News

22

Oct
2020
DataPLANT is happy to annouce a project coordinator

The DataPLANT NFDI was able to convince Cristina, a highly skilled person about to graduate in fundamental plant research as a project coordinator. She will help to work on DataPLANT mission to combine the technical expertise in the areas of basic plant research, information and computer sciences and infrastructure specialists for supporting plant scientists in the handling of research data in a customized way. She coordinates the DataPLANT consortium within the NFDI, which is concerned with supporting research data management in basic plant research. She is in close contact with the research community and the speakers of the consortium. She will interact closely with thematically related NFDI consortia and the NFDI Directorate. To this end, she already brings a wealth of experience in the plant community to bear to advance collaboration with various stakeholders in Germany and internationally. She also coordinates the governance of DataPLANT and assists the “Data Stewards” in supporting the researchers in the individual groups. In addition, she represents the spokespersons in committees and associations at federal and European level. Her profile: She holds a Master’s degree in plant sciences with a thesis on “Physiological and biochemical analyses of sugar transporter-dependent cold response of Arabidopsis thaliana”. Her further career as a plant physiologist began with her entry into the department of Prof. Neuhaus, where she started her PhD as a member of the BMBF-funded Betahiemis project. She already possesses excellent skills in the management of scientific projects. In the course of her research activities she was able to acquire knowledge in the management of large data sets and experience in scientific data analysis and data visualization. She has already come into contact with topics relevant to DataPLANT such as ontologies, data containers, FAIR data. She has a wide range of publishing experience and experience in fund acquisition, third-party funding management, and writing project reports. She is also familiar with committee work and the organization of conferences and workshops. Cristina will take her post in November. Further open positions in the DataPLANT NFDI which will appear in the coming weeks can be found on this web page and positions in the context of the general NFDI are posted at the NFDI webpage at nfdi.de.

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21

Oct
2020
DataPLANT participates in Second NFDI strategy workshops

The second NFDI strategy workshop focused on vision, values, mission as well as on the technical architecture of the NFDI. The workshop was organized by the NFDI Directorate. In the meantime the association has been successfully founded and registered. The directorate has also been completed in terms of personnel. The aim of the workshop was to sharpen the vision through the participating consortia: Why are we doing this and what kind of world do we dream of? There was also an exchange about the values: What are desirable characteristics of the NFDI that are shared by all members and guarantee responsible action? The mission should clarify: What are we doing, what is our goal for the NFDI and how do we want to proceed? The third theme should advance the reflection on a possible Technical Architecture: How is “the NFDI system” made up of different components and how do they interact? Because of the actual situation all was handled online using tools like break-out rooms and jamboards.

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5

Oct
2020
DataPLANT extends the Call-for-ARC to the wider community

The Annotated Research Context (ARC) is a conceptual combination of experimental data with associated annotation, metadata and description of computational workflows. It aims both as structuring the workflows on the local desktop of the user, allow for sharing and versioning and finally be the base of a data publication. The ARC covers the complete research cycle and includes experiment data described with the ISA model, reference knowledge, computational steps like software, code and scripts as information for the core data repositories on transcriptomics, proteomics, metabolomics and phenomics. In DataPLANT the ARCs will be the generic interface for compute and storage as well as publication and sharing.

