations.
3) Provide support and operations for the EraSysAPP projects seeding the European Infrastructure including: support for projects to found their local data management solution based on openSEEK and project-specific data analysis pipelines; a Support Team for technical curation, policy making, advice and training; and a PALs focus group of project representatives to work with the delivery team.
1) Develop a standards-based Data and Model Management Platform by combining the openBIS and SEEK platforms (openSEEK) with a Core Tool Pool of community software and archives.
2) Establish a sustainable European infrastructure using the platform, including a community Facility called EuroSEEK to host projects that do not want to operate their own local openSEEK platform. We will establish a Data & Model Management Network of community actions of experts, users and developers, sustainability mechanisms for the EuroSEEK Facility that federates national activities in countries in addition to the DMMCore countries; and a SysBioDMM Foundation to manage future membership funding of the resources and the community networks. We will actively engage in standards and work with standards and policy setting organisations.
3) Provide support and operations for the EraSysAPP projects seeding the European Infrastructure including: support for projects to found their local data management solution based on openSEEK and project-specific data analysis pipelines; a Support Team for technical curation, policy making, advice and training; and a PALs focus group of project representatives to work with the delivery team.
Planned Impact
Systems approaches to biology have the potential to transform biology and medicine and provide economic benefits through, for example, industrial biotechnology amd applications that detect drug project failure earlier and speed up therapeutic development: it is estimated that drug discovery costs could be reduced by $390m (£225m) development time to market shortened by three years (Strategy for UK Life Sciences, BIS). The UK alone has more than 50+ research groups and has invested £300m in awards, with an expectation of greater investment.
This project proposes to raise the capacity and capability of Systems Biology asset management by establishing a management platform for data, models and SOPs, enabling access to and management of results, radically improving the availability of the results and raising the quality of metadata practices. Thus the project has the potential to produce impact across Systems Biology and its application, and across a broad range of the life sciences through better management, quality control, and adherence to standards leading to greater reproducibility and reusability of models and data.
Our work plan makes a direct contribution towards making the widest possible economic and societal impact of Systems Biology , with dedicated programmes of community engagement and outreach. Specific impacts include:
- An off-the-shelf management platform (openSEEK) for European researchers exploiting prior developments. We have the potential to be the management system for SysBio projects worldwide. The platform has already made an impact internationally with instances in Europe, Russia and South America.
- A EuroSEEK hosted resource built using openSEEK to retain, find, track, and share European research results, thereby ensure a greater impact of Europe's research programmes internationally and to business, and facilitating data and knowledge exchange between researchers.
- Raised accessibility and profile of European software and data investments through their integration into the pan-European resource and training programme.
- An established Data and Model Management Facility Network of European Centres using: openSEEK as the flagship platform; EuroSEEK as a directory of researchers and research; and centre members as skilled data stewards. The network will bootstrap a European Research Infrastructure.
- Adoption of the platform, resources and practices by developing a Knowledge Network of early and mid-career researchers, User and Developer Forums and a Systems Biology Developers Foundry.
- Raised capacity through a training programme with bootcamps, workshops etc, through partnerships with organisations like Software Carpentry and GOBLET.
- Partnerships with scholarly communication stakeholders (publishers and open access repositories) to improve data and model publishing, incentivize researchers and yield better management practices.
- Active participation and leadership in domain specific standards bodies (e.g. COMBINE), selected communities (e.g. Research Data Alliance, BioSharing), and adaptation of our platforms and training to emerging standards and selected Research Infrastructures (e.g. ISBE, ELIXIR,EUDAT).
The greatest challenge to impact is sustaining the DMMCore outcomes and activities for the long term. We will work with funding agencies and the community to develop funding models, infrastructure support policies and contribution mechanisms. We will work with the UK's Software Sustainability Institute on sustainability strategies for the software and software training, and establish a not for profit Foundation as a focus for funding, running the EuroSEEK facility and open source software development.
This project proposes to raise the capacity and capability of Systems Biology asset management by establishing a management platform for data, models and SOPs, enabling access to and management of results, radically improving the availability of the results and raising the quality of metadata practices. Thus the project has the potential to produce impact across Systems Biology and its application, and across a broad range of the life sciences through better management, quality control, and adherence to standards leading to greater reproducibility and reusability of models and data.
Our work plan makes a direct contribution towards making the widest possible economic and societal impact of Systems Biology , with dedicated programmes of community engagement and outreach. Specific impacts include:
- An off-the-shelf management platform (openSEEK) for European researchers exploiting prior developments. We have the potential to be the management system for SysBio projects worldwide. The platform has already made an impact internationally with instances in Europe, Russia and South America.
- A EuroSEEK hosted resource built using openSEEK to retain, find, track, and share European research results, thereby ensure a greater impact of Europe's research programmes internationally and to business, and facilitating data and knowledge exchange between researchers.
- Raised accessibility and profile of European software and data investments through their integration into the pan-European resource and training programme.
- An established Data and Model Management Facility Network of European Centres using: openSEEK as the flagship platform; EuroSEEK as a directory of researchers and research; and centre members as skilled data stewards. The network will bootstrap a European Research Infrastructure.
- Adoption of the platform, resources and practices by developing a Knowledge Network of early and mid-career researchers, User and Developer Forums and a Systems Biology Developers Foundry.
- Raised capacity through a training programme with bootcamps, workshops etc, through partnerships with organisations like Software Carpentry and GOBLET.
- Partnerships with scholarly communication stakeholders (publishers and open access repositories) to improve data and model publishing, incentivize researchers and yield better management practices.
- Active participation and leadership in domain specific standards bodies (e.g. COMBINE), selected communities (e.g. Research Data Alliance, BioSharing), and adaptation of our platforms and training to emerging standards and selected Research Infrastructures (e.g. ISBE, ELIXIR,EUDAT).
The greatest challenge to impact is sustaining the DMMCore outcomes and activities for the long term. We will work with funding agencies and the community to develop funding models, infrastructure support policies and contribution mechanisms. We will work with the UK's Software Sustainability Institute on sustainability strategies for the software and software training, and establish a not for profit Foundation as a focus for funding, running the EuroSEEK facility and open source software development.
Organisations
- University of Manchester (Collaboration, Lead Research Organisation)
- Leiden University (Collaboration)
- ETH Zurich (Collaboration)
- Norwegian University of Life Sciences (NMBU) (Collaboration)
- SB Science Management UG (Collaboration)
- Infrastructure for Systems Biology Europe (Collaboration)
- New Forest Ventures Ltd (Collaboration)
- National Institute of Biology (Collaboration)
- U.S. Department of Energy (Collaboration)
- Russian Academy of Sciences (Collaboration)
- researchobject.org (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- University of Zurich (Collaboration)
- ELIXIR (Collaboration)
- Stellenbosch University (Collaboration)
- University of Rostock (Collaboration)
- Heidelberg Institute for Theoretical Studies (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
Publications
Stanford NJ
(2015)
The evolution of standards and data management practices in systems biology.
in Molecular systems biology
Waltemath D
(2014)
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
in Standards in Genomic Sciences
Wilkinson MD
(2016)
The FAIR Guiding Principles for scientific data management and stewardship.
in Scientific data
Wolstencroft K
(2017)
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.
in Nucleic acids research
Wolstencroft K
(2015)
SEEK: a systems biology data and model management platform.
in BMC systems biology
| Description | We have six major findings: 1. The FAIRDOM SEEK Open Software Platform, pluggable with a Core Pool of specialist software (JWS Online, LabArchives, BioVis, Cytoscape etc), specialist public archives (PubMed, Biomodels etc) and general purpose public archives (e.g. Zenodo, Figshare). An open source development community is being developed around the FAIRDOM-SEEK software. The Platform can be downloaded, installed and managed independently by researchers for their own customised needs to build project Hubs. The platform supports data from instruments (using openBIS software as well as other platforms) to web-based cross-repository cataloging (using the FAIRDOM-SEEK software), metadata collection (using our RightField software) and model simulation (using our partner's JWS Online Software). The platform has now been independently installed by over 140 groups and projects in: Spain, France, Belgium, Germany, Slovenia, Russia, USA, and South Africa. The software has regular releases with change logs, (currently we are at release 41). It is TRL9 and used by three European Research Infrastructures in the Life Sciences (ELIXIR, IBISBA and ISBE). 2. The FAIRDOMHub is a public data and model management Hub for projects, based on the SEEK Software Platform. A project "Commons" is a key recommendation of the EU ISBE Research Infrastructure. The ERASysAPP, ERASysBIO and SysMO ERANet projects were consolidated as areas on the FAIRDOMHub, and in January 2016 the Hub was updated to support self-managing independent projects. Currently over 200 projects have self-managed spaces on the Hub for managing their research assets either whilst working on them or at the point of publishing. over 1770 researchers are registered in the Hub's Yellow Pages from over 416 institutions, registering 5110 project assets. The COVID-19 Disease Map Consortium, (doi:https://doi.org/10.1101/647776) uses the FAIRDOMHub (https://fairdomhub.org/projects/190) to coordinate the 270+ international consortium in the ground-breaking work on curating SARS-CoV-2 virus-host interaction mechanism models. The BBSRC funded PlasMo Plant Systems-biology Modelling database of 500 models/data migrated to FAIRDOMHub in 2018 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6652102, (https://fairdomhub.org/projects/129) 3. The FAIRDOM Services of business analysis and stewardship advice, installation support and hosting, stewardship training, curation support, best practices and standards watch, and trouble shooting. Services are tiered to range from premium and super premium levels, funded support of specific initiatives and projects such as EU ERANET ERASysAPP to standard level support of independent users through forums and online resources. FAIRDOM is working with the ELIXIR EU Research Infrastructure to establish a network of affiliates offering FAIRDOM services. 