SysMO-DB2

Lead Research Organisation: University of Manchester
Department Name: Computer Science

Abstract

Systems biology is a biology-based inter-disciplinary study field combining experimental investigations and computational modeling to discover emergent properties of complex interactions in biological systems. SysMO is a European trans-national funding and research initiative on 'Systems Biology of Microorganisms'. The initiative's goal is to record and describe the dynamic molecular processes that occur in microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models. Each project is made up of a consortium of European institutions and each works towards different research outcomes on a variety of microorganisms, including bacteria, archaea (single-celled microorganisms) and yeast. The environmental conditions for each organism vary, growing in culture, soil, water and animal hosts. This diversity means that there are many different kinds of models and many different types of data collected. The SysMO initiative has been divided into two phases: SysMO1 funded eleven projects and 91 institutions; SysMO2 will fund seven projects, five of which are project continuations from phase 2 (so six projects are concluded) and two of which are new. The research outcomes (models, data, procedures), and the know-how and best practice developed by the scientists, are to be managed and pooled in order to: benefit the members of the programme during the running of the projects; disseminate and publish the results to the wider scientific community; and safeguard the results after the completion of the projects that maximises the 'shelf life' and utility of data generated by SysMO. SysMO-DB is a project to build and manage an incrementally developed web-based software platform to achieve this. SysMO-DB1, funded during the first phase, begun the development of a web-based platform - called the SEEK - for cataloguing the different outcomes of the projects, archiving data, procedures and models and integrating with the different project's local data management systems, including the standardisation of the information used to describe the data and models and the handling of project spreadsheets. The SEEK also includes a social network for the SysMO members and integrates with public repositories for data, models, analyses and publications such as JWS Online (for models); SABIO-RK (for data), myExperiment (for bioinformatics data analysis pipelines) and PubMed (for publications). SysMO-DB has also developed effective practices for working with SysMO scientists through the founding of a PALs focus group of researchers who shape the developments, data standards and protocols necessary for pooling and promote SEEK adoption in their own projects. The focus of SysMO-DB1 is on supporting the current projects. SysMO-DB2 continues and extends the work to cope with SysMO-phase changes and life after beyond and after SysMO: new and terminating projects, personnel change, publication outside the consortium and long-term preservation of results. SysMO-DB2 also plans to package up the software and methods so that they can be adopted and sustained by other programmes such as EraSysBio+. EraSysBio+ is a pan-European programme for 16 Systems Biology projects. It is similar in organisation to SysMO but radically different in terms of scope. Hence it differs in the data, model and process capabilities needed. As part of widening the adoption of the SysMO-DB approach the project will support EraSysBio+ in its first 18 months. The two projects from EraSysBio+ that focus on microorganisms will be fully integrated into the SysMO-DB work programme. For the full range of EraSysBio+ projects SysMO-DB2 will instantiate a new instance of the SEEK, provide advice and help launch a PALs scheme.

Technical Summary

SysMO is a European trans-national funding and research initiative on 'Systems Biology of Microorganisms'. The initiative's goal is to record and describe the dynamic molecular processes that occur in microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models. Each project is made up of a consortium of European institutions and each works towards different research outcomes on a variety of microorganisms under a variety of conditions leading to different kinds of models and different types of data collected. Phase 1, SysMO1, funded 11 projects. In phase 2, SysMO2 funds 7 projects, 5 continuations (6 projects are terminated) and 2 new. The SysMO-DB project aims to create and deploy a lightweight, technical infrastructure in order to: (i) pool the SysMO research capacities and its members' know-how, (ii) enable dissemination of results within and between projects, between participants, and to the scientific community, and (iii) support SysMO researchers in their routine work to manage their data, models and processes. SysMO-DB, addresses challenges in 5 areas: (i) developing and releasing the SysMO-DB SEEK software platform; (ii) managing the SEEK service; (iii) defining data exchange models, controlled vocabularies and curating models; (iv) establishing a strong user community engagement through a focus group of PALS; and (v) promoting adoption and sustaining the SEEK software, service and community. SysMO-DB2 extends the work to cope with new and terminating projects changes, long-term preservation and life beyond and after SysMO. SysMO-DB2 will package up the software and methods to be adoptable by other programmes such as EraSysBio+, pan-European programme for 16 Systems Biology projects. SysMO-DB2 will instantiate an EraSysBio+ instance of the SEEK, provide advice and help launch a PALs scheme. Two micro-organism projects will be fully integrated into the SysMO-DB.