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21

Sep
2020
DataPLANT: First General Assembly

On 21st September the DataPLANT participants gathered online to officially meet for the First General Assembly of the consortium. More then 40 people participated and discussed in the two hours session. At the beginning the DataPLANT mission got refined and explained and how it fits into the NFDI general objectives. The NFDI intends to build a national, sustainable data infrastructure for disciplinary sciences. All successful consortia will enjoy a funding for five years initially. After a successful interim evaluation it would be possible to extend the activities for another five years. DataPLANT intends to gain a significant coverage of researchers and groups in the field of fundamental plant research and to establish a sustainable funding scheme during this time. The NFDI consortia should help, advise and support “their disciplines” in standardization and research data management. To achieve that objective DataPLANT puts the so called Annotated Research Contexts (ARC) at it’s core. An ARC consists of an ordered combination of experimental data with annotation and descriptions of computational workflows. The ARCs will help to increase the level of annotation at the source and track provenance using community standards to maximize future data discoverability and reuse. With it will come new responsibilities for researchers. DataPLANT will homogenize formats, terminologies, guidelines, policies to simplify the RDM landscape which will lead to democratization of research data. To support the handling of ARCs storage, compute and authentication services will get integrated to facilitate usability and access. The services will focus on plant specific processing and analysis tools which cover the complete research cycle. ARCs will become the generic interface for compute and storage as well as for publication and sharing. The community with especially profit through specialized tools and workflows, more available storage, a full ARCs compatibility, automated metadata generation and public repository compatibility. These developments drive the digital change in science with the goal to establish an ARC publication as a full equivalent to a classical (paper) publication. ARCs are the base of the collaborative research platform and can be shared between researchers seamlessly (through a mixture of locally decentralized storage mixed with a collaborative centralized versioning). The ARCs become the easy to use single access point for the Swate tool which uses an annotation grammar of source names, characteristics, factors, parameters, sample name and data. The DataPLANT consortium is the representative of fundamental plant research within the NFDI. To facilitate a tight interaction with the community three boards got created and a General Assembly will gather from time to time. In between GA the boards will guide and advice DataPLANT. For transparency all documents of meetings will be published (slides, notes, decisions, …) The office will support the future board procedures and will be the first point of contact for the data stewards, the community and researchers interested in the consortium. For task areas (TA) will work in different means to support the community: TA1 will hire five standards experts whick will work on quality, standardization and interoperability. TA2 plans to deploy six developers and technicians to work on software, services and infrastructure for the community. TA3 hosts seven data stewards which will directly interact with the data champions and the wider community on transfer, application and education in the field. These TAs will get complemented by four people in coordination, management, support and services in TA4. Those plannings are estimates as DataPLANT got a nominal budget cut of 13.5% which translates in real terms (as the salaries are fixed to 2019 DFG figures) to 20 - 25% reduction. Further on the agreement of the applicant institution (University of Freiburg) with the DFG is about getting to be signed, the consortial agreement is still in circulation. To actually start in DataPLANT a first round of personnel is getting to be hired. The data champions will be contacted by the office in the coming weeks to refine the vision and prioritize requirements. They are the primary target for the “Call for ARCs” in the first round. This is meant to kick-off the data stewards service which is intended to communicate and realize the FAIR best practices, plan data management strategies for research projects and proposals and provide legal assistance for licensing and sharing of data. The general assembly got concluded by a talk of Prof. York Sure-Vetter, director of the NFDI. He gave a short overview on the state of the creation of the registered association and it’s inauguration in October. He motived the common goal of the improvement of research data management, the advancement of science and the change of academic culture to embrace open data publications.

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11

Sep
2020
DataPLANT governance: First round of board meetings held

During the beginning of September the board meetings were held, starting with the Senior ManagementBoard followed both by the Scientific and Technical bards. The first round of meetings got chaired bythe speaker, future meetings will be coordinated by a board chair supported by the office. It was decided to make the relevant informationtransparent; thus the slides and minutes are directly available via the linked PDFs. All information presented and decisions made will be made public in the future as well at least to all participants of DataPLANT. Until DataPLANT is officially started, the new web site is becoming available and the cooperation and participation tools are deciced upon, the documents will reside on the preliminary web site. The Senior Management Board directly reports to the General Assembly and represents the community inbetween GA meetings. It oversees all TA activities (with a focus on TA4) and finances and takes care of the strategy development. The Technical Board employs technical and infrastructuralexperts and moderates the various infrastructure requirements and data service offerings anddecides on resource distribution/allocation, future development of new offerings or thedeprovisioning of deprecated services. It will receive input mainly from TA2 and TA3. The scientific board consists mostly of plant scientists and computer scientists developing services and advises on standardization needs and develops foresight processes. It focuses on the TA1 and TA3.The boards take the input from both the general assembly and the senior managementboard and outside requests (e.g. from other consortia or the NFDI super structure). All boards willbe supported by the DataPLANT office; the post will be offered soon through the usual channels. Both technical and scientific boards moderate requests, which were notdecided within the respective body to the high-level decision-making committee, the seniormanagement board. The senior management board consists of all co-speakers of DataPLANTand reports to the general assembly. Whilst the senior management board strives to makeunanimous decisions, it will employ a simple majority vote principle where in case of a tie vote thecoordinator decides. The office handles the everyday business on behalf of the managementboard and the disbursement of funds of the sub NFDI. It is the first point of contact for the general NFDI processes, the facilitation of the inter NFDI exchange and the DataPLANT community (bothparticipants and new users). It acts on behalf of the management board in between meetings andbuffers incoming requests. The office takes care of the financial affairs of DataPLANT and reportsannually to the general assembly and back to the grant provider. Furthermore, it handles inter-NFDI affairs and supports the coordination of cross cutting topics. The DataPLANT governance and coordination is designed to be open for adaptation; the NFDI governance - which will get fixed through the association registration process in October - was identified as a joint topic relevant for all consortia. The suggested structures will be put into a regular reviewingscheme by the general assembly and the senior management board. Both inputs from theDataPLANT community as well as from the NFDI in general will be considered.