4. The FAIRDOM Community is a community of researchers and developers skilled in asset stewardship or tool-making, and engaging with communities important to Sys and Syn Bio researchers such as standards (e.g. COMBINE), publishers, funders and other RIs. Activities include face to face meetings and webinars; summer schools and specialist workshops. We ran a BioSamples Club; a SysBio software developers foundry; and VIP users (the PALS). The team partnered with training providers such as Software and Data Carpentry and community networks such as COMBINE, CaSyM, MultiScale Biology Network, GARNet and ELIXIR Data Management Network, and now partner primarily with ELIXIR Nodes 5. EU Research Infrastructures - FAIRDOM is a key component of three EU Research Infrastrctures - EU RI ISBE, where FAIRDOM became core data stewardship pillar for ISBE Interim Phase. We also developed stewardship policy for ERANet ERASysAPP programme, and we developed policy for data stewardship ISBE. - FAIRDOM-SEEK has been adopted by 6 ELIXIR Nodes for data management and cataloguing, and is the backbone of the German NFD14Health Covid-19 Study Hub (https://covid19.studyhub.nfdi4health.de). ELIXIR-Norway sub-contracted the FAIRDOM project to connect the SEEK platform with their National Life Science Infrastructure; ELIXIR Belgium won a national award to run FAIRDOM for their projects and employ developers to dedicated to the FAIRDOM project; ELIXIR France run a SEEK Installation for their projects and ELIXIR. FAIRDOM SEEK is now a component of ELIXIR's RDMKit toolkit developed by the EU ELIXIR-CONVERGE project. FAIRDOM is a component of the EOSC-Life EU Cluster and has been used in ELIXIR communities for Plant Phenotyping. - FAIRDOM-SEEK forms the IBISBAHub for the outcomes of the IBISBA Consortium and the roadmapped IBISBA ESFRI. - FAIRDOM-SEEK is the basis of a workflow collaboratory for Life Sciences WorkflowHub.eu developed through EU grant awards: EOSC Life Cluster Project, the BioExcel Centre of Excellence. EOSC Life is a Cluster project uniting 13 EU Research Infrastructures in the Life Sciences. Despite being only beta launched in Sept 2021, WorkflowHub.eu is recognised as a world leading workflow registry and is part of the EU COVID Data Portal https://www.covid19dataportal.org. It was highlighted as the prime success by the review panel of EOSC-Life. Beyond Systems Biology the platform has been adopted by the EU Biodiversity Portal BioVeL and the Synthesys+ for natural history collections (a project of the ESFRI DISSCo). 6. The FAIRDOM Association e.V., is a legally registered Not Profit Organisation (NPO) Association to further the aims of FAIRDOM and support its products, services and activities, able to have its own employees and able to win and distribute funds. On 12th December 2016 the Association was incorporated in front of a notary in Berlin. A founding member is Professor Andrew Millar (Director of the SynthSys Centre at the University of Edinburgh) who is not funded by the DMMCore award. Having a legal entity did not prove effective for funding and sustainability in practice and in 2021 the Association was dissolved in favour of using ELIXIR as its prime coordination mechanism. |
| Exploitation Route | The purposet of the project is a public and open source infrastructure and the associated stewardship services to support Systems Biology projects with their data and model management allowing for intensive community engagement, training, advice and support services. All the software is open source, with an open developer community. The FAIRDOMHub is a free public resource hosted. The project was all about the use of the platforms, the Hub, know-how and the building of user, collaborator and developer communities. We first established the FAIRDOM Association e.V. to a member-serving and community-serving organisation, since set aside in favour of collaboration and sustainability through the EU ELIXIR Research Infrastructure and its national nodes. The project included establishing a sustainable European infrastructure to extend the network services to the wider European systems biology community and seed a European wide Data and Model Management Network to support and promote data and model management and capacity building, disseminating knowledge and standards, interacting with community related policy and standards setting and coordinating with related e-infrastructures such as ELIXIR, IBISBA and ISBE. This latter point proved essential for FAIRDOM's sustainability as well as its position in National projects in Germany (NFD14Health, LiSyM cancer, Leipzig Health Atlas), Norway and Belgium. We developed the necessary toolset and set up a data and model management platform for Systems Biology projects working closely with both the user and the developer communities. We also document and disseminate the outcomes and activities especially to funding agencies, projects and centres, assuring the success of the sustainable business model and funding models for the long term. Provide training in the usage of the tools and platform, as well as in its operations and further development. We are increasingly being used as a platform outside of Systems and Synthetic Biology. We repositioned our underlying FAIRDOM-SEEK project Hub and Cataloging platform as a general, customisable infrastructure, particularly for supporting the sharing of computational workflows, leading to the WorkflowHub. We have been successful in securing funds for continuing the development and support of the FAIRDOM platform through EU awards (Synthesys+, BioExcel2, EOSC Life, ELIXIR-CONVERGE, IBISBA1.0 and PREP-IBISBA). Our Belgium, Norway and German collaborators have also secured national funds to contribute to our sustainability. |
| Sectors | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| URL | http://www.fair-dom.org |
| Description | The COVID-19 Disease Map Consortium, (doi:https://doi.org/10.1101/647776) uses the FAIRDOMHub (https://fairdomhub.org/projects/190) to coordinate the 270+ international consortium in the ground-breaking work on curating SARS-CoV-2 virus-host interaction mechanism models. The DMMCore project was rebranded FAIRDOM. FAIR stands for "Findable, Accessible, Interoperable, Reusable". FAIRDOM stands for "FAIR Data, Operations, Models" and "FAIR sharing and credit" between researchers. The BBSRC grant was part of a multi-award programme with BMBF (Germany) and SystemX (Switzerland). We worked closely with these partners as a joint delivery team. Impacts The FAIRDOM Consortium continues to thrive post the completion of this award. It has been expanded to include partners in Sweden, Belgium, Slovenia and Norway as well as UK, Switzerland, Netherlands, Germany, and South Africa. Each contributes resources through shared and coordinated development and we have successful secured funding at national and European levels. 1. The FAIRDOM-SEEK Open Software Platform for data and model management. An open source development community has been developed around this software. The Platform can be downloaded, installed and managed independently by researchers for their own customised needs. 140+ independent SEEK installations are known. Highlights include take-up by: Environmental Molecular Sciences Laboratory a large national scientific user facility (800 scientists, 1500 instruments) at Pacific Northwest National Laboratory (PNNL) in Washington State, USA; the de.NBI German Bioinformatics Network; Norway's Centre for Digital Life; large EU consortia (e.g. NMTrypl, EmPowerPutid, Mycosynvac) and national projects such as in Germany: Virtual Liver Network, LiSyM (Liver System Medicine), LiSyM Cancer, the German NFD14Health programme and the Leipzig Health Atlas. ELIXIR Norway integrated FAIRDOM with their National EInfrastructure for Life Sciences, ISBE.SI have integrated FAIRDOM with the pISA filestore and ELIXIR Belgium have established their own Hub. Two UK Synthetic Biology Centres (SynBioChem and SynthSys) used the platform. A prime impact route has been through the European Research Infrastructures and the European Open Science Cloud, where the SEEK has been adopted - see below for more details. 2. The FAIRDOMHub public and free data and model management project Hub based on the Platform hosted by our German partners HITS. 380+ projects are currently registered and include all the projects of the ERANets SysMO and ERASysAPP programme from DMMCore as well as projects from the German Bioinformatics Infrastructure de.NBI and many independent projects. 2215+ users are registered with 5000+ assets and 480+ Investigations. Growth in additional projects continues at a steady 20-30% per annum. An important impact is the retention of results from projects. In 2017 50% of SysMO-DB projects were still actively posting content many years after end of that programme. The Plant Systems-biology Modelling database and portal (plasmo.ed.ac.uk) The PlaSMo repository contained over 100 described models and nearly 400 data and model files when its funding ended. We migrated the PlaSMo models to FAIRDOMHub where they are still available today (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6652102/) Since January 2016 the Hub supports independent, self-managing projects. From 2019 FAIRDOMHub featured in several demonstrators for the European Cluster project EOSC-Life, a huge project which clusters the 13 Life Science Research Infrastructures of Europe, and the German NFDI programme. 3. The FAIRDOM Services for business analysis and stewardship advice, installation support and hosting, stewardship training, curation support, best practices and standards watch, and trouble shooting. We have to balance support for immediate users, investment in bigger users, and the building of the materials that make data management more accessible independently. We are building up a portfolio of projects through: "pre-sales" consultations with strategic projects; National and Community networks; National infrastructures and Centres; EFSRIs and EOSC. We extended our reach to Synthetic Biology, Systems Medicine and general bio-data. We developed a pilot FAIRDOMHub as a "publisher companion" for manuscripts with mathematical models and/or experimental data, first with those who collaborate with JWS Online's curation services: FEBSJ has accepted publications in which we link data and models to the Hub, using DOIs With the European RI ISBE we conducted a community survey in availability and usage of standards, and general data management practices. We have summarised the key findings and published a commentary paper: DOI 10.15252/msb.20156053 We have the reproducibility of Systems Biology models with the development of the Research Objects packaging and support for the COMBINE Archive file format, model simulation and versioning. 4. The FAIRDOM Community of researchers and developers skilled in stewardship and tool-making, standards, and other stakeholders: publishers, funders and other RIs. We developed a Knowledge Hub of materials, guides; useful sites; data management checklists ; community standards; repositories and commons; specialised software; publications; webinars; reports; presentations; tutorials. A video promoted data stewardship and we ran a webinar series in 2016. We ran the Samples Club (with RIs BBMRI-ERIC, ISBE and ELIXIR) which developed a new model for samples adopted by the Human Cell Atlas project at the EBI, and the SysBio Developers Foundry which brought together developers working in the systems and synthetic biology communities. Since 2018 we have concentrated on working with National networks (in Sweden, Norway, Belgium, SA, Netherlands, Germany, France, UK) and pan-national EFSRIs and the EOSC-Life Cluster project at the European Level, incorporating FAIRDOM into projects as partners. This gives us access to 1000s of users (see below). We are also part of the ELIXIR Community on Systems Biology, which has taken over from the ISBE ESFRI. 