Planned Impact

SysMO-DB is about rapidly, retrospectively and sensitively creating and deploying a lightweight, technical infrastructure in order to: (i) pool the SysMO research capacities and its members' know-how, (ii) enable a seamless dissemination of results within and between projects, between participants of the model-hypothesis-experiment-model systems biology cycle, and to the scientific community, (iii) support SysMO researchers in their routine work to manage their data, models and SOPs and the data, models and SOPs relevant to their work. Currently SysMO-DB is an inward-looking, gated community. By the end of SysMO2 must be outward-looking and open to wider membership and public access in order to make the greatest impact outside the bounds of the SysMO partners. The expected outcome is an information exchange system for Systems Biology in Europe that: (i) works and is adopted and used; (ii) matches the practical needs of experimentalists and modellers and helps them work together; (iii) has a network of people who know how to use it and who spread the word about it; and (iv) is adopted by other programmes and communities. Thus the objectives of the proposal are targeted at ensuring, enabling and driving impact for many stakeholders: for the SysMO projects, for academic and industrial researchers outside the programme and for organisations and initiatives that need a similar information platform. Computer scientists will benefit from an opportunity to deploy Web 2.0 and Web 3.0 technologies in the field. The stakeholders will benefit in a number of ways. SysMO members will have a safe haven for their data, assistence and training in data and model metadata management, access to modern, labour-saviing bioinformatics technologies such as workflows, access to previously unrecognised resources and access to new techniques for data comparison, model validation etc. They will benefit from the visibility of, and access to, pooled assets and membership of a social network of researchers and their capabilities. This latter point could lead to new means of forming cooperations. The managers of public repositories will benefit from well curated assets that are suitably fit for deposition at the point of publication, and the SysMO members benefit from a new publication route. Managers and participants of similar intiatives will benefit from access to new technology and a new platform that they can deploy and adapt. Researchers outside SysMO will benefit from the secured results of SysMO. Thus the Systems Biology research community will benefit from advances in technology and knowledge for new avenues of work and collaboration. The proposal intrinsically incorporates a plan to ensure impact broadily categorised into these areas. - The platform itself for the exchange of SysMO outcomes during the initiative and the preservation of outcomes at each projects' completion - The development of the platform such that it can be readily sustained after the project ends, and readily extended and adopted by other initiatives - The PALS and programme of user engagement to ensure that the platform is fit for purpose and the SysMO community (and beyond) are capable of adopting it - A programme of dissemination of the SysMO-DB SEEK platform and the development of cooperations with key stakeholders such as the EMBL-EBI 'omics data resource managers.
 
Description The SysMO-DB2 project (http://www.sysmo-db.org) followed from SysMO-DB1. It established and continued to develop and support a data, model and SOP management platform to support the long-term retention, exchange, sharing and publishing of the outcomes of the multi-partner projects of the first and second round of the ERANet SysMO (Systems Biology for MicroOrganisms, http://sysmo.net/) programme and selected projects of the ERASysBio+ programme.

In partnership with HITS, Heidelberg (Germany) and U Stellenbosch (South Africa), the project:
- further developed the SEEK platform for the lightweight management of data, models and SOPs in Systems Biology (http://www.seek4science.org). This has functionalities for project management (yellow pages), organising outcomes using the ISA framework, catalogues ad repositories for digital assets arising from Sys Bio research, seamless integration with Systems Biology simulators and gateways to third party data archives. It is standards driven.

- further developed the SysMO-SEEK and established the ERANet ERASysBio SEEK resources for the projects to register, interlink, retain and share their results (https://seek.sysmo-db.org/) which then moved to the FAIRDOMHub.org in the DMMCore project (See DMMCore entry).

- continued to develop a methodology for lightweight data gathering using Just Enough Results Model (JERM)

- further developed tools (Rightfield, http://www.rightfield.org.uk) for making JERM templates and spreadsheet tools to help biologists with data curation

- further developed the JWS Online Sys Bio model database and simulation system.

- ran summer schools, workshops, tutorials and training programmes

- extended and ran a PALs knowledge network of young researchers in the SysMO projects who became skilled data managers, champions and scouts for the platform.

- assisted projects to curate their data and models, with over 70 site visits in total

- participated in Systems Biology Standards activities, notably the COMBINE and ISA standards.

- worked with funding councils implement data sharing policy and data management strategy.