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31

Aug
2020
DataPLANT pre kick-off coordination meeting

The (co-)applicant group of DataPLANT (speakers of the consortium) met in Annweiler/Trifels from Thursday to Saturday (27th till 29th August) to discuss the kick-off of the governance and to prepare the various boardmeetings which will be held in the coming weeks. The senior menagement board will have it’s inaugural meeting the 3rd September, followed by the scientific and technical board meetings. These meetings are part of the NFDI and DataPLANT community governance. The coordination meeting discussed the final grant and the implications from the budget cuts announced earlier. These will influence the scope and width of workpackages. Futher topics were the rules of compensation within the consortium and the hiring of personnel for each task area starting from now. Open posts will get announced through the central NFDI platform as well as at the upcoming GAIN event. The second half of the meeting was dedicated to shape the vision of DataPLANT and elaborate on a first set of templates and services to start with. The Annotated Research Context (ARC) is at the core DataPLANT and alltask areas are grouped around it.A preliminary core workflow got sketched: The data is acquired from someinstrument and then getting annotated with the help of a first versionof the Swate toolpublicly available. It allows to pick parameters from known ontologiesand helps to find appropriate parameters (see best practices). If those are missing, they could be added andautomatically being recorded for extension. The standardization processwill pick those up and discuss them with the appropriate committee. Inthe first iteration the user works locally in the proposed ARC filestructure which could either be created through a template ZIP or viathe Excel tool. To allow a versioning in that iterative process a GIT isproposed and a versioning service will be offered by the infrastructureproviders. The data will be later on stored in an object storage.Certain metadata will be copied to the elastic search component asattributes for the bucket used. The ISATAB is getting stored alongsidethe data as well (assay branch within the ARC). It the experiment gotfinalized a further workflow step will be offered to replicate thespecified ARC (composition of data, metadata and workflow description)into the data (publication) repository. This could be a communityrepository (EBI, NCBI, ENA) or another service provided throughDataPLANT. After the assay branch is available within the ARCcomputational workflow e.g. through Galaxy can follow (which requires anappropriate account provided through DataPLANT Hub). The DataPLANT Hubwill allow for simple and complex search on the community data madeavailable through it. The data stewards will be enabled to help with thetemplating of experiments.

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26

Aug
2020
DataPLANT took part in the 1st NFDI strategic workshop

DataPLANT participated in the first NFDI strategy workshop initiated and coordinated by the NFDI directorate. The workshop intended to find joint solutions and to tackle the further development of the NFDI focusing on cross-cutting topics. Not every cross-cutting issue is necessarily dealt with to the same extent by all consortia. DataPLANT e.g. indicated to cooperate on Research Data Commons (Infrastructures), (Meta)Data, findability, provenance, quality management and assurance as well as legal aspects. Further fields of common interest are user-driven developments, training and education and how to stimulate cultural change. DataPLANT plans to foster the cultural change towards the wide acceptance of data publications. In the upcoming phase the governance and sustainibility, internationalisation, policy advice and consultation will be jointly developed. Furthermore suggestions were taken up, according to which there should be a discussion on how best to integrate the consortia of the next round and whether tools/methods/filetypes might be suitable as an additional cross-cutting theme. In the meantime the Terms and Conditions for Funding Agreements with the German Research Foundation (DFG) on Consortia within the National Research Data Infrastructure were published and are to be implemented by the applicant institutions. The same applies for the “Mittelweiterleitungsvertrag” (rules for the transfer of funds) which defines the relationship between the (co-)applicants.

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9

Jul
2020
DataPLANT participated in the 2nd NFDI conference

DataPLANT - a NFDI initiative focused on fundamental plant research - participated in the NFDI Conference 2020 held on 8th and 9th July 2020 online. DataPLANT was presented beside all the other consortia proposed for funding or in the planning stage. The presentations gave the respective intentions and scientific communities supported in parallel tracks. The abstracts (DataPLANT abstract) contain an overview on the consortium and the scientific communities addressed as well as information on the focus, user needs and objectives of the (planned) consortium. In addition to contributions from the GWK, the DFG and the NFDI board of directors, the abstracts presented the current state of discussion, planning and development. The conference aimed at three objectives: Information provided by the DFG on the concept and the overarching goals of the NFDI, as well as on the key points of the proposal submission for the second and third rounds; networking among the consortia proposed and planned for funding; and presentation of the head of the newly founded NFDI Directorate, Professor Dr. York Sure-Vetter. In the future, the Directorate will support the self-organisation and networking of the consortia on cross-consortium services, on subject-related or data-like offerings and on other challenges.