5. EU RI Impact Our most significant method for impact has been our strategic affiliation with European research Infrastructures. DMMCore sponsored the widening of FAIRDOM's impact to the ISBE Systems Biology Research Infrastructure. • FAIRDOM was adopted as a core component of the interim phase ISBE Light and led the stewardship pillar. We authored the ISBE data management strategy and recommendations and serve on the ISBE Light Steering Committee. We represented ISBE at international meetings and are working with the Intergovernmental Working Group to secure sustainability. Work on the DMMCore extended FAIRDOM's reach to the ESFRI Research Infrastructure ISBE. ISBE has since folded into ELIXIR Research Infrastructure - a mature and powerful intergovernmental organisation of 23 countries for managing Life Science data. • ELIXIR is the intergovernmental European Research Infrastructure for Life Science Data. It is made up of 23 national nodes, a hub and 250+ organisations. FAIRDOM-SEEK is an official Node resource of 3 Nodes (Belgium, Germany and UK) and is used by other Nodes (Sweden, Slovenia, Norway, Netherlands, France) in their data management. It is incorporated into data management for the ELIXIR Systems Biology and Plants communities and is being developed as a data broker to EBI deposition databases. The FAIRDOMHub is a recognised resource of the German node. ELIXIR-Norway sub-contracted the FAIRDOM project to connect the SEEK platform with their National Life Science Infrastructure; ELIXIR Belgium won a national award to run FAIRDOM for their projects (DataHub) and employ developers to rededicate to the FAIRDOM project; ELIXIR France run a SEEK Installation for their projects. Germany has won a number of national awards for projects using the SEEK, notably LiSyM Cancer and German NFD14Health, specialising in Systems Medicine. Sweden's SciLifeLab has adopted the SEEK as its metadata management platform. FAIRDOM is incorporated into the RDMKit ELIXIR's RDM toolkit launched in March 2021 (rdmkit.elixir-europe.org), funded by the EU ELIXIR-CONVERGE project. • The SEEK is the underlying platform for the WorkflowHub, the ELIXIR and EOSC-Life Workflow registry. EOSC-Life is a cluster EU project uniting 13 Biomedical Research Structures in Europe. The WorkflowHub was beta released in Sept 2020 and commended in the EOSC-Life mid-term review as an outstanding achievement. The WorkflowHub is already established as a critical piece of EOSC infrastructure. • FAIRDOM-SEEK is the platform for the IBISBAHub, which handles for the outcomes of the IBISBA Research Infrastructure for Industrial Biotechnology. • FAIRDOM-SEEK is used by MIT's BioMicro's Data Management Platform. • Beyond Systems Biology the platform was been adopted by the EU Biodiversity Portal BioVeL and has since been adopted by Synthesys+ for natural history collections (a project of the ESFRI DISSCo) for its Specimen Data Refinery. At the policy level we co-authored the ERASysAPP SRA and the data management plan and advised on the follow-on proposal EU Cofund ERACoBioTech. In ERACoBioTech we co-authored the data management planning. The German FAIRDOM Association partners were been subcontracted to support 8/22 of the first round funded ERACoBioTech projects from in June 2018. Interactions with funding agencies and ESFRI Research Infrastructure include contributions to policy and stewardship advocacy in EU RIs, national councils (SynBio Leadership Council Roadmap) EU initiatives (e.g. ScienceEurope, European Open Science Cloud) and international initiatives (Force11/BD2K DCIP). We established a not for profit Foundation FAIRDOM e.V, incorporated in Germany. However this proved to be an administrative burden and complicated. We have reverted to working within the framework of ELIXIR for our collaboration. 8. COVID-19 FAIRDOM contributed to the work towards the COVID pandemic in three specific ways • The FAIRDOM-SEEK is the backbone of the German NFD14Health Covid-19 Study Hub • The FAIRDOMHub was adopted by The COVID-19 Disease Map Consortium, an open collaboration of 250+ people to build a comprehensive, standardized knowledge repository of SARS-CoV-2 virus-host interaction mechanisms (doi:https://doi.org/10.1101/647776). It uses the FAIRDOMHub (https://fairdomhub.org/projects/190) to regularly release newly curated models; • The SARS-CoV-2 Galaxy Consortium (https://doi.org/10.1371/journal.ppat.1008643) uses the WorkflowHub (https://workflowhub.eu/projects/3) (2020) and releases reproducible Workflow Research Objects to be shared across the research community. The WorkflowHub was launched 6 months ahead of schedule to register and disseminate COVID-19 related computational workflows. WorkflowHub and FAIRDOMHub are listed in the EU COVID Data portal https://covid19dataportal.org/ The FAIRDOM-SEEK is a flagship for new models of scholar communication, for Research Objects and for the FAIR (Findable, Accessible, Interoperable, Reusable) movement which is now a widespread policy of national and international funders, journals and communities. FAIR was launched by the (Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18) in which FAIRDOM is given as an example. |
| First Year Of Impact | 2008 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Societal,Economic,Policy & public services |
| Description | ERACoBioTech Data Management Planning |
| Geographic Reach | Europe |
| Policy Influence Type | Membership of a guideline committee |
| URL | https://www.cobiotech.eu/ |
| Description | ERASysAPP Strategic Research Agenda - Systems Biology in Europe 2016 |
| Geographic Reach | Europe |
| Policy Influence Type | Citation in other policy documents |
| Impact | The Strategic Research Agenda - Systems Biology in Europe 2016 addresses five key issues. -Funding collaborative research: need for novel types of funding schemes -Academia and industry: make SMEs aware of the opportunities of systems biology -Data and model management: make research assets re-usable over longer periods of time -Education and training: introduce computational modelling and data integration in curricula -Research infrastructures: make optimal use of European research infrastructures Each chapter results in a number of concrete recommendations that are directed to scientists, funding organisations, industry and policy makers. |
| URL | https://www.erasysapp.eu/publications/strategy-documents |
| Description | EU's Targeted Stakeholders' Consultation on Long Term Sustainability of Research Infrastructures (January 2016) |
| Geographic Reach | Europe |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | FAIR in practice - Jisc report on the Findable Accessible Interoperable and Reuseable Data Principles |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| URL | https://zenodo.org/record/1245568#.XIf-tLjgp3i |
| Description | Science Europe |
| Geographic Reach | Europe |
| Policy Influence Type | Citation in other policy documents |
| Impact | The former Science Europe Scientific Committee for the Life, Environmental and Geo Sciences organised a workshop in Brussels on 1 and 2 December 2015. Representatives from Science Europe Member Organisations (both research funding and research performing organisations), the publishing community, various research organisations and universities, evaluators and researchers, were invited to share their diverse perspectives and to brainstorm the issue. The 'state of the art' in terms of crediting multidisciplinary research, the needs of various stakeholders, solutions, bottlenecks and recommendations for funders, researchers, policy makers and publishers were discussed in-depth. It was universally agreed that systems such as crediting appropriately, supporting data re-use and rewarding multidisciplinary science need updating. There is a need to determine standardised criteria for evaluating multidisciplinary science, and a need to apply them successfully in evaluation panels and in recruitment. In order to achieve this, guidelines should be provided for researchers, funders, evaluation panels and publishers on how to credit and to cite specific contributions, data, tools and software in an improved way. Data and tools were especially highlighted; informal mentions of software and datasets should end and proper citation should be used in the future. Individual researchers should take steps themselves to ensure that they highlight all of their contributions. In addition to the typical peer-reviewed publications, researchers should disseminate their 'other research outputs', such as collaborative work, shared data, new methods or techniques, software, media outputs and other such contributions. These should in turn be evaluated along with the traditional outputs. The full list of recommendations are listed at the end of the report, and include further suggestions about how to more accurately credit and better evaluate multidisciplinary research. Some of the promising new tools and methods being developed, were presented and discussed. The benefits of applying new methods for assessing the specific contributions of researchers and accurately awarding them for their scholarly input to the data-driven multidisciplinary research of the current and future scientific landscape would be wide-ranging. Collectively, such new approaches will foster multidisciplinary science and support research-driven innovation. |
| URL | http://www.scienceeurope.org/wp-content/uploads/2016/06/SE_LEGS_Careerpaths_Workshop_Report.pdf |
| Description | The Open Research Data Task Force "Realising the potential of open research data" |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| URL | https://www.universitiesuk.ac.uk/policy-and-analysis/research-policy/open-science/Pages/open-researc... |
| Description | AgroServ |
| Amount | £14,252,873 (GBP) |
| Funding ID | 10038927 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 08/2027 |
| Description | BioDT |
| Amount | £11,951,059 (GBP) |
| Funding ID | 10038930 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2022 |
| End | 04/2025 |
| Description | Bioindustry 4.0 |
| Amount | £10,007,922 (GBP) |
| Funding ID | 10048146 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2023 |
| End | 12/2026 |
| Description | COST Association |
| Amount | € 2,000,000 (EUR) |
| Funding ID | COST Action CA15110 |
| Organisation | European Cooperation in Science and Technology (COST) |
| Department | COST Action |
| Sector | Public |
| Country | Belgium |
| Start | 03/2016 |
| End | 03/2020 |
| Description | Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) |
| Amount | £10,300,000 (GBP) |
| Funding ID | BB/M017702/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2014 |
| End | 11/2019 |
| Description | ELIXIR-CONVERGE |
| Amount | € 5,000,000 (EUR) |
| Funding ID | 871075 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 02/2020 |
| End | 01/2023 |
| Description | EOSC Enhance: Enhancing the EOSC portal and connecting thematic clouds |
| Amount | € 1,999,700 (EUR) |
| Funding ID | 871160 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 12/2019 |
| End | 11/2021 |
| Description | EOSC-Life, Providing an open collaborative space for digital biology in Europe |
| Amount | € 23,745,996 (EUR) |
| Funding ID | INFRAEOSC-04-2018, H2020-EU.1.4.1.1, 824087 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 03/2019 |
| End | 02/2023 |
| Description | FAIR-CURES-RO |
| Amount | $77,149 (USD) |
| Funding ID | subcontract from FAIR4CURES NIH Data Commons |
| Organisation | Elsevier |
| Sector | Private |
| Country | Netherlands |
| Start | 09/2018 |
| End | 08/2020 |
| Description | IBISBA 1.0: Industrial Biotechnology Innovation and Synthetic Biology Accelerator |
| Amount | € 5,000,000 (EUR) |
| Funding ID | H2020-INFRAIA-2017, 730976 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 12/2017 |
| End | 11/2021 |
| Description | INFRADEV-3-2015, 676559, ELIXIR-EXCELERATE |
| Amount | € 19,000,000 (EUR) |
| Funding ID | INFRADEV-3-2015, 676559 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 09/2015 |
| End | 08/2019 |
| Description | PREP-IBISBA Industrial Biotechnology Innovation and Synthetic Biology Accelerator Preparatory Phase |
| Amount | € 3,995,065 (EUR) |
| Funding ID | 871118 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 01/2020 |
| End | 12/2023 |
| Description | SYNTHESYS PLUS Synthesis of systematic resources |
| Amount | € 11,325,200 (EUR) |
| Funding ID | INFRAIA-01-2018-2019, H2020-EU.1.4.1.2, 823827 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 02/2019 |
| End | 01/2023 |
| Title | Common Workflow Language |
| Description | The Common Workflow Language (CWL) is a specification for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. CWL is designed to meet the needs of data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy, Physics, and Chemistry. CWL is developed by a multi-vendor working group consisting of organizations and individuals aiming to enable scientists to share data analysis workflows. The CWL project is maintained on Github and follows the Open-Stand.org principles for collaborative open standards development. Legally CWL is a member project of Software Freedom Conservancy and is formally managed by the elected CWL leadership team, however every-day project decisions are made by the CWL community which is open for participation by anyone. We are founding members of CWL; co-developed the specification, develop tools such as the CWL Viewer (View.commonwl.org) and promote the adoption of CWL internationally particularly through our EU projects in the Life Sciences. CWL is based on work we undertook in the Taverna Workflow system, developed in the OMII project and developed since in EU projects. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Its the Common Workflow Language adopted extensively by the commerical and and open source sector across disciplines, and in particular adopted by the Life Sciences. It is basis of the European Open Science Cloud Life Science Collaboratory (EOSCLife) and several other ESFRIs. |