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.
Exploitation Route The platform was adopted by 14/15 SysMO 1 and 2 and EraSysBio+ Microorganism projects and has gone on to be widely adopted in other programmes, notably the Virtual Liver Network, ERANet ERASysBio+ projects, and the ERANet ERASysAPP.
The SysMO-SEEK resource continued to be used by over half the SysMO projects, even after the funds, the programmes and the projects ended. Many groups are including the platform in their new grant proposals. We successfully retained the outcomes of the SysMO 1and 2 programmes as planned. During SysMO-DB2 The platform was adopted by 10+ independent projects (e.g. Unicellsys, JenAge, RosAge, SBCancer, Sybacol projects) and local group instances were established at the VU Amsterdam for Yeast Glycolysis, Systems Science for Health in Birmingham and Magdeburg Centre for Systems Biology. Commercially, SEEK was the basis of a component of Eagle Genomics Ltd's ElasticAP platform, that got redeveloped into the Eaglecore platform.
The SysMO-DB project directly lead to the BBSRC DMMCore award, a consortium of 4 EU funding councils to: Establish a sustainable European Infrastructure to extend the network services to the wider European systems biology community; Develop the necessary toolset and set up a data and model management platform for systems biology project, building on SEEK and openBIS (SystemsX); and document and disseminate the outcomes and activities to funding agencies, projects and centres with the goal of establishing a sustainable business model for this infrastructure. The project was rebadged as FAIRDOM, established a legal entity (the FAIRDOM Association e.V) and has extended its scope, partnerships and funding streams. The SEEK Platform has been rebadged as FAIRDOM-SEEK.
Since the establishment of the FAIRDOM project by the DMMCore award, 130+ projects now use the FAIRDOMHub (a public Commons which subsumes the SysMO and ERASysAPP SEEKs) and 50+ projects use the software platform in their own instances. The platform forms part of the German de.NBI bionformatics infrastructure and has been adopted by two UK Synthetic Biology Centres (SynthSys and SYNBIOCHEM), the EMSL Facility at the USA PNNL. Projects across Europe, South Africa, and in Siberia have adopted the platform. See the DMMCore Research Fish entry for further details.
Work on the SysMO-DB project directly lead to participation in the ESFRI Research Infrastructure ISBE - Infrastructure for Systems Biology Europe, and we lead the Data and model management work package setting out Europe's plans for this area. This in turn led to FAIRDOM-SEEK adoption in two further ESFRIs - by (6) ELIXIR Nodes and by IBISBA. It also forms the basis of a workflow collaboratory for Life Sciences being developed through three EU grant awards: EOSC LifeCluster Project, the BioExcel Centre of Excellence and the Synthesys+ for natural history collections (a project of the ESFRI DISSCo). The SEEK platform is now the basis of the EU EOSC Life workflow collaboratory, starting March 2019. EOSC Life is a Cluster project uniting 13 EU Research Infrastructures in the Life Sciences. See the DMMCore entry for further details.
The JWS Online Sys Bio model database and simulation system continues to offer data and simulation facilities.
The PALs knowledge network and the workshop/tutorial programme have been adopted by other projects - notably the Dutch DTL Centre and the German Virtual Liver Network. the knowledge network is being extended through the FAIRDOM Initiative, partially funded by the BBSRC DMMCOre Award.
Our work on COMBINE (MIRIAM, SED-ML) and ISA standards is adopted by the wider community for data and model management.
The SEEK platform has also been adopted outside of Sys Bio. The software platform underpins the EU Biodiversity Virtual eLaboratory Portal (http://www.biovel.eu) and the Manchester Web Ergonomics Laboratory.
The RightField platform has been adopted in archaeology, cultural studies and environmental sciences. It forms the basis of the Populous Ontology development tool (http://www.e-lico.eu/populous.html).
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.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