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26

Jun
2020
DataPLANT's funding got granted by the GWK / Kick-Off in Progress

DataPLANT has been informed that the Joint Science Conference (GWK) has followed the recommendation of the NFDI Expert Panel and today decided to support the [NFDI 7/1 DataPLANT] proposal (press release of the GWK). Furthermore, it was informed that the GWK has not yet made a final decision on the amount of funding to be granted per consortium. This decision will be taken on the basis of a consultation of the NFDI expert panel, which will take place on 9 July. An official notification from the University of Freiburg as consortium leader in DataPLANT is also available. In parallel to the ongoing planning for the project kick-off, DataPLANT has entered into coordination with the NFDI directorate and exchange with the other funded consortia on consortium agreement, recruitment and cross-cutting topics. Further on DataPLANT participates in the joint NFDI workshop on meta data.

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16

Jun
2020
DataPLANT signs the "Leipzig-Berlin-Erklärung zu NFDI-Querschnittsthemen der Infrastrukturentwicklung"

DataPLANT is a co-signatory of the “Leipzig-Berlin Declaration on NFDI Cross-Sectional Issues in Infrastructure Development” and regards this joint document as the basis for the necessary mutual coordination based on sustainable processes and structures. For example, topics that are relevant to several expert consortia are to be worked on cooperatively and across individual consortia in the interests of sustainable interoperability. Further questions from the areas of infrastructure, integration of service providers and sustainable financing are to be discussed as well. In addition, legal issues relating to the preservation, sharing and re-use of digital objects are of relevance to all consortia. Therefore, key issues concerning licences, the handling of sensitive data, IT law, data protection and confidentiality of data should be addressed for the whole NFDI. A central challenge for all consortia is the sustainable long-term access to research data. This includes topics such as data provenance and sovereignty of data, sustainability and security of data, tools and services, as well as persistent identifiers (e.g. DOIs or ePICs) and the certification of data repositories and archives. This includes in particular the securing of technical access and productive subsequent use options for the original research and creation context (re-use). Suitable measures for the management of research software must also be agreed. This includes the operation of development and archiving repositories, the management of metadata for referencing and citation, and the standardized description of software code.

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19

May
2020
Positive vote of the reviewer panel to the DataPLANT application

Yesterday, on 18 May, the announced decision of the NFDI Selection Committee’s panel of experts reached us. In this decision, which has yet to be confirmed by the GWK on June 26, DataPLANT was recommended for funding along with eight other consortia. We are pleased that we have been able to successfully follow our vision for RDM in fundamental plant research together with you and hope that we will master the last mile as well. Further feedback on the grant application is announced for August at the latest. As nine consortia are recommended to be funded in this round instead of the seven originally announced, it cannot yet be said whether this will have an impact on the planned budget. The planning will be accordingly cautious. The NFDI expert panel’s advice is based in particular on the results of the evaluation and the applicant’s comments on the evaluation results. In order to be able to adequately evaluate the applications reviewed in seven expert colloquia, the NFDI expert panel also paid special attention to the framework conditions for setting up the NFDI in a scientifically guided procedure. As a result of its selection process, the NFDI Expert Panel recommends the following nine consortia from the first round of calls for proposals to the Joint Science Conference (GWK) for funding: NFDI4Ing, NFDI4Health, NFDI4Biodiversity, NFDI4Culture, KonsortSWD, GHGA, NFDI4Cat, NFDI4Chem, and DataPLANT. A total of 22 consortia took part in the first round, with two further rounds to follow this year and next year. A total of up to 30 consortia are to be funded in the full development stage, with approximately 70 million euros available for direct project costs. In the meantime, this provisional website has been set up to promote the information of the community about our consortium and ongoing activities. Additionally, we have set up a Twitter account “@nfdi4plants” to tweet about upcoming events and activities. For the time being we continue to use the mailing list we set and subscribed all participants as a classic information channel. At the same time, we have entered into “cross-cutting activities” and are participating, for example, in the exchange on metadata in the NFDI at an event scheduled for the beginning of July.