| URL | http://commonwl.org |
| Title | Research Objects |
| Description | "Research Objects" describes an emerging approach to the publication, and exchange of scholarly information on the Web that aims to improve its reuse and reproducibility by: Supporting the publication of more than just PDFs, making data, code, and other resources first class citizens of scholarship Recognizing that sometimes there is a need to publish collections of these resources together as one shareable, cite-able resource. Enriching these resources and collections with any and all additional information required to make research reusable, and reproducible! Research objects are not just data, not just collections, but any digital resource that aims to go beyond the PDF for scholarly publishing. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2010 |
| Provided To Others? | Yes |
| Impact | The notion of a Research Object has had a significant impact in the publishing and scholarly communications world -- the NIH BD2K Commons Initiative is based on Research Objects -- Research Objects formed the basis of the workflow reproducibility and preservation EU project Workflow4ever (http://www.wf4ever-project.org) which had an excellent rated final review. -- Research Objects have influenced the publisher community: NPG, F1000, GigaScience, Mozilla Science, Elsevier all have RO activities -- ROs won the Vision award in the 2nd Beyond the PDF International Conference -- RO principles are being incorporated in the EU RI ELIXIR interoperability workplan and the Force11.org Organisation. -- We have been invited to give numerous keynotes on ROs. |
| URL | http://www.researchobject.org |
| Title | WorkflowHub |
| Description | WorkflowHub is a Computational Workflow registry that is workflow management system agnostic, where workflows may remain in their native repositories in their native forms. It has been sponsored by a collection of European projects including Synthesys+, EOSC-Life, IBISBA and BioExcel. Although developed for Life Sciences it is discipline agnostic. It is based on the FAIRDOM-SEEK platform. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | An open community of 50+ participants from 10 countries work together to co-develop the Hub. To respond to the COVID-19 crisis the Hub was established and launched 6 months early in April 2021 to support the sharing of COVID-19 processing pipelines. It had its beta release in Sept 2021. It is incorporated into the ELIXIR European Research Infrastructure for Life Science data Tools ecosystem, is a registered resource in the European Open Science Cloud Portal and an official service of ELIXIR-UK The registry is now part of the EU COVID Data Portal https://www.covid19dataportal.org and was highlighted as the prime success by the review panel of EOSC-Life. It currently has 194 well curated workflows from 10 different systems and 249 contributors, 84 teams |
| URL | https://workflowhub.eu |
| Title | FAIRDOMHub |
| Description | The FAIRDOMHub is a public data and model management "Commons" resource for Systems Biology Projects. It is based on the openSEEK Software Platform. It is hosted at Heidelberg Institute for Theoretical Studies. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Previous to January 2016 the Hub specifically supported the ERANets SysMO and ERASysBio+. In January 2016, as a result of the BBSRC DMMCore project (along with contributions from BMBF and SystemX) the Commons is now open to all researchers. 58 projects are currently registered on FAIRDOMHub along with over 700 researchers from 193 institutions |
| URL | http://www.fairdomhub.org |
| Title | WorkflowHub |
| Description | WorkflowHub is a Computational Workflow registry that is workflow management system agnostic, where workflows may remain in their native repositories in their native forms. It has been sponsored by a collection of European projects including Synthesys+, EOSC-Life, IBISBA and BioExcel. Although developed for Life Sciences it is discipline agnostic. It is based on the FAIRDOM-SEEK platform. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | An open community of 49 participants from 10 countries work together to co-develop the Hub. To respond to the COVID-19 crisis the Hub was established and launched 6 months early in April 2021 to support the sharing of COVID-19 processing pipelines. It had its beta release in Sept 2021 and is already incorporated into the ELIXIR European Research Infrastructure for Life Science data Tools ecosystem. The registry is now part of the EU COVID Data Portal https://www.covid19dataportal.org and was highlighted as the prime success by the review panel of EOSC-Life. It currently has 83 well curated workflows from 5 different systems and 110 contributors. |
| URL | https://workflowhub.eu |
| Description | Centre for Digital Life, Norway |
| Organisation | Norwegian University of Life Sciences (NMBU) |
| Country | Norway |
| Sector | Academic/University |
| PI Contribution | FAIRDOMHub and software adopted as platform adopted by the Centre for Digital Life and a range of Norwegian Systems Biology Projects: GenoSysFat, DigiSal, NbioPharm and DCod national projects, supported by FAIRDOM team. |
| Collaborator Contribution | Adopted Plans to use FAIRDOM as the recommended data management resource for all of the Norwegian Digital Life projects. This is 6 projects in the first round, with an additional grouping of projects to be announced in 2017 Pathway to partnership with ELIXIR-Norway who provide the NELS data platform for the Digital Life projects. This may well lead to new funding and a longer term partnership. The successful adoption of our platform by DigiSal has been a route to ELIXIR-Norway/NMBU becoming a FAIRDOM Facility. Participants in the FAIRDOM Knowledge Hub Expected to become members of FAIRDOM Association e.V. |
| Impact | See the contributions arising from the SysMO-DB1, SysMO-DB2 and DMMCore BBSRC awards. https://f1000research.com/articles/7-968/v1 Multi-disciplinary (systems biology) |
| Start Year | 2015 |
| Description | ELIXIR |
| Organisation | ELIXIR |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | ELIXIR UK is the National Node for the ELIXIR Europe Research Infrastructure. In new work we are developjng a workflow colaboratory for European Life Sciences in the EOSC Life Cluster project. This is based on myExperiment (developed with the myGrid platform), the Common workflow Language and based on the FAIRDOM-SEEK platform developed by the DMMCore project. |
| Collaborator Contribution | An extensive cooperation across Europe for Research Data in Life Sciences, an intergovernmental infrastructure of 21 nation states represented by National Nodes. ELIXIR-UK co-leads TWO of the five Platforms - Interoperability and Training. We chair the Training Coordinators Group, run the Training portal and pioneered train the trainer and carpentry workshops across the National Nodes. In interoperability we lead the Bioschemas.org metadata markup initiative across the nodes, identifier services workflow interoperability. The Node participates in numerous cross-node cooperations and has won funds for 5 Implementation studies channelling funds to its members. |
| Impact | An extensive cooperation across Europe for Research Data in Life Sciences, an intergovernmental infrastructure of 21 nation states represented by National Nodes. ELIXIR-UK co-leads TWO of the five Platforms - Interoperability and Training. We chair the Training Coordinators Group, run the Training portal and pioneered train the trainer and carpentry workshops across the National Nodes. In interoperability we established the Bioschemas.org metadata markup initiative across the nodes, identifier services workflow interoperability. The Node participates in numerous cross-node cooperations and has won funds for 5 Implementation studies channelling funds to its members. Through this partnership Node members are beneficiaries in EU H2020 INFRA projects: CORBEL, EXCELERATE, EOSCpilot |
| Start Year | 2013 |
| Description | ELIXIR |
| Organisation | ELIXIR |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | ELIXIR UK is the National Node for the ELIXIR Europe Research Infrastructure. In new work we are developjng a workflow colaboratory for European Life Sciences in the EOSC Life Cluster project. This is based on myExperiment (developed with the myGrid platform), the Common workflow Language and based on the FAIRDOM-SEEK platform developed by the DMMCore project. |
| Collaborator Contribution | An extensive cooperation across Europe for Research Data in Life Sciences, an intergovernmental infrastructure of 21 nation states represented by National Nodes. ELIXIR-UK co-leads TWO of the five Platforms - Interoperability and Training. We chair the Training Coordinators Group, run the Training portal and pioneered train the trainer and carpentry workshops across the National Nodes. In interoperability we lead the Bioschemas.org metadata markup initiative across the nodes, identifier services workflow interoperability. The Node participates in numerous cross-node cooperations and has won funds for 5 Implementation studies channelling funds to its members. |
| Impact | An extensive cooperation across Europe for Research Data in Life Sciences, an intergovernmental infrastructure of 21 nation states represented by National Nodes. ELIXIR-UK co-leads TWO of the five Platforms - Interoperability and Training. We chair the Training Coordinators Group, run the Training portal and pioneered train the trainer and carpentry workshops across the National Nodes. In interoperability we established the Bioschemas.org metadata markup initiative across the nodes, identifier services workflow interoperability. The Node participates in numerous cross-node cooperations and has won funds for 5 Implementation studies channelling funds to its members. Through this partnership Node members are beneficiaries in EU H2020 INFRA projects: CORBEL, EXCELERATE, EOSCpilot |
| Start Year | 2013 |
| Description | EMSL - Pacific Northwest National Laboratory, USA |
| Organisation | U.S. Department of Energy |
| Department | Pacific Northwest National Laboratory |
| Country | United States |
| Sector | Public |
| PI Contribution | Our FAIRDOM Platform (SEEK4Science and openBIS) funded by the BBSRC SysMODB1, SysMODB2 and DMMCore recommended for adoption by the EMSL Facility for their data and model management. |
| Collaborator Contribution | Recruiting a FAIRDOM developer to help with our development Associate member of FAIRDOM and member of the Samples Club, member of FAIRDOM Developers Forum Steven Wiley serves on our SAB; Inaugural FAIRDOM webinar speaker |
| Impact | See outcomes of BB/M013189/1 DMMCore: Data and Model Management Core for ERASysAPP & Europe |
| Start Year | 2015 |
| Description | ETH Zurich Center for Information Sciences and Databases |
| Organisation | ETH Zurich |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Partners in the DMMCore project - now called FAIRDOM (http://www.fair-dom.org) Within ERANET ERASysAPP, the data and model management efforts started during ERANets SysMO1 and ERASysBIO and further developed during SysMO2, were applied in the research projects. Additionally, a combined EU RI ISBE / ERASysAPP Data and Model Management Project was funded by BMBF, SystemsX and BBSRC. This project "FAIRDOM" (www.fair-dom.org) was funded to support the ERASysAPP research groups and to establish a European one stop infrastructure which bundles data and model management expertise and offers support in this field as well as to train future data managers and coordinate further tool developments in data management systems. |
| Collaborator Contribution | Contribute the openBIS data management platform to the FAIRDOM Infrastructure. Full partners in the development and delivery of the data and model management platform and support for users. |
| Impact | See outcomes of BB/M013189/1 DMMCore: Data and Model Management Core for ERASysAPP & Europe |
| Start Year | 2014 |