URL http://www.sysmo-db.org/
 
Description The platform was adopted by 14/15 SysMO 1 and 2 and EraSysBio+ Microorganism projects and has gone on to be widely adopted in other programmes, notably the Virtual Liver Network, ERANet ERASysBio+ projects, and the ERANet ERASysAPP. The SysMO-SEEK resource continued to be used by over half the SysMO projects, even after the funds, the programmes and the projects ended. Many groups are including the platform in their new grant proposals. We successfully retained the outcomes of the SysMO 1and 2 programmes as planned. During SysMO-DB2 The platform was adopted by 10+ independent projects (e.g. Unicellsys, JenAge, RosAge, SBCancer, Sybacol projects) and local group instances were established at the VU Amsterdam for Yeast Glycolysis, Systems Science for Health in Birmingham and Magdeburg Centre for Systems Biology. Commercially, SEEK was the basis of a component of Eagle Genomics Ltd's ElasticAP platform, that got redeveloped into the Eaglecore platform. The SysMO-DB project directly lead to the BBSRC DMMCore award, a consortium of 4 EU funding councils to: Establish a sustainable European Infrastructure to extend the network services to the wider European systems biology community; Develop the necessary toolset and set up a data and model management platform for systems biology project, building on SEEK and openBIS (SystemsX); and document and disseminate the outcomes and activities to funding agencies, projects and centres with the goal of establishing a sustainable business model for this infrastructure. The project was rebadged as FAIRDOM, established a legal entity (the FAIRDOM Association e.V) and has extended its scope, partnerships and funding streams. The SEEK Platform has been rebadged as FAIRDOM-SEEK. Since the establishment of the FAIRDOM project by the DMMCore award, 130+ projects now use the FAIRDOMHub (a public Commons which subsumes the SysMO and ERASysAPP SEEKs) and 50+ projects use the software platform in their own instances. The platform forms part of the German de.NBI bionformatics infrastructure and has been adopted by two UK Synthetic Biology Centres (SynthSys and SYNBIOCHEM), the EMSL Facility at the USA PNNL. Projects across Europe, South Africa, and in Siberia have adopted the platform. See the DMMCore Research Fish entry for further details. Work on the SysMO-DB project directly lead to participation in the ESFRI Research Infrastructure ISBE - Infrastructure for Systems Biology Europe, and we lead the Data and model management work package setting out Europe's plans for this area. This in turn led to FAIRDOM-SEEK adoption in two further ESFRIs - by (6) ELIXIR Nodes and by IBISBA. It also forms the basis of a workflow collaboratory for Life Sciences being developed through three EU grant awards: EOSC LifeCluster Project, the BioExcel Centre of Excellence and the Synthesys+ for natural history collections (a project of the ESFRI DISSCo). The SEEK platform is now the basis of the EU EOSC Life workflow collaboratory, starting March 2019. EOSC Life is a Cluster project uniting 13 EU Research Infrastructures in the Life Sciences. See the DMMCore entry for further details. The JWS Online Sys Bio model database and simulation system continues to offer data and simulation facilities. The PALs knowledge network and the workshop/tutorial programme have been adopted by other projects - notably the Dutch DTL Centre and the German Virtual Liver Network. the knowledge network is being extended through the FAIRDOM Initiative, partially funded by the BBSRC DMMCOre Award. Our work on COMBINE (MIRIAM, SED-ML) and ISA standards is adopted by the wider community for data and model management. The SEEK platform has also been adopted outside of Sys Bio. The software platform underpins the EU Biodiversity Virtual eLaboratory Portal (http://www.biovel.eu) and the Manchester Web Ergonomics Laboratory. The RightField platform has been adopted in archaeology, cultural studies and environmental sciences. It forms the basis of the Populous Ontology development tool (http://www.e-lico.eu/populous.html). 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.
First Year Of Impact 2010
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description BB/M013189/1 DMMCore: Data and Model Management Core for ERASysAPP & Europe
Amount £1,015,804 (GBP)
Funding ID BB/M013189/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2014 
End 10/2019
 
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 EU FP7 ESFRI ISBE Infrastructure for Systems Biology Europe
Amount € 350,000 (EUR)
Funding ID 312455 
Organisation European Commission 
Department Seventh Framework Programme (FP7)
Sector Public
Country European Union (EU)
Start 08/2012 
End 09/2015
 
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 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 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
 
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 
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 50+ groups in Europe, Russia, South Africa, USA, and the UK. EU Projects that adopt the platform include: EmPowerPutida and Mycosynvac; national projects include the German Systems Medicine for Liver project and the de.NBI German Bioinformatics Network, and the Norway's Digital Life programme. 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. Combined with the openBIS system, it is the platform for two UK Synthetic Biology Centre's data management (SynBioChem and SynthSys). 90+ projects are currently registered on FAIRDOMHub.org Commons, a centralised public community instance of the SEEK4Science Platform. Work on the SysMO-DB project and the SEEK directly lead to participation in the ESFRI Research Infrastructure ISBE Light - Infrastructure for Systems Biology Europe, and we have lead the Data and model management work package setting out Europe's plans for this area. The SEEK4Science software and associated software, FAIRDOMHub Commons and its support services form a core pillar of the ISBE Light Interim phase. Commercially, SEEK was the prototype component of Eagle Genomics Ltd's eaglecore platform, adopted by GeneXplain and is currently being reviewed by 3 commercial organisations. 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. The SysMO-DB project also directly lead to the DMMCore award (renamed the FAIRDOM project), a consortium of 4 EU funding councils to: Establish a sustainable European Infrastructure to extend the network services to the wider European systems biology community; Develop the necessary toolset and set up a data and model management platform for systems biology project, building on SEEK and openBIS (SystemsX); and document and disseminate the outcomes and activities to funding agencies, projects and centres with the goal of establishing a sustainable business model for this infrastructure. FAIRDOM is funded by the UK through the BBSRC BB/M013189/1 DMMCore: Data and Model Management Core for ERASysAPP and Europe project. 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