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28

Feb
2020
Reply to the reviewer panel's protocol sent to the DFG

Today the DataPLANT consortium sent the three pages reply to the reviewers remark and used the chance to clarify a couple of open questions. We got a quite positive feedback on our concept of data stewards as a central support element to the fundamental plant research community. This core element makes the training and recruitment of suitable people a central task of the DataPLANT consortium. The successful training of the Data Stewards essentially requires basic skills in the standardized handling of data, their modeling and analysis, as well as a solid domain understanding of quantitative plant biology, especially the methods used in this research field. In addition, practical skills in handling different software packages, analysis and workflow tools as well as in teaching and training are required. To ensure the training of the Data Stewards from the start of DataPLANT, we propose a strategy with a mixture of direct and long-term measures. Corresponding training and further education opportunities are already included in the curricula of the applicant institutions. It is also planned to make existing courses of study (e.g. in the field of data science) more flexible so that the basic training of data stewards can be provided within the framework of these courses of study. A new development of tailor-made courses of study is also conceivable in the long term. With regard to both measures, the applicants were able to secure the support of the partner universities in preliminary discussions. For example, the course of study Quantitative Plant Biology at CEPLAS is a valuable addition to the recruitment of personnel. The review panel rightfully suggests that the services to be developed in DataPLANT should be flexible enough to ensure sustainability. A central goal in the design of the DataPLANT Hub is to provide flexible, demand-oriented and sustainable support for research data management throughout the entire research cycle. An essential aspect of the hub is the abstraction of workflows using the Common Workflow Language (CWL), which is widely used in all scientific fields, in order to enable researchers to execute workflows on any platform and to avoid the mentioned dependencies. The intended annotation of workflows with metadata as well as the quality measures for workflows to be developed act as additional abstraction mechanisms. Currently, GALAXY is a mature and widely used workflow platform on which the DataPLANT Hub and other measures of the consortium can be based at an early stage. Nevertheless, a sole dependency on GALAXY is actively avoided by abstraction and open creation of the DataPLANT Hub. DataPLANT aims to mirror the fundamental plant research community across all status groups in research and provider institutions. In order to ensure diversity, DataPLANT will implement the following multi-track strategy: 1) continuous recruitment of new participants and active recruitment of suitable individuals with a special focus on diversity from the growing plant community and beyond; 2) Exemplary role in the design of the initial governance: The governance will broadly staffed with members from the group of participants with respect to diversity, especially regarding career level, reputation and gender balance. We are also able to involve scientifically very experienced and proven personalities whose experience with clusters of excellence DataPLANT will benefit from. 3) Development of promotion and qualification opportunities (especially in the context of the training of Data Stewards) that allow participants at early career stages to become involved in DataPLANT at an early stage and to take on responsibility. 4) Active use of the explicit diversity measures of the participating institutions. Similar to the review panel, we consider the operating and financing model of DataPLANT to be a major challenge for long-term sustainability. While initially the services are offered free of charge for participants through project financing, for a permanent offer there is the necessity to put needs and arising costs for the refinancing of resources into relation. Supporting individual researchers and research associations in applying for FDM funding is a key aspect of DataPLANT. Our vision is that the mechanisms developed in DataPLANT will manifest themselves sustainably in the community. DataPLANT brings its ideas and efforts to the overarching NFDI structure (e.g., via the cross cutting topics) and is itself open to being integrated into the emerging frameworks of the NFDI and its approaches. We are in continuous exchange with other consortia on these topics. First approaches to solutions already result from the integration of the providers into collaborative national, national and international infrastructures.

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11

Feb
2020
DataPLANT advised on grant application and discusses compensation models with participants

The NFDI starts to shape the future scientific landscape and should be taken into account when planning research projects and cooperations. Together with a participant, the “Plant Genome and Systems Biology” group at the Helmholtz-Zentrum München DataPLANT discussed possible forms of support regarding both infrastructure services and consulting. Such cooperations would require agreed upon compensation models. Both parties acknowledged the fact of challenges regarding cost compensation models which comply with non-profit/public-benefit requirements and capable of being integrated into the central NFDI governance structure. Calculation of costs and refinancing becomesunavoidable at some point to allow sustainable cooperation. Different funding streams need to betaken into account. Every institution has funds to pay for commercial third-party services andconsulting, but it is nearly impossible to proper receive such funds as a research institution.Direct flows of money in a consortium of differently organized and funded research institutions isan issue to be iterated and solved via the corresponding cross-cutting topic. The data stewardservices can be clearly accounted for. Thus, it could be an option to use vouchers or coupons onservices in exchange for redirected financing via a grant application. An endorsement model couldbe established to foster such developments, where research funding agencies see the NFDI asa service broker. The NFDI structure ensures good scientific practice by offering certified serviceswhich are in turn applied for by research groups. The funding agencies would divert a certainamount of support to the NFDI in relation to the equivalent of the services requested. A base levelfunding e.g. either through universities or the NFDI would compensate for consultation to non-successful applications. Such options need to be discussed and developed together with allstakeholders within DataPLANT, the general NFDI level, and the appropriate political sphere.Efficient ways of reimbursement without overhead and bureaucracy are needed to offer asustainable model for long-term cooperation and viability. The concept outlined in the DFG NFDI workshop last year end of August including the concept of the NFDI as a registered society could be a feasible way for a non-profit oriented operation model for the individual consortia.