| Description | Heidelberg Institute for Theoretical Studies |
| Organisation | Heidelberg Institute for Theoretical Studies |
| Country | Germany |
| Sector | Charity/Non Profit |
| PI Contribution | HITS are our partners in the SysMO-DB and SysMO-DB2 projects. We were both funded under the ERANet SysMO; them by BMBF, us by BBSRC. Partners in the DMMCore project - now called FAIRDOM (http://www.fair-dom.org) Within ERANET ERASysAPP, the data and model management efforts started during ERANets SysMO1 and ERASysBIO and further developed during SysMO2, were applied in the research projects. Additionally, a combined EU RI ISBE / ERASysAPP Data and Model Management Project was funded by BMBF, SystemsX and BBSRC. This project FAIRDOM; (www.fair-dom.org) was funded to support the ERASysAPP research groups and to establish a European one stop infrastructure which bundles data and model management expertise and offers support in this field as well as to train future data managers and coordinate further tool developments in data management systems. |
| Collaborator Contribution | See the contributions arising from the SysMO-DB1, SysMO-DB2 and DMMCore BBSRC awards. HITS are our co-development partners of the SEEK4Science Data and Model Management platform, associated software and curation, and co-partners in the delivery of the FAIRDOM data and model stewardship programme. HITS co-founded the FAIRDOM Association e.V, the not for profit set up to run FAIRDOM's products and services |
| Impact | See the outputs and outcomes arising from the SysMO-DB1 and SysMO-DB2 BBSRC awards. See outputs and outcomes from BB/M013189/1 DMMCore: Data and Model Management Core for ERASysAPP and Europe |
| Start Year | 2008 |
| Description | ISBE Light: Infrastructure for Systems Biology in Europe |
| Organisation | Infrastructure for Systems Biology Europe |
| Country | European Union (EU) |
| Sector | Learned Society |
| PI Contribution | ISBE aims to develop the social, technical and physical infrastructure to support Systems Biology. Its preparatory stage ran from Aug 2012 to Aug 2015, and it has now entered its "interim" ISBE-Light phase of construction with a best effort to operate three pillars: stewardship, training and modelling services. In the prep phase FAIRDOM: ran the work package on Data and Model Management; authored the ISBE data and model management capability framework and strategy which includes the support of a project Commons - now the FAIRDOMHub; authored the ISBE 12 Recommendations for data and model management that form the core of the data management recommendations for ERASysAPP beyond the 5 year funding period (ERASysAPP D4.7); contributed to EU's Targeted Stakeholders' Consultation on Long Term Sustainability of Research Infrastructures (January 2016); and co-authored the ISBE Business Case. FAIRDOM components were showcased in the ISBE publication "Success Stories in Systems Biology": SEEK, Virtual Liver Network and JWS Online. We attended 22 ISBE meetings during the lifetime of FAIRDOM. FAIRDOM is a core component of the interim phase ISBE Light as the stewardship pillar which was fundamental to the ISBE Business Case (ratified Jan 2016). We work with ISBE-spain to make an integrated online presence by linking the FAIRDOMHub's Yellow Pages "people commons" with the ISBE Community portal and offering complementary content. FAIRDOM serves on the ISBE-Light Management Committee and we represent ISBE at international meeting such as the Technology Track ISMB2015 (Dublin 2015, ~50 session attendees) and the ISBE booth at the BioMedBridges workshop (Nov 2015, ~200 registered participants). ISBE-Light has a hub and spoke model of national nodes funded by national funds and on national roadmaps. FAIRDOM is working with ISBE in two directions: 1. Through ISBE's national funder's effort to secure national funds 2. With emerging ISBE national nodes as FAIRDOM Facilities. |
| Collaborator Contribution | The ISBE Intergovernmental Working Group (IWG) is the funders group working top down at the government level to negotiate financial support for ISBE and secure a MoU with nation states to contribute to a central hub. Currently 9 countries are in discussion. This is a potential funding source for FAIRDOM. Emerging ISBE national nodes are potential FAIRDOM Facilities The Netherlands and Slovenia have succeeded in putting ISBE on their national roadmaps. They are applying for national funding and are active in project and proposal consortia. These nodes can act as delivery partners for the FAIRDOM Association |
| Impact | ISBE.nl and ISBE.si ISBE nodes are partnering with FAIRDOM and have adopted the FAIRDOMHub platform to support their projects. |
| Start Year | 2015 |
| Description | ISBE.nl |
| Organisation | Infrastructure for Systems Biology Europe |
| Department | Infrastructure for Systems Biology Europe Netherlands |
| Country | Netherlands |
| Sector | Learned Society |
| PI Contribution | ISBE.nl is the Dutch ISBE node, led by the VU and Wageningen, both FAIRDOMHub users. ISBE.nl has recently adopted FAIRDOMHub as its data and model stewardship resource. It is the systems biology model services partner in the EU CORBEL (Horizon 2020 INFRADEV-4-2014-2015, 654248) project which seeks to establish cross- research infrastructure cooperation and interoperability for the 14 RIs in the biomedical sector. CORBEL has recently concluded an open call for Pilots that includes 9 using ISBE services through ISBE.nl. FAIRDOM Webinars are included on the CORBEL training portal. https://www.on-course.eu). |
| Collaborator Contribution | ISBE.nl is the Dutch ISBE node, led by the VU and Wageningen, both FAIRDOMHub users. ISBE.nl has recently adopted FAIRDOMHub as its data and model stewardship resource. It is the systems biology model services partner in the EU CORBEL (Horizon 2020 INFRADEV-4-2014-2015, 654248) project which seeks to establish cross- research infrastructure cooperation and interoperability for the 14 RIs in the biomedical sector. CORBEL has recently concluded an open call for Pilots that includes 9 using ISBE services through ISBE.nl. FAIRDOM Webinars are included on the CORBEL training portal. https://www.on-course.eu). |
| Impact | ISBE.nl has recently adopted FAIRDOMHub as its data and model stewardship resource. |
| Start Year | 2017 |
| Description | Leiden University |
| Organisation | Leiden University |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Leiden are our co-development partners of the metadata platform for the SEEK4Science Data and Model Management platform, associated software and curation, and co-partners in the delivery of the FAIRDOM data and model stewardship programme. |
| Collaborator Contribution | Leiden are our co-development partners of the metadata platform for the SEEK4Science Data and Model Management platform, associated software and curation, and co-partners in the delivery of the FAIRDOM data and model stewardship programme in the Netherlands. Representatives of the DTL (Dutch TechCentre for Lifesciences). |
| Impact | See outcomes of SysMO-DB2 and BB/M013189/1 DMMCore: Data and Model Management Core for ERASysAPP; Europe |
| Start Year | 2013 |
| Description | National Institute of Biology, Slovenia |
| Organisation | National Institute of Biology |
| Country | Slovenia |
| Sector | Charity/Non Profit |
| PI Contribution | ISBE.si is based at the National Institute of Biology. They are integrating their pISA data platform with our FAIRDOMHub and building web-lab assays to support data management from the experimental design till modeling and simulations and the pre-processing of the data before they can enter the modeling stage. They also cooperating with FAIRDOM on training. We are cooperating on supporting Systems Biology projects in Slovenia in funding programmes such as ERA CoFund ERACoBioTech. We aim that Slovenia will join the FAIRDOM Association e.V in 2017 |
| Collaborator Contribution | ISBE.si is based at the National Institute of Biology. They are integrating their pISA data platform with the FAIRDOMHub and building web-lab assays to support data management from the experimental design till modeling and simulations and the pre-processing of the data before they can enter the modeling stage. They also cooperating with FAIRDOM on training. |
| Impact | - An integrated pISA data platform with the FAIRDOMHub - web-lab assays to support data management - training materials |
| Start Year | 2016 |
| Description | New Forest Ventures Ltd (NFVL) |
| Organisation | New Forest Ventures Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | A UK marketing consultancy in the life science IT marketplace with expertise in positioning products, software and marketing. NFVL were contacted to develop FAIRDOM's sustainability and marketing plans and prepared the Articles of Association for the favoured legal entity FAIRDOM Association. NFVL are a Founding member of the Association |
| Collaborator Contribution | A UK marketing consultancy in the life science IT marketplace with expertise in positioning products, software and marketing. NFVL were contacted to develop FAIRDOM's sustainability and marketing plans and prepared the Articles of Association for the favoured legal entity FAIRDOM Association. NFVL are a Founding member of the Association |
| Impact | FAIRDOM Association e.V. |
| Start Year | 2016 |
| Description | Oxford eResearch Centre |
| Organisation | University of Oxford |
| Department | Oxford E-Research Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | - For the FAIRDOM project (BBSRC SysMO-DB1, SysMO-DB2, DMMCore) we use the OeRC ISA Structure as the backbone of the SEEK4Science software we use for the FAIRDOMHub Commons. - For ELIXIR-UK, OeRC are partners in metadata interoperability services, notably Biosharing.org |
| Collaborator Contribution | - For the FAIRDOM project (BBSRC SysMO-DB1, SysMO-DB2, DMMCore) we use the OeRC ISA Structure as the backbone of the SEEK4Science software we use for the FAIRDOMHub Commons. Co-developing ISA2 - For ELIXIR-UK, OeRC are partners in metadata interoperability services, notably Biosharing.org |
| Impact | see outcomes of: SysMO-DB2, DMMCore: Data and Model Management Core for ERASysAPP & Europe, and Delivering ELIXIR-UK |
| Start Year | 2008 |
| Description | Research Object |
| Organisation | researchobject.org |
| Sector | Charity/Non Profit |
| PI Contribution | researchobject.org is a grass roots community to develop and disseminate Research Objects, their concept, adoption, and other latest developments. It was established by Prof Goble's e-Science group and is now a global community with academic and commercial members. |
| Collaborator Contribution | The community have developed specifications, implementations and run a series of international workshops. |
| Impact | Specifications of Research Objects, including RO-Crate http://www.researchobject.org/2019-11-15-ro-crate-1-0/ funding from Elsevier, incorporation into data repositories (DataVerse, Mendeley Data) and the NIH Data Commons Core to the development of the workflow collaboratory for the EOSCLife project (European Open Science Cloud Life). A component of the EU EOSC FAIR Digital Object Framework Multidisciplinary - chiefly the life sciences, biodiversity and computer science |
| Start Year | 2013 |
| Description | Rostock |
| Organisation | University of Rostock |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Aligned CombineArchive with Research Objects BiVes model visualisation tool integrated into SEEK SED-ML script database for storing simulation descriptions that reproduce figures in scientific journals. Hosted Martin Scharm from Rostock at Manchester, UK, 18 May-24 July 2015 Co-organised our ERASysAPP Workshop Reproducible and Citable Data and Models, 14-16 Sept 2015, Rostock, Germany co-organised Sys Bio Developers Foundry, Developers Forum, Heidelberg, Germany, 6-7 October 2014 Established a dedicated Rostock training platform |
| Collaborator Contribution | Aligned CombineArchive with Research Objects BiVes model visualisation tool integrated into SEEK SED-ML script database for storing simulation descriptions that reproduce figures in scientific journals. Martin Scharm visited from Rostock at Manchester, UK, 18 May-24 July 2015 Co-organised our ERASysAPP Workshop Reproducible and Citable Data and Models, 14-16 Sept 2015, Rostock, Germany co-organised Sys Bio Developers Foundry, Developers Forum, Heidelberg, Germany, 6-7 October 2014 |
| Impact | CombineArchive with Research Objects https://sems.uni-rostock.de/2015/09/webcat-exports-research-objects/ COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon and Nicolas Le Novère, BMC Bioinformatics201415:369, DOI: 10.1186/s12859-014-0369-z Martin Peters, Johann J. Eicher, Dawie van Niekerk, Dagmar Waltemath and Jacky L. Snoep (2017). "The JWS online simulation database". Bioinformatics. doi: 10.1093/bioinformatics/btw831 Co-organised our ERASysAPP Workshop Reproducible and Citable Data and Models, 14-16 Sept 2015, Rostock, Germany, https://www.erasysapp.eu/standardsworkshop2015 |
| Start Year | 2012 |
| Description | SB ScienceManagement UG (haftungsbeschränkt) (SBSM) |
| Organisation | SB Science Management UG |
| Country | Germany |
| Sector | Private |
| PI Contribution | A Germany consultancy specialising in project management and consulting for third party funding to researchers, institutions and industrial partners with focus on systems and synthetic biology. SBSM advised on and undertook the administrative processes of incorporating the FAIRDOM Association e.V. in Germany and act as our office. We offer them a training platform and partnerships in future proposals. |
| Collaborator Contribution | SBSM advised on and undertook the administrative processes of incorporating the FAIRDOM Association e.V. in Germany and act as our office. This work was undertaken pro bono. SBSM plan FAIRDOM training services and led OBTAIN grant proposal we were a partner of. We plan collaborations on training services and H2020 proposal development. SBSM coordinate the CHARME COST Action |
| Impact | Incorporated the FAIRDOM Association e.V. in Germany and act as our office. New proposals being developed |
| Start Year | 2016 |
| Description | SYNBIOCHEM Centre |
| Organisation | University of Manchester |
| Department | Synthetic Biology Research Centre for Synthetic Biology of Fine and Speciality Chemicals |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Centre has adopted the FAIRDOM-openSEEK platform and running an on-site independent Hub installation with FAIRDOM's assistance. They have joined the FAIRDOM Developers Forum |
| Collaborator Contribution | The Centre has adopted the FAIRDOM-openSEEK platform and running an on-site independent Hub installation with FAIRDOM's assistance. They have funded a full-time FTE to assist with on-boarding FAIRDOM into the Centre They have joined the FAIRDOM Developers Forum |
| Impact | A Synthetic Biology configured FAIRDOM openSEEK platform RA Le Feuvre, P Carbonell, A Currin, M Dunstan, D Fellows, AJ Jervis, NJW Rattray, CJ Robinson, N Swainston, M Vinaixa, A Williams, C Yan, P Barran, R Breitling, GG Chen, JL Faulon, C Goble, R Goodacre, DB Kell, J Micklefield, NS Scrutton, P Shapira, E Takano, NJ Turner, SYNBIOCHEM Synthetic Biology Research Centre, Manchester-A UK foundry for fine and speciality chemicals production, 2016, Synthetic and Systems Biotechnology Volume 1 Issue 4 Pages 271-275 |
| Start Year | 2014 |
| Description | SynthSys Centre, UK |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Our FAIRDOM Platform (SEEK4Science and openBIS) funded by the BBSRC SysMODB1, SysMODB2 and DMMCore recommended for adoption by the Synthsys Centre for their data and model management. Practical evaluation of SEEK and OpenBIS for biological data management in SynthSys; first report (https://www.era.lib.ed.ac.uk/handle/1842/12236) |
| Collaborator Contribution | Millar's Group at the SynthSys Centre, UK, http://www.synthsys.ed.ac.uk/ Users and members of the FAIRDOM Programme, adopting the FAIRDOM platform and contributing to the Knowledge Network. Integrating SEEK with DSpace Institutional Repository Members of the Developers Forum, Samples Club, Sys Bio Developers Foundry, Developers Forum Andrew Millar serves on the FAIRDOM SAB Andrew Millar co-established the Not for profit FAIRDOM Association e.V. and serves as the vice chair SynthSys co-founded the UK SynBio Data Club established by FAIRDOM |
| Impact | Practical evaluation of SEEK and OpenBIS for biological data management in SynthSys; first report (https://www.era.lib.ed.ac.uk/handle/1842/12236) See outcomes of BB/M013189/1 DMMCore: Data and Model Management Core for ERASysAPP and Europe |
| Start Year | 2014 |
| Description | The Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia |
| Organisation | Russian Academy of Sciences |
| Department | Siberian Branch |
| Country | Russian Federation |
| Sector | Academic/University |
| PI Contribution | Prof. Kolchanov uses the FAIRDOM SEEK platform to manage data from German-Russian cooperation projects, in particular the Glycon project. The SEEK helps them to run distributed projects. The most important plus is the exchange of experimental procedures, resulting data and models. They also use SEEK for educational purposes at the Faculty of Natural Science in the Novosibirsk State University. Over the years, Novosibirsk has attracted further users of the SEEK platform. FAIRDOM Hub now has 2 projects with 4 Russian partners. We will continue to provide teaching at Russian summer schools for attracting additional users to the FAIRDOMHub. |
| Collaborator Contribution | Contributions to FAIRDOM: training and summer schools, and advocacy |
| Impact | See outcomes of DMMCore. Many summer schools. for example: 8th Young Scientists School "Systems biology and Bioinformatics" held on 22-25th August 2016 in Novosibirsk, Russia. http://conf.bionet.nsc.ru/sbb2016/wp-content/uploads/sites/8/2016/08/Programma-4.pdf ) (110 participants). |
| Start Year | 2014 |
| Description | U Stellenbosch, SA |
| Organisation | University of Stellenbosch |
| Country | South Africa |
| Sector | Academic/University |
| PI Contribution | Long term partners in the SysMO-DB1, SysMO-DB2 and DMMCore BBSRC funded projects. The programme is now called FAIRDOM. Within ERANET ERASysAPP, the data and model management efforts started during ERANets SysMO1 and ERASysBIO and further developed during SysMO2, were applied in the research projects. Additionally, a combined EU RI ISBE / ERASysAPP Data and Model Management Project was funded by BMBF, SystemsX and BBSRC. This project "FAIRDOM" (www.fair-dom.org) was funded to support the ERASysAPP research groups and to establish a European one stop infrastructure which bundles data and model management expertise and offers support in this field as well as to train future data managers and coordinate further tool developments in data management systems. |
| Collaborator Contribution | Stellenbosch provide the model curation and the JWS Online model simulation platform fully integrated into the FAIRDOM Software Platform SEEK4Science (http://www.seek4science.org), and the FAIRDOM Web-based Community Commons FAIRDOMHub (http://www.fairdomhub.org) |
| Impact | Numerous. See BBSRC SysMO-DB1, SysMO-DB2 and DMMCore Grant awards |
| Start Year | 2008 |
| Description | University of Zurich (UZH) |
| Organisation | University of Zurich |
| Department | Department of Biochemistry |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | Partners in the DMMCore project - now called FAIRDOM (http://www.fair-dom.org) Within ERANET ERASysAPP, the data and model management efforts started during ERANets SysMO1 and ERASysBIO and further developed during SysMO2, were applied in the research projects. Additionally, a combined EU RI ISBE / ERASysAPP Data and Model Management Project was funded by BMBF, SystemsX and BBSRC. This project "FAIRDOM" (www.fair-dom.org) was funded to support the ERASysAPP research groups and to establish a European one stop infrastructure which bundles data and model management expertise and offers support in this field as well as to train future data managers and coordinate further tool developments in data management systems. |
| Collaborator Contribution | Contribute the openBIS data management platform to the FAIRDOM Infrastructure. Full partners in the development and delivery of the data and model management platform and support for users. |
| Impact | See entry BB/M013189/1 DMMCore: Data and Model Management Core for ERASysAPP & Europe |
| Start Year | 2014 |
| Title | FAIRDOMHub |
| Description | The FAIRDOMHub is a Public Hub managed and supported by the FAIRDOM consortium. It is a web-accessible registry for storing, sharing and publishing research assets of biology projects. The assets include FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models. FAIRDOMHub includes special support for the Systems Biology community. It is an instance of the FAIRDOM-SEEK platform. FAIRDOMHub enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2010 |
| Open Source License? | Yes |
| Impact | 2031 people registered, 273 projects hosted, 469 institutions registered, support for 122 programmes including: ISBE.NL, Covid-19 disease map - Bioinformatics analysis and computational modelling, nfdi4health - German National Research Data Infrastructure for Personal Health Data, Center for Digital Life Norway, ERA CoBioTech, ERA SysAPP and ERA SysBio. Hosts the PlasMo archive after that project lost its funding and the international COVID-19 Disease Map consortium. hosts 3821 Datafiles, 622 models and 432 Standard operating procedures from 416 scientific investigations. FAIRDOMHub is a registered service of the ELIXIR-DE national node and a service of the ELIXIR European Research Infrastructure for Life Science Data. |
| URL | https://fairdomhub.org |
| Title | IBISBAHub |
| Description | IBISBA is designed to accelerate end-to-end bioprocess development, linking best-in-class R&D facilities to provide seamless multi-technology services. Focusing on the different R&D phases in bioprocess development, IBISBA offers services related to computer-assisted design of biocomponents, construction of enzymes and microbial strains, the fermentation, downstream processing and project knowledge asset management. IBISBAHub is a asset repository, workflow and SOP library and Trans National Access outputs repository for the IBISBA European Research Infrastructure IBISBA. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | THe IBISBAHub forms a central component of the EU ESFRI EU-IBISBA digital infrastructure |
| URL | https://hub.ibisba.eu/ |
| Title | JWS Online |
| Description | JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models. It was also developed in SysMO-DB2 award and continues to be developed in the DMMCore award. |
| Type Of Technology | Webtool/Application |
| Impact | JWS Online is associated with the FEBS journal - models to be published are held in JWS Online Construct your own model With the new JWS Online model builder you can build a model from scratch using a simple interface. Models can be simulated directly in the JWS Online simulator. The builder adheres very closely to the SBML model specification and supports the MIRIAM and SBO standards for annotation, and provides a useful online annotation tool. Simulate models Simulate curated kinetic models from the JWS Online database, or non-curated models built or uploaded to JWS Online. JWS Online supports time evolutions, steady-state simulations, structural analysis, metabolic-control analysis, parameter scans, and reaction plots. SBML compliant JWS Online now uses a database implementation with a native format that mirrors the SBML specification. This minimises changes in SBML structure during the upload-edit-save cycle. JWS Online supports uploading and modification of existing models in SBML or JWS format. Martin Peters, Johann J. Eicher, Dawie van Niekerk, Dagmar Waltemath and Jacky L. Snoep (2017). "The JWS online simulation database". Bioinformatics. doi: 10.1093/bioinformatics/btw831 |
| URL | http://jjj.biochem.sun.ac.za/ |
| Title | Just Enough Results Model |
| Description | The JERM describes the relationships between data, models, SOPs, samples, specimens and publications for Systems Biology. It is used as part of the SEEK4Science Platform which in turn is the basis of the metadata for the FAIRDOM platform which in turn is the basis of the FAIRDOMHub Commons for Systems Biology projects and for over 30 other projects using the FAIRDOM platform in their own installations. The JERM It adheres to the ISA de facto standard for organising investigations, studies and assays. It was started in the SysMO-DB1 award, developed further in the SysMO-DB2 award and continues to be developed in the DMMCore award. JERM 2.0 was released in Sept 2017. |
| Type Of Technology | Software |
| Year Produced | 2008 |
| Open Source License? | Yes |
| Impact | It is used as part of the SEEK4Science Platform metadata infrastructure and is feeding into the European Open Science Cloud Pilot (EOSCpilot) Data Catalogue interoperability EDMI minimum information model. |
| URL | http://jermontology.org/ |
| Title | RightField |