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10

Feb
2020
DataPLANT receives positive feedback from the DFG, but still work ahead

DataPLANT was present at the 3rd NFDI Community Workshop - Services for Research Data Management in Neuroscience hosted at the 10th Februar at Ludwig Maximilians University Munich to exchange with other NFDI consortia and discuss common topics like infrastructure provisioning. The NFDI4Neuro as well as the NFDI4BIMP intend to hand in their proposals in this year’s round of applications. The main topic of this community workshop was the exchange on infrastructure for the NFDI and especially on the providers’ perspective. The provider’s perspective in the NFDI was elaborated by the BioDATEN science data center. Providers of research IT infrastructures are faced by significant technological changes especially fostered by resource virtualization. Many of the modern services and workflows are operated in an increasingly cloud-like fashion where data and compute moves into centralized, aggregated resources. Such shared resources allow to faster host new projects. The necessary exess capacity is much easier to maintain and justify in centralized resources as the shared overhead to provide is typically much less than in independent systems. Grant providers start to understand the changed technological landscape and to adopt their funding schemes allowing to buy-in into existing resources preferred to establishing single ones per new project. Users are faced by difficult to forecast requirements. It is often impossible for them to define the exactly “right” configuration of a required resource (sizing challenge). These challenges are answered by the IT industry and science driven cloud and aggregated HPC offerings. The aggregation of resources into larger ones can focus the increased efforts for market analysis, system selection, proper procurement and operation of (large scale) IT infrastructures onto few experts. Further on such a strategy would eliminate the contradiction of typical project run times versus the (significant) delay for equipment provisioning and the usual write down time spans of that equipment. The massive changes in the IT landscape and of the user expectations increase the pressure for re-orientation of university (scientific) computer centers. For many of them cooperation is the chance to significantly widen their scope of IT services. It helps to keep up with the demand by the scientific communities and to offer a relevantly complete service portfolio. Organizationally, it allows for specialization and community focus. When defining future strategies and operation models they might find a new meaning in supporting research data management by providing efficient infrastructures and consultation to the various scientific communities. Further on it offers them the opportunity to participate in infrastructure calls. These developments offer for the researchers the offloading of non-domain specific tasks and services. Suitable governance structures are to be implemented to ensure a persistent relevance of future computer centers through user participation and feedback loops. Close cooperation and consultation (like already done in Freiburg for the bwForCluster NEMO and for the storage infrastructure bwSFS) helps all stakeholders to have suitable, up to date infrastructures tailored to their needs. Such structures are in their infancy for the NFDI, but future NFDI wide coordination should advance this topic. The financing of IT infrastructures for the various scientific communities is often grant driven (and inherently not sustainable) for sustainable long term services and research data management. The future would see a changed flow of funding from simple project driven and organization centered practice to demand-driven streams to different providers.Large infrastructure initiatives like de.NBI or the NFDI need not only to solve the role of personnel employment (permanent vs. project based) but to define suitable business and operation models compatible with the VAT regulations and the federal and state requirements for cash flows in mixed consortia.