| Description | RightField is an open-source tool for adding ontology term selection to Excel spreadsheets. RightField is used by a 'Template Creator' to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. RightField was started in the SysMO-DB1 award, developed further in the SysMO-DB2 award and continues to be developed in the DMMCore award |
| Type Of Technology | Software |
| Year Produced | 2010 |
| Open Source License? | Yes |
| Impact | Rightfield is used as part of the Extract-Transform-Load pipeline for the FAIRDOM SEEK platform used by the SysMO-DB BBSRC projects. It has been downloaded over 620 times. The RightField platform has been adopted in archeaology, cultural studies and environmental sciences. It forms the basis of the Populous Ontology development tool, developed by Manchester and the EBI. |
| URL | http://www.rightfield.org.uk |
| Title | SEEK4Science / FAIRDOM-SEEK |
| Description | The SEEK platform is a web-based resource for sharing heterogeneous scientific research datasets,models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved. Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology. SEEK is incorporating semantic technology allowing sophisticated queries over the data, yet without getting in the way of your users. |
| Type Of Technology | Software |
| Year Produced | 2009 |
| Open Source License? | Yes |
| Impact | The SEEK4Science platform was adopted by the all of the ERANet SysMO I and II projects it was designed for and has gone on to be widely adopted in other programmes, notably the German Virtual Liver Network and its follow-on Liver Systems Medicine project, ERANet's ERASysBio+ projects, and ERASysAPP. The Platform is now developed under the FAIRDOM Initiative (funded by the DMMCore project partners, including the BBSRC) http://www.fair-dom.org, were it has been rebadged as FAIRDOM-SEEK The software platform has been independently adopted by 140+ groups in Europe, Russia, South Africa, USA, and the UK. EU Projects that adopt the platform include: include the German Systems Medicine for Liver project and the de.NBI German Bioinformatics Network, the Leipzig Health Atlas, the University Medical Center Gottingen and the CESGO research sharing platform. The platform has been adopted by the Environmental Molecular Sciences Laboratory a large national scientific user facility at Pacific Northwest National Laboratory (PNNL) in Washington State, USA. Since 2017 there have been over 10K Docker image downloads FAIRDOMHub.org Commons is a centralised public community instance of the SEEK4Science Platform (see FAIRDOMHub entry). Work on the SEEK directly lead to participation in the ESFRI Research Infrastructure ISBE Light - Infrastructure for Systems Biology Europe, and the ESFRI IBISBA for Industrial Biotechnology (see IBISBAHub entry). The SEEK is also used for project asset management by 6 ELIXIR Nodes and forms the platform for WorkflowHub (see WorkflowHub entry). the SEEK is now managed by a Collective of ELIXIR Nodes (UK, BE, NL, DE, NO) and Stellenbosch University SA. Commercially, SEEK was the prototype component of Eagle Genomics Ltd's eaglecore platform and adopted by GeneXplain . Practical evaluation of SEEK and openBIS for biological data management in SynthSys; first report (https://www.era.lib.ed.ac.uk/handle/1842/12236) recommended the platform. Wruck et al. Data management strategies for multinational large-scale systems biology projects. Briefings in Bioinformatics 2012 stated that Out of the box it provides the most useful features for large scale biology projects. |
| URL | http://www.seek4science.org |
| Title | WorkflowHub |
| Description | WorkflowHub is a Computational Workflow registry that is workflow management system agnostic, where workflows may remain in their native repositories in their native forms. It has been sponsored by a collection of European projects including Synthesys+, EOSC-Life, IBISBA and BioExcel. Although developed for Life Sciences it is discipline agnostic. It is based on the FAIRDOM-SEEK platform. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | An open community of 50+ participants from 10 countries work together to co-develop the Hub. To respond to the COVID-19 crisis the Hub was established and launched 6 months early in April 2021 to support the sharing of COVID-19 processing pipelines. It had its beta release in Sept 2021. It is incorporated into the ELIXIR European Research Infrastructure for Life Science data Tools ecosystem, is a registered resource in the European Open Science Cloud Portal and an official service of ELIXIR-UK The registry is now part of the EU COVID Data Portal https://www.covid19dataportal.org and was highlighted as the prime success by the review panel of EOSC-Life. It currently has 194 well curated workflows from 10 different systems and 249 contributors, 84 teams |
| Title | myExperiment |
| Description | Public repository for retaining and sharing scientific workflows. Social sharing platform. myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2008 |
| Open Source License? | Yes |
| Impact | First and arguably only public sharing platform for any workflow system. Over 1000 citations (combined, google scholar) of myExperiment papers. on 12/03/2017 myExperiment has: 10633 registered members, 393 groups, 3894 workflows, 1238 files, 479 packs Used by many EU projects (e.g. BioVeL, SCAPE, HELIO, VPH, IBISBA), US (e.g. FLOSS), companies (e.g. RapidMiner, KNIME) and open platforms (Galaxy) as their workflow repository. over 22 workflow systems represented in repository. In 2018 was proposed by the EU Research Infrastructure ELIXIR as the registry for the European Open Science Cloud. in 2019 four EU projects - BioExcel2, EOSC Life, Synthesys+ and IBISBA1.0 - have pooled together to redevelop myExperiment into myExperiment 2.0 based on the FAIRDOM-SEEK (SEEK4Science) platform developed by the DMMCore and SysMO BBSRC awards. |
| URL | http://myexperiment.org |
| Description | Alan Turing Institute Symposium on Reproducibility, Sustainability, and Preservation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynote on What is reproducibility? Alan Turing Institute Symposium on Reproducibility, Sustainability, and Preservation, Oxford, UK, 6th-7th April 2016 Keynote |
| Year(s) Of Engagement Activity | 2016 |
| Description | COMBINE 2016 Invited talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | COMBINE is the grassroots Systems and Synthetic Biology standards organisation Invited talk FAIRDOM - FAIR Asset management and sharing experiences in Systems and Synthetic Biology COMBINE 2016, Newcastle, 19th September. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://co.mbine.org/events/COMBINE_2016 |
| Description | CaSym Winter School, March 30th 2017, Ljubljana, Slovenia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | CaSym Winter School, March 30th 2017, Ljubljana, Slovenia |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://cfgbc.mf.uni-lj.si/events/courses/2017winterschool/programme.html |
| Description | Combined CHARME - EMBnet and NETTAB 2016 Workshop on "Reproducibility, standards and SOP in bioinformatics", Rome, Italy, 25th-26th October 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Reproducibility, standards and SOP in bioinformatics Combined CHARME - EMBnet and NETTAB 2016 Workshop, October 25-26, 2016, Rome, Italy The Workshop 'Reproducibility, standards and SOP in bioinformatics' is co-organised by the COST European Action CHARME (CA15110), EMBnet (The Global Bioinformatics Network) and NETTAB (International Workshop Series on Network Tools and Applications for Biology). It is hosted by the ELIXIR-ITA Node and will be held at the Italian CNR (National Research Council) head quarter, in Rome. The workshop will be preceded by a GOBLET/ELIXIR-ITA Tutorial and a ELIXIR Hacktahon on Monday 24th and followed by the EMBnet Annual General Meeting on Thursday 27th and Friday 28th. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.igst.it/nettab/2016/ |
| Description | Dagstuhl Seminar 16041 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Research Objects, SEEK4Science and FAIRDOM. Dagstuhl Seminar 16041 Reproducibility of Data-Oriented Experiments in e-Science, 25-29 January 2016 Invited Talk and invitation only meeting 1 week long working produced a report on reproducibility |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.dagstuhl.de/en/program/calendar/semhp/?semnr=16041 |
| Description | EOSCpilot workshop How FAIR friendly is your Data Catalogue? Open Science Fair, 6-8 Sept 2017, Athens |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | EOSCpilot workshop How FAIR friendly is your Data Catalogue? Open Science Fair, 6-8 Sept 2017, Athens How FAIR friendly is your data catalogue? You are here Home Organisers Rafael Jimenez - ELIXIR, Donatella Castelli - CNR, Natalia Manola - Athena Research & Innovation Centre, Carole Goble - University of Manchester Duration 3 hours This workshop will build upon the work planned by the EOSCpilot data interoperability task and the BlueBridge workshop held on April 3 at the RDA meeting. We will investigate common mechanisms for interoperation of data catalogues that preserve established community standards, norms and resources, while simplifying the process of being/becoming FAIR. Can we have a simple interoperability architecture based on a common set of metadata types? What are the minimum metadata requirements to expose FAIR data to EOSC services and EOSC users? Workshop abstract Research communities and specially research infrastructures are making a concerted effort to homogenize, collect their (meta)data and publish them in the open through community specific data catalogues. This is a good start towards making data FAIR, but how can we ensure availability of domain specific FAIR data and data-analysis services through a common virtual research environment like the European Open Science Cloud (EOSC)? From vertical domains (e.g., research infrastructures) to horizontal approaches (e.g., OpenAIRE, DataCite) which cover national settings and libraries/repositories, we see different content, data models, interfaces, frameworks, architectures and vocabularies being used. The EOSCpilot data interoperability task aims to establish principles, propose recommendations and demonstrate how FAIR data hosted by domain specific data repositories can be exposed to EOSC to be used and reused by EOSC services and users. This workshop will build upon the work planned by the EOSCpilot data interoperability task and the BlueBridge workshop held on April 3 at the RDA meeting. We will investigate common mechanisms for interoperation of data catalogues that preserve established community standards, norms and resources, while simplifying the process of being/becoming FAIR. Can we have a simple interoperability architecture based on a common set of metadata types? What are the minimum metadata requirements to expose FAIR data to EOSC services and EOSC users? Target Audience Research Infrastructures, e-Infrastructures, libraries, policy makers, funders, researchers. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://eoscpilot.eu/events/open-science-fair-6-8-september-2017-athens/how-fair-friendly-your-data-... |
| Description | G7 Open Science Working Group |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | G7 Open Science Working Group, UKRI/BEIS appointed expert member attended meetings in 2019, 2020, 2021. |
| Year(s) Of Engagement Activity | 2019,2020,2021 |
| Description | GARNet-Egenis Big Data Workshop, Totnes, UK, 21-22 April 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | This workshop brings together prominent biologists, data scientists, database leads, publishers, representatives of learned societies and funding bodies to discuss ways of harnessing and integrating large plant data to foster discovery. Over the last decade, data infrastructures such as cloud, grids and repositories have garnered attention and funding as crucial tools to facilitate the re-use of existing datasets. This is a complex task, and within plant science a variety of strategies have been developed to collect, combine and mine research data for new purposes. This workshop aims to review these strategies, identify examples of best practices and successful re-use both within and beyond plant science, and discuss both technical and institutional conditions for effective data mining. Workshop |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://garnetcommunity.org.uk/sites/default/files/GARNetEgenis_Book.pdf |
| Description | Intelligent Systems for Molecular Biology (ISMB), Dublin. July 10th - 14th 2015. Presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | FAIR data and model management for systems biology. Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology (ECCB) Dublin. July 10th - 14th 2015. Presentation the major conference in Bioinformatics. |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://www.iscb.org/ismbeccb2015 |
| Description | Invited Webinar in an NSF series |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | USA NSF Convergence Accelerator Series Tracks A&B webinar, 19th May 2021. |
| Year(s) Of Engagement Activity | 2021 |
| URL | http://spatial.ucsb.edu/2021/Carole-Goble |
| Description | Invited talk 1st Conference of the European Association of Systems Medicine, 26-28 October 2016, Berlin |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Invited talk on FAIR Data, Operations and Model management for Systems Biology and Systems Medicine Projects 1st Conference of the European Association of Systems Medicine, 26-28 October 2016, Berlin |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://www.easym.eu/ |
| Description | Keynote - 25th Pacific Symposium in Biocomputing 2020 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynote: Building the FAIR Research Commons for Life Sciences: the pain, the glory |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://psb.stanford.edu/previous/psb20/ |
| Description | Keynote at FAIRplus Innovation and SME Forum |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | FAIRplus Innovation and SME Forum keynote, Topic: FAIR History and the Future |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://fairplus-project.eu/get-involved/SME-innovation-forum |
| Description | Keynote at Symposium: The Future of a Data-Driven Society, Maastricht University, 25 Jan 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Review: Symposium The Future of a Data-Driven Society Every day we hear about how artificial intelligence and big data technologies are changing our daily lives, and changing the world. What more will the future bring, and will society be ready for it? The conversation on 'The future of a data-driven society', was held on the day before the Dies Natalis. The event featured keynote lectures by inspiring leaders and competitions for world-changing visions and outstanding research proposals. Keynote lectures Prof. Carole Goble from the University of Manchester set out her vision on the future of science. Prof. Carole Goble emphasised the importance of sharing and publicising research data according to the FAIR principles (Findable, Accessible, Interoperable, Reusable), and demonstrated which steps she takes to do so. Prof. Lucy Suchman from Lancaster University. Prof. Lucy Suchman is an anthropologist with extensive experience and expertise relating to the interaction between people and computers. She explained her recent study into the role of robots in geriatric care, and presented a new approach to technological design within the field of healthcare. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.maastrichtuniversity.nl/events/symposium-future-data-driven-society |
| Description | Keynote: 17th Italian Research Conference on Digital Libraries (IRCDL) 2021 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 17th Italian Research Conference on Digital Libraries (IRCDL) 2021, 18th February 2021, 150+ o The swings and roundabouts of a decade of fun and games with Research Objects |
| Year(s) Of Engagement Activity | 2021 |
| URL | http://ircdl2021.dei.unipd.it/ |
| Description | Keynote: 1st First International Workshop on Reproducible Open Science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | 1st First International Workshop on Reproducible Open Science @ Theory and Practice of Digital Librarie Conference, 9 Sept 2016, Hannover, Germany. Invited Keynote What is Reproducibility? The R* brouhaha (and how Research Objects can help) |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://repscience2016.research-infrastructures.eu/ |
| Description | Keynote: FAIRe Data Infrastructures Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynote FAIRe Data Infrastructures Workshop, 15 October 2020 Title: How are we Faring with FAIR (and what FAIR is not) |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.gmds.de/aktivitaeten/medizinische-informatik/projektgruppenseiten/faire-dateninfrastrukt... |
| Description | Keynote: First virtual workshop on Research data management for Linked Open Science - DaMaLOS 2020 @ ISWC 2020 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynpte First virtual workshop on Research data* management for Linked Open Science - DaMaLOS 2020, Virtual, 02 Nov 2020 at ISWC 2020, The swings and roundabouts of a decade of fun and games with Research Objects |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://zbmed.github.io/damalos/ |
| Description | Keynote: ISWC2017 SemSci Workshop, Vienna, 21 October 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | SemSci 2017: Enabling Open Semantic Science 1st International Workshop co-located with ISWC 2017, October 2017, Vienna, Austria In the past few years, a push for open reproducible research has led to a proliferation of community efforts for publishing raw research objects like datasets, software, methodologies, etc. These efforts underpin research outcomes much more explicitly accessible. However, the actual time and effort required to achieve this new form of scientific communication remains a key barrier to reproducibility. Furthermore, scientific experiments are becoming increasingly complex, and ensuring that research outcomes become understandable, interpretable, reusable and reproducible is still a challenge. The goal of this workshop is to incentivise practical solutions and fundamental thinking to bridge the gap between existing scientific communication methods and the vision of an reproducible and accountable open science. Semantic Web technologies provide a promising means for achieving this goal, enabling more transparent and well-defined descriptions for all scientific objects required for this new form of science and communication. We are particularly interested in four kinds of contributions: Novel approaches that analyze how publications link to their described methods and research outputs Novel approaches that use the research outputs of a scientific publication to facilitate its understanding and reuse (e.g., generating explanations of results, interactive visualizations, linking to datasets and methods, etc.) Novel approaches that help comparing and relating software, datasets and methods used in different publications Novel approaches to apply Semantic Web and Linked Data techniques to scientific workflows. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://semsci.github.io/semSci2017/ |
| Description | Leiden Bioscience Lecture, 24 November 20 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Reproducibility, Research Objects and Reality, Leiden Bioscience Lecture, 24 November 2016 Research Seminar |
| Year(s) Of Engagement Activity | 2016 |
| Description | Multiscale Biology Network Springboard meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | FAIR Data and Model Management for Systems Biology (and SOPs too!) Multiscale Biology Network Springboard meeting, Nottingham. June 1st 2015. Invited talk to build links with the Multiscale Biology Network community |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://multiscalebiology.org.uk/ |
| Description | NFAIS Incorporating Research Objects in Scholarship: Greater Discoverability, Access and Use, Virtual Workshop, December 12, 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk NFAIS Incorporating Research Objects in Scholarship: Greater Discoverability, Access and Use, Virtual Workshop, December 12, 2017, Date: Tuesday, December 12, 2017 Time: 1:00 pm - 3:45 pm (EDT) Location: Virtual Half-Day Workshop For some time now, various stakeholders have started to think about and collaborate on efforts to pull enriched objects into the scholarly article through the use of identifiers-including but not limited to data sets, code, annotations, and more. In doing so, research would become more readily discoverable, reusable and reproducible, and the data and other research elements would ultimately become key components of the new scholarly record. Incorporating digital research objects requires a challenging framework that involves shared responsibilities among all stakeholders in the scholarly communications ecosystem. While discussions have been going on since as early as 2014, and the FAIR guiding principles (findable, accessible, interoperable, and re-usable) for data management were developed through stakeholder cross-collaboration, this workshop explores where we are today, what work has been done, and what is still needed to move this complex conversation forward. In this half-day virtual workshop, we will examine the researcher, publisher and discovery tool perspective, as well as the challenges and work underway to include these key components within the scholarly record. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.nfais.org/index.php?option=com_mc&view=mc&mcid=72&eventId=537176 |
| Description | Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015. The project ran this workshop with colleagues in Rostock and HITS aimed at researchers in Systems Biology The meeting spawned contact with LifeGlimmer, and also Jon Olav Vik from Norway. As a result FAIRDOM gained a new large-scale project (GenoSysFat), and also a new contributing partner which they support for data and model management (DigiSal) which led onto a close partnership with Norway's Digital Life programme and ELIXIR-Norway |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://fair-dom.org/2015/09/22/reproducible-and-citable-data-and-models-workshop/ |
| Description | SSBSS 2017, July 17 2017, Cambridge, UK 4th International Synthetic & Systems Biology Summer School |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Robinson College, University of Cambridge, UK on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results, and to interact with their peers, in a friendly and constructive environment. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://ssbss2017.taosciences.org/ |
| Description | SWAT4HCLS 2017 Keynote |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynote presentation at International Conference, SWAT4HCLS 2017, 5th Dec 2017, Rome |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.swat4ls.org/workshops/rome2017/programme/ |
| Description | Science Europe LEGS Committee: Career Pathways in Multidisciplinary Research: How to Assess the Contributions of Single Authors in Large Teams |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Crediting informatics and data folks in life science teams Science Europe LEGS Committee: Career Pathways in Multidisciplinary Research: How to Assess the Contributions of Single Authors in Large Teams, 1-2 Dec 2015, Brussels Invited Talk resulted in a report http://www.scienceeurope.org/wp-content/uploads/2016/06/SE_LEGS_Careerpaths_Workshop_Report.pdf |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.scienceeurope.org/scientific-committees/life-sciences/publications-of-the-life-sciences-c... |
| Description | Workshop on Managing Digital Research Objects in an Expanding Science Ecosystem, 15 Nov 2017, Bethesda, USA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshop - Managing Digital Research Objects in an Expanding Science Ecosystem Date: Oct 24, 2017 "Managing Digital Research Objects in an Expanding Science Ecosystem" Wednesday, November 15th, 2017 9:00 am - 5:00 pm EST Lister Hill National Center for Biomedical Communications U.S. National Library of Medicine/NIH 8600 Rockville Pike, Bethesda, MD 20894 "We are at a tipping point in the development of a common conceptual framework and set of tools and components which will revolutionize the management of scientific data." Keynote Speaker Presenting the Global Challenge Peter Wittenberg, Co-Editor of Recommendations for Implementing a Virtual Layer for Management of the Complete Life Cycle of Scientific Data Sessions on Developing Frameworks that Address the Challenge Identifiers as an integral Part of the Scholarly Record Creating and Maintaining Standards for Object Identifiers, Persistent Identifiers for Data Sets, Industry Incorporation of Identifiers Using multiple, interlinked, and evolving research artifacts to advance research Scientific Use Case Analysis, Metadata Harmonization, Linked Open Data Approach, Sustainable Environment/Actionable Data Connecting Users with Digital Research Objects Filling the Gaps and Moving the Agenda Forward |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.codata.org/news/216/62/Workshop-Managing-Digital-Research-Objects-in-an-Expanding-Science... |