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13

Jan
2020
DataPLANT receives positive feedback from the DFG, but still work ahead

BioDATEN and DAplus+ are jointly involved in the nationwide NFDI process with DataPLANT Consortium (in the area of Fundamental Plant Research). End of January the review of the DFG assessment of the of the application and the oral presentation in Bonn (Link to the older message) in early December arrived. The reviewers gave a widely positive feedback, from which we deduce that DataPLANT is still in the group for consideration of funding. We would like to thank our collaborators from the Galaxy team, especially Anika Erxleben and from the Technical University in Kaiserslautern and Jülich Research Center. The feedback addresses various areas of the proposal, such as “Maturity and relevance”, “Research data management” and “Internal structure and sustainability”. Besides very positive remarks there are also some critical passages that should be considered in the answer. Some snippets from the review: “The consortium is thematically closely focused on fundamental plant science research. This strong focus and the fact that, in addition to model plants, some cultivated plant species are also taken into account is seen as a clear strength of this consortium” … “The planned implementation of processes for metadata validation seems to make sense and the claim to improve the quality of existing metadata instead of discarding it is commendable. The assessment of the quality of raw data is a interesting additional approach, which, in view of the interpretation of the results by the users carefully must be developed. The quality of the already implemented and the level of measures planned beyond this is very high. One of the planned measures is the establishment of ‘data stewards’ as flexible on-site assistants to be deployed, who are very demanding but also … is very positive.” … “The consortium’s efficient internal structure is impressive, consisting of the various stakeholder groups and the clearly defined bodies, including the ‘Data stewards’ and ‘Data champions’. The topic ‘efficiency and sustainability’ is well received in the application addressed.” The “Diversity” of the consortium lead, which was quite one-sided in the current application, needs to be improved in the further process. The consortium is now requested to respond to individual points in a three-page statement in reply to the reviewers remarks. In particular, the focus of the answer will lie on points such as “How are the data stewards recruited, trained and meaningfully distributed institutionally and made available to the participants” or “Possibilities of generalising the workflow approach”. The improvement of “diversity” should in particular expressed in a broader governance structure to be formulated jointly with the consortium. This will also incorporate initial experiences from the BioDATEN science data center.

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9

Dec
2019
DataPLANT NFDI application defended in Bonn

DataPLANT was initiated by BioDATEN in Baden-Wuerttemberg and DaPLUS of Kaiserslautern and Jülich to create a NFDI consortium on fundamental plant research. It took part in the next round together with other consortia like NFDI4AGRI, NFDI4Earth and NFDI4BioDiversity. On the 2nd and 3rd of December 2019 the DataPLANT consortium has been in Bonn and presented and defended the NFDI application. The perceived feedback on the first day was quite positive. On the second day, we received in a further individual round a couple of more detailed questions on certain aspects. We are optimistic that we left a solid impression, whereby a general assessment and classification is difficult at this stage of the overall procedure. DataPLANT is a comparably small consortium compared to other larger ones. In January 2020, we expect a written statement, to which we can react again with a three-page comment. On this basis, the reviewers will make a recommendation by the end of May 2020. The formal decision will probably be made at the end of July 2020.

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18

Oct
2019
Next step in the NFDI building process: Grant application submitted

On Tuesday the 15th October the DataPLANT NFDI consortium submitted it’s proposal to the DFG. The consortium in Fundamental Plant Research consists of roughly 30 participants including universities and large research institutions distributed over the country. A significant proportion of the participants originate from Baden-Württemberg and the BioDATEN Science Data Center. Further co-applicants are the Technical University of Kaiserslautern and the Forschungszentrum Jülich. The central aim of the DataPLANT consortium is to advance research data management in it’s designated community and generate added value in the field of basic plant research. Successful collaboration and use of data of different modalities – from many sources and experiments, pre-processed or analysed with a variety of algorithms – requires contextualization of the data. The FAIR Data 1 and Linked Open Data Principles provide critical guidelines for research data management. Various consortia have therefore made proposals for best practice and compliance with these principles, but it is almost always the initiative of individual researchers to implement them. Therefore, comprehensive information on the required quality for use by third parties is rarely available. Researchers have been shown to require practical assistance in exploiting the fragmented and complex resource landscape. This increases the need for a tailor-made (infra)structure for research data management. By combining technical expertise in the fields of fundamental plant research, information and computer sciences and infrastructure specialists, DataPLANT will support plant scientists in every RDM concerns. DataPLANT will create a service environment to contextualize research data according to the FAIR principles with minimal additional effort and to support the entire research cycle in modern plant biology. The tailor-made service landscape in DataPLANT will consist of technical-digital assistance as well as on-site personnel assistance. DataPLANT thus creates a central entry point and a valuable subject-specific data and knowledge resource. In combination with teaching and training concepts, data literacy is strengthened and a long-term motivation for the creation of well-indicated data objects is generated. By integrating plant science into the NFDI network as a whole, DataPLANT is driving the digital transformation and democratization of research data in the field.

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30

Aug
2019
Participation in the NFDI governance workshop in Bonn

A colleague from Freiburg took part in the NFDI Governance workshop hosted by the DFG in Bonn. The objectives of the workshop were the discussion of possible legal forms for the NFDI structure and giving an overview of the steps up to the application date of 15th October 2019. In the morning there was a presentation by a consulting law firm, which was mandated by the DFG to examine possible paths of governance and legal models. In the afternoon, questions were discussed under moderation by DFG representatives, which should be taken into account for the proposals. Fundamental questions arose, which were taken up by the DFG. From DataPLANT’s perspective, a number of questions need to be clarified regarding governance in the NFDI. These range from the role of discipline-specific sub-NFDIs in the overall context to the provision of certain basic and extended services and their billing. Comprehensive services such as training or infrastructure could be provided jointly, e.g. via a common training portal or defined interfaces for data provision and search. There will be a certain compulsion for standardisation, which should be moderated by the NFDI. Future operating and business models will have to be defined, clarifying the rights and roles of science and providers in discipline-specific sub-NFDIs. In the same way, commitment is to be established, for example through SLAs. It should be defined how billing models or refinancing of common (basic) infrastructures such as storage and compute could look like. The legal situation and role of the provider with regard to a sustainable assurance of operation should be defined. Further objectives of the workshop were to identify problem areas and topics as well as relevant fields of action and assign them to the various actors (DFG, consortia, the superordinate NFDI governance structure). The establishment of the NFDI is breaking new ground in many respects: It will provide a networked structure under the provisions of the law on grants, it requires cooperation and control components for support. Through the NFDI a professionalization of research data management is intended and it should provide appropriate services, taking into account tax law requirements. The insights of the workshop will get included into the section on the structure and governance part of the consortium in the grant application.

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5

Jul
2019
Forming the consortium in the NFDI process: DaPLUS+ and BioDATEN Science Data Center

Together with colleagues from Tübingen, Konstanz, Freiburg, Heidelberg, … parts of the BioDATEN community joined forces with the DaPLUS+ consortium from Kaiserlautern, Jülich and Düsseldorf to paticipate in the process to create a National Research Data Infrastructure. The newly formed consortium centers around plant data in bioinformatics and handed in a binding “Letter of Interest”. In modern hypothesis-driven science, researchers increasingly rely on effective research data management services and infrastructures that facilitate the acquisition, processing, exchange and archival of research data sets, to enable the linking of interdisciplinary expertise and the combination of different analytical results. The immense additional insight obtained through comparative and integrative analyses provides additional value in the examination of research questions that goes far beyond individual experiments. Specifically, in the research area of fundamental plant research that this consortium focuses on, modern approaches need to integrate analyses across different system levels (such as genomics, transcriptomics, proteomics, metabolomics, phenomics). This is necessary to understand system-wide molecular physiological responses as a complex dynamic adjustment of the interplay between genes, proteins and metabolites. As a consequence, a wide range of different technologies as well as experimental and computational methods are employed to pursue state-of-the-art research questions, rendering the research objective a team effort across disciplines. The overall goal of DataPLANT is to provide the research data management practices, tools, and infrastructure to enable such collaborative research in plant biology. In this context, common standards, software, and infrastructure can ensure availability, quality, and interoperability of data, metadata, and data-centric workflows and are thus a key success factor and crucial precondition in barrier-free, high-impact collaborative plant biology research. Toward this, the key objectives pursued by this consortium are: A specific community standard for fundamental plant research (meta)data and workflow annotation, based on generic, existing and emerging standards (e.g., ISA model, MIAPPE) and ontologies in plant science. Assistive mechanisms and services to build, link and maintain the complete research context during data acquisition, curation, analysis, and publication. Mechanisms for collaborative research based on enrichment and automatized crosslinking of plant-research specific (meta)data to facilitate research context management. A cloud-based open reference implementation of these mechanisms and services, and a central hosted instance thereof. A robust, federated infrastructure both for data computation and management covering the complete data lifecycle. Comprehensive training of community members through workshops and summer schools and providing open training material. The final grant application is due to the 15th October.

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30

May
2019
The Berlin Memorandum on cross-cutting topics

A colleague from Kaiserslautern joined the event co-organized by other NFDI consortia in Berlin.

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15

May
2019
"BioDATEN" and "DaPLUS+" at NFDI conference in Bonn

Both the not yet started Science Data Center “BioDATEN” and the DaPLUS+ initiative were present at the two days NFDI conference held in mid of May in Bonn. The Science Data Center BioDATEN - Bioinformatics DATa ENvironment is a community effort in standardization, services and sustainable research data management. It plans to combine the tools and services provided in frameworks like Galaxy with efforts towards standardization and research data management. DaPLUS+ was formed by colleagues in fundamental plant research from Technical University in Kaiserlautern and Juelich research center.

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